--- _id: '13271' abstract: - lang: eng text: "In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,\r\nfor parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems." acknowledgement: I am grateful to Boguslaw Zegarliński for asking me the questions in [3] and for helpful communication. I also want to thank Paata Ivanisvili for drawing [25] to my attention and for useful correspondence. Many thanks to the anonymous referee for the valuable comments and for pointing out some errors in an earlier version of the paper. This work is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. article_processing_charge: No article_type: original author: - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Zhang H. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. 2023. doi:10.1007/s00023-023-01345-7 apa: Zhang, H. (2023). Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-023-01345-7 chicago: Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-023-01345-7. ieee: H. Zhang, “Some convexity and monotonicity results of trace functionals,” Annales Henri Poincare. Springer Nature, 2023. ista: Zhang H. 2023. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. mla: Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare, Springer Nature, 2023, doi:10.1007/s00023-023-01345-7. short: H. Zhang, Annales Henri Poincare (2023). date_created: 2023-07-23T22:01:15Z date_published: 2023-07-08T00:00:00Z date_updated: 2023-12-13T11:33:46Z day: '08' department: - _id: JaMa doi: 10.1007/s00023-023-01345-7 ec_funded: 1 external_id: arxiv: - '2108.05785' isi: - '001025709100001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2108.05785 month: '07' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6 grant_number: M03337 name: Curvature-dimension in noncommutative analysis publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Some convexity and monotonicity results of trace functionals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13258' abstract: - lang: eng text: Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation. acknowledgement: 'This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).' article_number: '4153' article_processing_charge: Yes article_type: original author: - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Stepan full_name: Simsa, Stepan id: 409d615c-2f95-11ee-b934-90a352102c1e last_name: Simsa orcid: 0000-0001-6687-1210 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 2023;14. doi:10.1038/s41467-023-39625-9 apa: Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., & Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39625-9 chicago: Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39625-9. ieee: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153. mla: Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications, vol. 14, 4153, Springer Nature, 2023, doi:10.1038/s41467-023-39625-9. short: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023). date_created: 2023-07-23T22:01:11Z date_published: 2023-07-12T00:00:00Z date_updated: 2023-12-13T11:42:38Z day: '12' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41467-023-39625-9 ec_funded: 1 external_id: isi: - '001029450400031' pmid: - '37438341' file: - access_level: open_access checksum: 5aceefdfe76686267b93ae4fe81899f1 content_type: application/pdf creator: dernst date_created: 2023-07-31T11:32:36Z date_updated: 2023-07-31T11:32:36Z file_id: '13337' file_name: 2023_NatureComm_Kleshnina.pdf file_size: 1601682 relation: main_file success: 1 file_date_updated: 2023-07-31T11:32:36Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13336' relation: research_data status: public scopus_import: '1' status: public title: The effect of environmental information on evolution of cooperation in stochastic games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '13263' abstract: - lang: eng text: "Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models." acknowledgement: This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413]. article_processing_charge: Yes article_type: original author: - first_name: Van Giang full_name: Trinh, Van Giang last_name: Trinh - first_name: Belaid full_name: Benhamou, Belaid last_name: Benhamou - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 citation: ama: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 2023;39(Supplement_1):i513-i522. doi:10.1093/bioinformatics/btad262' apa: 'Trinh, V. G., Benhamou, B., Henzinger, T. A., & Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad262' chicago: 'Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad262.' ieee: 'V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” Bioinformatics, vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.' ista: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.' mla: 'Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics, vol. 39, no. Supplement_1, Oxford Academic, 2023, pp. i513–22, doi:10.1093/bioinformatics/btad262.' short: V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522. date_created: 2023-07-23T22:01:12Z date_published: 2023-06-30T00:00:00Z date_updated: 2023-12-13T11:41:52Z day: '30' ddc: - '000' department: - _id: ToHe doi: 10.1093/bioinformatics/btad262 ec_funded: 1 external_id: isi: - '001027457000060' pmid: - '37387165' file: - access_level: open_access checksum: ba3abe1171df1958413b7c7f957f5486 content_type: application/pdf creator: dernst date_created: 2023-07-31T11:09:05Z date_updated: 2023-07-31T11:09:05Z file_id: '13335' file_name: 2023_Bioinformatics_Trinh.pdf file_size: 641736 relation: main_file success: 1 file_date_updated: 2023-07-31T11:09:05Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: Supplement_1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: i513-i522 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Bioinformatics publication_identifier: eissn: - 1367-4811 issn: - 1367-4803 publication_status: published publisher: Oxford Academic quality_controlled: '1' related_material: link: - relation: software url: https://github.com/giang-trinh/trap-mvn scopus_import: '1' status: public title: 'Trap spaces of multi-valued networks: Definition, computation, and applications' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 39 year: '2023' ... --- _id: '13316' abstract: - lang: eng text: Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN. acknowledgement: 'This work was supported by JSPS KAKENHI grant #18K062291, and the Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the Takeda Science Foundation, and Life Science Foundation of Japan to JT.' article_number: e84850 article_processing_charge: Yes article_type: original author: - first_name: Junko Y. full_name: Toshima, Junko Y. last_name: Toshima - first_name: Ayana full_name: Tsukahara, Ayana last_name: Tsukahara - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Takuro full_name: Tojima, Takuro last_name: Tojima - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Akihiko full_name: Nakano, Akihiko last_name: Nakano - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: ama: Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 2023;12. doi:10.7554/eLife.84850 apa: Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano, A., & Toshima, J. (2023). The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.84850 chicago: Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.84850. ieee: J. Y. Toshima et al., “The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network,” eLife, vol. 12. eLife Sciences Publications, 2023. ista: Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima J. 2023. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 12, e84850. mla: Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife, vol. 12, e84850, eLife Sciences Publications, 2023, doi:10.7554/eLife.84850. short: J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano, J. Toshima, ELife 12 (2023). date_created: 2023-07-30T22:01:02Z date_published: 2023-07-21T00:00:00Z date_updated: 2023-12-13T11:37:36Z day: '21' ddc: - '570' department: - _id: DaSi doi: 10.7554/eLife.84850 external_id: isi: - '001035372800001' pmid: - '37477116' file: - access_level: open_access checksum: 2af111a00cf5e3a956f7f0fd13199b15 content_type: application/pdf creator: dernst date_created: 2023-07-31T07:43:00Z date_updated: 2023-07-31T07:43:00Z file_id: '13324' file_name: 2023_eLife_Toshima.pdf file_size: 11980913 relation: main_file success: 1 file_date_updated: 2023-07-31T07:43:00Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2023' ... --- _id: '13317' abstract: - lang: eng text: We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction. acknowledgement: "LE, JH, and VR were supported by ERC Advanced Grant “RMTBeyond” No. 101020331. SS was supported by KAKENHI Grant Number JP22J14935 from the Japan Society for the Promotion of Science (JSPS) and Forefront Physics and Mathematics Program to Drive Transformation (FoPM), a World-leading Innovative Graduate Study (WINGS) Program, the University of Tokyo.\r\nOpen access funding provided by The University of Tokyo." article_number: '128' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Shoki full_name: Sugimoto, Shoki last_name: Sugimoto - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Volodymyr full_name: Riabov, Volodymyr id: 1949f904-edfb-11eb-afb5-e2dfddabb93b last_name: Riabov - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Sugimoto S, Henheik SJ, Riabov V, Erdös L. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 2023;190(7). doi:10.1007/s10955-023-03132-4 apa: Sugimoto, S., Henheik, S. J., Riabov, V., & Erdös, L. (2023). Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-023-03132-4 chicago: Sugimoto, Shoki, Sven Joscha Henheik, Volodymyr Riabov, and László Erdös. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics. Springer Nature, 2023. https://doi.org/10.1007/s10955-023-03132-4. ieee: S. Sugimoto, S. J. Henheik, V. Riabov, and L. Erdös, “Eigenstate thermalisation hypothesis for translation invariant spin systems,” Journal of Statistical Physics, vol. 190, no. 7. Springer Nature, 2023. ista: Sugimoto S, Henheik SJ, Riabov V, Erdös L. 2023. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 190(7), 128. mla: Sugimoto, Shoki, et al. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics, vol. 190, no. 7, 128, Springer Nature, 2023, doi:10.1007/s10955-023-03132-4. short: S. Sugimoto, S.J. Henheik, V. Riabov, L. Erdös, Journal of Statistical Physics 190 (2023). date_created: 2023-07-30T22:01:02Z date_published: 2023-07-21T00:00:00Z date_updated: 2023-12-13T11:38:44Z day: '21' ddc: - '510' - '530' department: - _id: LaEr doi: 10.1007/s10955-023-03132-4 ec_funded: 1 external_id: arxiv: - '2304.04213' isi: - '001035677200002' file: - access_level: open_access checksum: c2ef6b2aecfee1ad6d03fab620507c2c content_type: application/pdf creator: dernst date_created: 2023-07-31T07:49:31Z date_updated: 2023-07-31T07:49:31Z file_id: '13325' file_name: 2023_JourStatPhysics_Sugimoto.pdf file_size: 612755 relation: main_file success: 1 file_date_updated: 2023-07-31T07:49:31Z has_accepted_license: '1' intvolume: ' 190' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Journal of Statistical Physics publication_identifier: eissn: - 1572-9613 issn: - 0022-4715 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Eigenstate thermalisation hypothesis for translation invariant spin systems tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 190 year: '2023' ... --- _id: '13278' abstract: - lang: eng text: We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity "breaks" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms. article_number: '006' article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Rammelmüller, Lukas last_name: Rammelmüller - first_name: David full_name: Huber, David last_name: Huber - first_name: Matija full_name: Čufar, Matija last_name: Čufar - first_name: Joachim full_name: Brand, Joachim last_name: Brand - first_name: Hans-Werner full_name: Hammer, Hans-Werner last_name: Hammer - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 2023;14(1). doi:10.21468/scipostphys.14.1.006 apa: Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., & Volosniev, A. (2023). Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.14.1.006 chicago: Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.14.1.006. ieee: L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev, “Magnetic impurity in a one-dimensional few-fermion system,” SciPost Physics, vol. 14, no. 1. SciPost Foundation, 2023. ista: Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1), 006. mla: Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics, vol. 14, no. 1, 006, SciPost Foundation, 2023, doi:10.21468/scipostphys.14.1.006. short: L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev, SciPost Physics 14 (2023). date_created: 2023-07-24T10:48:23Z date_published: 2023-01-24T00:00:00Z date_updated: 2023-12-13T11:39:32Z day: '24' ddc: - '530' department: - _id: MiLe doi: 10.21468/scipostphys.14.1.006 external_id: arxiv: - '2204.01606' isi: - '001000325800008' file: - access_level: open_access checksum: ffdb70b9ae7aa45ea4ea6096ecbd6431 content_type: application/pdf creator: dernst date_created: 2023-07-31T08:44:38Z date_updated: 2023-07-31T08:44:38Z file_id: '13328' file_name: 2023_SciPostPhysics_Rammelmueller.pdf file_size: 1163444 relation: main_file success: 1 file_date_updated: 2023-07-31T08:44:38Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '1' keyword: - General Physics and Astronomy language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: SciPost Physics publication_identifier: issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' scopus_import: '1' status: public title: Magnetic impurity in a one-dimensional few-fermion system tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '13274' abstract: - lang: eng text: Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics. acknowledgement: We thank Baofang Song as well as the developers of Channelflow for sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful discussions. This work was supported by a grant from the Simons Foundation (662960, B. H.). article_number: '034002' article_processing_charge: No article_type: original author: - first_name: Chaitanya S full_name: Paranjape, Chaitanya S id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87 last_name: Paranjape - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 - first_name: Yohann full_name: Duguet, Yohann last_name: Duguet - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002 apa: Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023). Direct path from turbulence to time-periodic solutions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.131.034002 chicago: Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002. ieee: C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” Physical Review Letters, vol. 131, no. 3. American Physical Society, 2023. ista: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002. mla: Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:10.1103/physrevlett.131.034002. short: C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023). date_created: 2023-07-24T09:43:59Z date_published: 2023-07-21T00:00:00Z date_updated: 2023-12-13T11:40:19Z day: '21' department: - _id: GradSch - _id: BjHo doi: 10.1103/physrevlett.131.034002 external_id: arxiv: - '2306.05098' isi: - '001052929900004' intvolume: ' 131' isi: 1 issue: '3' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.05098 month: '07' oa: 1 oa_version: Preprint project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Direct path from turbulence to time-periodic solutions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2023' ... --- _id: '13261' abstract: - lang: eng text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression. acknowledgement: This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship. article_processing_charge: No article_type: original author: - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Hongtao full_name: Chen, Hongtao last_name: Chen - first_name: Lev full_name: Barinov, Lev last_name: Barinov - first_name: Benjamin full_name: Zoller, Benjamin last_name: Zoller - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor citation: ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 2023;380(6652):1357-1362. doi:10.1126/science.adf5568 apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adf5568 chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568. ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” Science, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023. ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362. mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:10.1126/science.adf5568. short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362. date_created: 2023-07-23T22:01:12Z date_published: 2023-06-29T00:00:00Z date_updated: 2023-12-13T11:41:07Z day: '29' department: - _id: EdHa doi: 10.1126/science.adf5568 external_id: isi: - '001106405600028' intvolume: ' 380' isi: 1 issue: '6652' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/science.adf5568 month: '06' oa: 1 oa_version: Preprint page: 1357-1362 project: - _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b grant_number: 343-2022 name: A mechano-chemical theory for stem cell fate decisions in organoid development publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 380 year: '2023' ... --- _id: '13336' article_processing_charge: No author: - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina citation: ama: 'Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564' apa: 'Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564' chicago: 'Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564.' ieee: 'M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.' ista: 'Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564.' mla: 'Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023, doi:10.5281/ZENODO.8059564.' short: M. Kleshnina, (2023). date_created: 2023-07-31T11:30:46Z date_published: 2023-06-20T00:00:00Z date_updated: 2023-12-13T11:42:37Z day: '20' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.8059564 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8059564 month: '06' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13258' relation: used_in_publication status: public status: public title: 'kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13443' abstract: - lang: eng text: 'The ages of solar-like stars have been at the center of many studies such as exoplanet characterization or Galactic-archeology. While ages are usually computed from stellar evolution models, relations linking ages to other stellar properties, such as rotation and magnetic activity, have been investigated. With the large catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index, Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology relations. Stellar ages are obtained with two stellar evolution codes that include treatment of angular momentum evolution, hence using Prot as input in addition to classical atmospheric parameters. We explore two different ways of predicting stellar ages on three subsamples with spectroscopic observations: solar analogs, late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive relations between Sph and ages between 1 and 5 Gyr, and other stellar properties. For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the model with Prot and Sph with median differences of 0.1% and 0.2%, respectively. We also apply Machine Learning techniques with a Random Forest algorithm to predict ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs together, predicted ages are on average within 5.3% of the model ages and improve to 3.1% when including Prot. These are very promising results for a quick age estimation for solar-like stars with photometric observations, especially with current and future space missions.' acknowledgement: 'This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the NASA Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555. We acknowledge that this research was supported in part by the National Science Foundation under grant No. NSF PHY-1748958. S.M. acknowledges support from the Spanish Ministry of Science and Innovation (MICINN) with the Ramón y Cajal fellowship No. RYC-2015-17697, the grant No. PID2019-107061GB-C66, and through AEI under the Severo Ochoa Centres of Excellence Programme 2020–2023 (CEX2019-000920-S). S.M. and D.G.R. acknowledge support from the Spanish Ministry of Science and Innovation (MICINN) with the grant No. PID2019-107187GB-I00. Z.R.C. acknowledges support from National Aeronautics and Space Administration via the TESS Guest Investigator Program (grant No. 80NSSC18K18584). The work presented here was partially supported by the NASA grant NNX17AF27G. A.R.G.S. acknowledges the support by FCT through national funds and by FEDER through COMPETE2020 by the following grants: UIDB/04434/2020 and UIDP/04434/2020. A.R.G.S. is supported by FCT through the work contract No. 2020.02480.CEECIND/CP1631/CT0001. R.A.G., L.A., and S.N.B. acknowledge the support from PLATO and GOLF CNES grants. S.N.B. acknowledges support from PLATO ASI-INAF agreement No. 2015-019-R.1-2018.' article_number: '131' article_processing_charge: Yes article_type: original author: - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Zachary R. full_name: Claytor, Zachary R. last_name: Claytor - first_name: Ângela R. G. full_name: Santos, Ângela R. G. last_name: Santos - first_name: Rafael A. full_name: García, Rafael A. last_name: García - first_name: Louis full_name: Amard, Louis last_name: Amard - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: Enrico full_name: Corsaro, Enrico last_name: Corsaro - first_name: Alfio full_name: Bonanno, Alfio last_name: Bonanno - first_name: Sylvain N. full_name: Breton, Sylvain N. last_name: Breton - first_name: Diego full_name: Godoy-Rivera, Diego last_name: Godoy-Rivera - first_name: Marc H. full_name: Pinsonneault, Marc H. last_name: Pinsonneault - first_name: Jennifer full_name: van Saders, Jennifer last_name: van Saders citation: ama: Mathur S, Claytor ZR, Santos ÂRG, et al. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 2023;952(2). doi:10.3847/1538-4357/acd118 apa: Mathur, S., Claytor, Z. R., Santos, Â. R. G., García, R. A., Amard, L., Bugnet, L. A., … van Saders, J. (2023). Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/acd118 chicago: Mathur, Savita, Zachary R. Claytor, Ângela R. G. Santos, Rafael A. García, Louis Amard, Lisa Annabelle Bugnet, Enrico Corsaro, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/acd118. ieee: S. Mathur et al., “Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations,” The Astrophysical Journal, vol. 952, no. 2. American Astronomical Society, 2023. ista: Mathur S, Claytor ZR, Santos ÂRG, García RA, Amard L, Bugnet LA, Corsaro E, Bonanno A, Breton SN, Godoy-Rivera D, Pinsonneault MH, van Saders J. 2023. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 952(2), 131. mla: Mathur, Savita, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal, vol. 952, no. 2, 131, American Astronomical Society, 2023, doi:10.3847/1538-4357/acd118. short: S. Mathur, Z.R. Claytor, Â.R.G. Santos, R.A. García, L. Amard, L.A. Bugnet, E. Corsaro, A. Bonanno, S.N. Breton, D. Godoy-Rivera, M.H. Pinsonneault, J. van Saders, The Astrophysical Journal 952 (2023). date_created: 2023-08-01T14:19:16Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T12:00:15Z day: '01' ddc: - '520' department: - _id: LiBu doi: 10.3847/1538-4357/acd118 external_id: isi: - '001034185700001' file: - access_level: open_access checksum: f12452834d7ed6748dbf5ace18af4723 content_type: application/pdf creator: dernst date_created: 2023-08-02T07:42:26Z date_updated: 2023-08-02T07:42:26Z file_id: '13448' file_name: 2023_AstrophysicalJour_Mathur.pdf file_size: 4192386 relation: main_file success: 1 file_date_updated: 2023-08-02T07:42:26Z has_accepted_license: '1' intvolume: ' 952' isi: 1 issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: American Astronomical Society quality_controlled: '1' status: public title: Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 952 year: '2023' ... --- _id: '13259' abstract: - lang: eng text: Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency. acknowledgement: Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical support with tissue culture; and A. Furuta for technical support in bulk RNA-seq analysis. We also thank the Single-cell Omics Laboratory for technical consultation in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and 22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and by the Shiseido Female Researcher Science Grant to M.I. This work was partially supported by RIKENE pigenome Control Program, Medical Research Center Initiative for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N. article_processing_charge: Yes article_type: original author: - first_name: Nao full_name: Ogura, Nao last_name: Ogura - first_name: Yohei full_name: Sasagawa, Yohei last_name: Sasagawa - first_name: Tasuku full_name: Ito, Tasuku id: d5a17a4a-e534-11eb-93ec-91fa2aa9bd57 last_name: Ito orcid: 0000-0002-2482-9089 - first_name: Toshiaki full_name: Tameshige, Toshiaki last_name: Tameshige - first_name: Satomi full_name: Kawai, Satomi last_name: Kawai - first_name: Masaki full_name: Sano, Masaki last_name: Sano - first_name: Yuki full_name: Doll, Yuki last_name: Doll - first_name: Akira full_name: Iwase, Akira last_name: Iwase - first_name: Ayako full_name: Kawamura, Ayako last_name: Kawamura - first_name: Takamasa full_name: Suzuki, Takamasa last_name: Suzuki - first_name: Itoshi full_name: Nikaido, Itoshi last_name: Nikaido - first_name: Keiko full_name: Sugimoto, Keiko last_name: Sugimoto - first_name: Momoko full_name: Ikeuchi, Momoko last_name: Ikeuchi citation: ama: Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 2023;9(27):eadg6983. doi:10.1126/sciadv.adg6983 apa: Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi, M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg6983 chicago: Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai, Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg6983. ieee: N. Ogura et al., “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus,” Science Advances, vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983, 2023. ista: Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 9(27), eadg6983. mla: Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances, vol. 9, no. 27, American Association for the Advancement of Science, 2023, p. eadg6983, doi:10.1126/sciadv.adg6983. short: N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll, A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science Advances 9 (2023) eadg6983. date_created: 2023-07-23T22:01:11Z date_published: 2023-07-07T00:00:00Z date_updated: 2023-12-13T11:59:29Z day: '07' ddc: - '580' doi: 10.1126/sciadv.adg6983 external_id: isi: - '001030983100012' pmid: - '37418524' file: - access_level: open_access checksum: f59217e1083767777318b5d0cc5e141d content_type: application/pdf creator: dernst date_created: 2023-08-01T06:40:35Z date_updated: 2023-08-01T06:40:35Z file_id: '13338' file_name: 2023_ScienceAdvance_Ogura.pdf file_size: 1759993 relation: main_file success: 1 file_date_updated: 2023-08-01T06:40:35Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '27' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: eadg6983 pmid: 1 publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2023' ... --- _id: '13976' abstract: - lang: eng text: Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery. acknowledgement: "Our article is dedicated to all freedom-loving people around the world and to the people of Ukraine who fight for our freedom. Special thanks to Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful review, valuable criticism, and useful suggestions while preparing this manuscript, and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered their time. No funding supported work on this article." article_processing_charge: Yes article_type: original author: - first_name: Walter full_name: Wolfsberger, Walter last_name: Wolfsberger - first_name: Karishma full_name: Chhugani, Karishma last_name: Chhugani - first_name: Khrystyna full_name: Shchubelka, Khrystyna last_name: Shchubelka - first_name: Alina full_name: Frolova, Alina last_name: Frolova - first_name: Yuriy full_name: Salyha, Yuriy last_name: Salyha - first_name: Oksana full_name: Zlenko, Oksana last_name: Zlenko - first_name: Mykhailo full_name: Arych, Mykhailo last_name: Arych - first_name: Dmytro full_name: Dziuba, Dmytro last_name: Dziuba - first_name: Andrii full_name: Parkhomenko, Andrii last_name: Parkhomenko - first_name: Volodymyr full_name: Smolanka, Volodymyr last_name: Smolanka - first_name: Zeynep H. full_name: Gümüş, Zeynep H. last_name: Gümüş - first_name: Efe full_name: Sezgin, Efe last_name: Sezgin - first_name: Alondra full_name: Diaz-Lameiro, Alondra last_name: Diaz-Lameiro - first_name: Viktor R. full_name: Toth, Viktor R. last_name: Toth - first_name: Megi full_name: Maci, Megi last_name: Maci - first_name: Eric full_name: Bortz, Eric last_name: Bortz - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Patricia M. full_name: Morton, Patricia M. last_name: Morton - first_name: Paweł P. full_name: Łabaj, Paweł P. last_name: Łabaj - first_name: Veronika full_name: Romero, Veronika last_name: Romero - first_name: Jakub full_name: Hlávka, Jakub last_name: Hlávka - first_name: Serghei full_name: Mangul, Serghei last_name: Mangul - first_name: Taras K. full_name: Oleksyk, Taras K. last_name: Oleksyk citation: ama: 'Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders: Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045' apa: 'Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. GigaScience. Oxford Academic. https://doi.org/10.1093/gigascience/giad045' chicago: 'Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience. Oxford Academic, 2023. https://doi.org/10.1093/gigascience/giad045.' ieee: 'W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,” GigaScience, vol. 12. Oxford Academic, 2023.' ista: 'Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12.' mla: 'Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience, vol. 12, Oxford Academic, 2023, doi:10.1093/gigascience/giad045.' short: W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko, M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro, V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero, J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023). date_created: 2023-08-06T22:01:13Z date_published: 2023-07-27T00:00:00Z date_updated: 2023-12-13T12:01:46Z day: '27' department: - _id: FyKo doi: 10.1093/gigascience/giad045 external_id: isi: - '001081086100001' pmid: - '37496156' intvolume: ' 12' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/gigascience/giad045 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: GigaScience publication_identifier: eissn: - 2047-217X publication_status: epub_ahead publisher: Oxford Academic quality_controlled: '1' scopus_import: '1' status: public title: 'Scientists without borders: Lessons from Ukraine' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2023' ... --- _id: '13973' abstract: - lang: eng text: We construct families of log K3 surfaces and study the arithmetic of their members. We use this to produce explicit surfaces with an order 5 Brauer–Manin obstruction to the integral Hasse principle. acknowledgement: "This paper was completed as part of a project which received funding from the\r\nEuropean Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie grant agreement No. 754411." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Julian full_name: Lyczak, Julian id: 3572849A-F248-11E8-B48F-1D18A9856A87 last_name: Lyczak citation: ama: Lyczak J. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. 2023;73(2):447-478. doi:10.5802/aif.3529 apa: Lyczak, J. (2023). Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier. https://doi.org/10.5802/aif.3529 chicago: Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier, 2023. https://doi.org/10.5802/aif.3529. ieee: J. Lyczak, “Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces,” Annales de l’Institut Fourier, vol. 73, no. 2. Association des Annales de l’Institut Fourier, pp. 447–478, 2023. ista: Lyczak J. 2023. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. 73(2), 447–478. mla: Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” Annales de l’Institut Fourier, vol. 73, no. 2, Association des Annales de l’Institut Fourier, 2023, pp. 447–78, doi:10.5802/aif.3529. short: J. Lyczak, Annales de l’Institut Fourier 73 (2023) 447–478. date_created: 2023-08-06T22:01:12Z date_published: 2023-05-12T00:00:00Z date_updated: 2023-12-13T12:03:04Z day: '12' ddc: - '510' department: - _id: TiBr doi: 10.5802/aif.3529 ec_funded: 1 external_id: arxiv: - '2005.14013' isi: - '001000279500001' file: - access_level: open_access checksum: daf53fc614c894422e4c0fb3d2a2ae3e content_type: application/pdf creator: dernst date_created: 2023-08-07T07:19:42Z date_updated: 2023-08-07T07:19:42Z file_id: '13977' file_name: 2023_AnnalesFourier_Lyczak.pdf file_size: 1529821 relation: main_file success: 1 file_date_updated: 2023-08-07T07:19:42Z has_accepted_license: '1' intvolume: ' 73' isi: 1 issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 447-478 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Annales de l'Institut Fourier publication_identifier: issn: - 0373-0956 publication_status: published publisher: Association des Annales de l'Institut Fourier quality_controlled: '1' scopus_import: '1' status: public title: Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 73 year: '2023' ... --- _id: '13974' abstract: - lang: eng text: The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common point. In this paper, we prove a trengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result generalizes to a result about simplices in Rd, d≥2. acknowledgement: "Part of the research leading to this paper was done during the 16th Gremo Workshop on Open Problems (GWOP), Waltensburg, Switzerland, June 12–16, 2018. We thank Patrick Schnider for suggesting the problem, and Stefan Felsner, Malte Milatz, and Emo Welzl for fruitful discussions during the workshop. We also thank Stefan Felsner and Manfred Scheucher for finding, communicating the example from Sect. 3.3, and the kind permission to include their visualization of the point set. We thank Dömötör Pálvölgyi, the SoCG reviewers, and DCG reviewers for various helpful comments.\r\nR. Fulek gratefully acknowledges support from Austrian Science Fund (FWF), Project M2281-N35. A. Kupavskii was supported by the Advanced Postdoc.Mobility Grant no. P300P2_177839 of the Swiss National Science Foundation. Research by P. Valtr was supported by the Grant no. 18-19158 S of the Czech Science Foundation (GAČR)." article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Bernd full_name: Gärtner, Bernd last_name: Gärtner - first_name: Andrey full_name: Kupavskii, Andrey last_name: Kupavskii - first_name: Pavel full_name: Valtr, Pavel last_name: Valtr - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. Discrete and Computational Geometry. 2023. doi:10.1007/s00454-023-00532-x apa: Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2023). The crossing Tverberg theorem. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00532-x chicago: Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00532-x. ieee: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” Discrete and Computational Geometry. Springer Nature, 2023. ista: Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2023. The crossing Tverberg theorem. Discrete and Computational Geometry. mla: Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry, Springer Nature, 2023, doi:10.1007/s00454-023-00532-x. short: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, Discrete and Computational Geometry (2023). date_created: 2023-08-06T22:01:12Z date_published: 2023-07-27T00:00:00Z date_updated: 2023-12-13T12:03:35Z day: '27' department: - _id: UlWa doi: 10.1007/s00454-023-00532-x external_id: arxiv: - '1812.04911' isi: - '001038546500001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1812.04911 month: '07' oa: 1 oa_version: Preprint project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '6647' relation: earlier_version status: public scopus_import: '1' status: public title: The crossing Tverberg theorem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13975' abstract: - lang: eng text: "We consider the spectrum of random Laplacian matrices of the form Ln=An−Dn where An\r\n is a real symmetric random matrix and Dn is a diagonal matrix whose entries are equal to the corresponding row sums of An. If An is a Wigner matrix with entries in the domain of attraction of a Gaussian distribution, the empirical spectral measure of Ln is known to converge to the free convolution of a semicircle distribution and a standard real Gaussian distribution. We consider real symmetric random matrices An with independent entries (up to symmetry) whose row sums converge to a purely non-Gaussian infinitely divisible distribution, which fall into the class of Lévy–Khintchine random matrices first introduced by Jung [Trans Am Math Soc, 370, (2018)]. Our main result shows that the empirical spectral measure of Ln converges almost surely to a deterministic limit. A key step in the proof is to use the purely non-Gaussian nature of the row sums to build a random operator to which Ln converges in an appropriate sense. This operator leads to a recursive distributional equation uniquely describing the Stieltjes transform of the limiting empirical spectral measure." acknowledgement: "The first author thanks Yizhe Zhu for pointing out reference [30]. We thank David Renfrew for comments on an earlier draft. We thank the anonymous referee for a careful reading and helpful comments.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria)." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Andrew J full_name: Campbell, Andrew J id: 582b06a9-1f1c-11ee-b076-82ffce00dde4 last_name: Campbell - first_name: Sean full_name: O’Rourke, Sean last_name: O’Rourke citation: ama: Campbell AJ, O’Rourke S. Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability. 2023. doi:10.1007/s10959-023-01275-4 apa: Campbell, A. J., & O’Rourke, S. (2023). Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability. Springer Nature. https://doi.org/10.1007/s10959-023-01275-4 chicago: Campbell, Andrew J, and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random Laplacian Matrices.” Journal of Theoretical Probability. Springer Nature, 2023. https://doi.org/10.1007/s10959-023-01275-4. ieee: A. J. Campbell and S. O’Rourke, “Spectrum of Lévy–Khintchine random laplacian matrices,” Journal of Theoretical Probability. Springer Nature, 2023. ista: Campbell AJ, O’Rourke S. 2023. Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability. mla: Campbell, Andrew J., and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random Laplacian Matrices.” Journal of Theoretical Probability, Springer Nature, 2023, doi:10.1007/s10959-023-01275-4. short: A.J. Campbell, S. O’Rourke, Journal of Theoretical Probability (2023). date_created: 2023-08-06T22:01:13Z date_published: 2023-07-26T00:00:00Z date_updated: 2023-12-13T12:00:50Z day: '26' ddc: - '510' department: - _id: LaEr doi: 10.1007/s10959-023-01275-4 external_id: arxiv: - '2210.07927' isi: - '001038341000001' has_accepted_license: '1' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10959-023-01275-4 month: '07' oa: 1 oa_version: Published Version publication: Journal of Theoretical Probability publication_identifier: eissn: - 1572-9230 issn: - 0894-9840 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Spectrum of Lévy–Khintchine random laplacian matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13257' abstract: - lang: eng text: The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study. acknowledgement: "We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784." article_number: '035111' article_processing_charge: No article_type: original author: - first_name: A. full_name: Shekhter, A. last_name: Shekhter - first_name: R. D. full_name: Mcdonald, R. D. last_name: Mcdonald - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 citation: ama: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. Physical Review B. 2023;108(3). doi:10.1103/PhysRevB.108.035111 apa: Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., & Modic, K. A. (2023). Magnetotropic susceptibility. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.035111 chicago: Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.035111. ieee: A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” Physical Review B, vol. 108, no. 3. American Physical Society, 2023. ista: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111. mla: Shekhter, A., et al. “Magnetotropic Susceptibility.” Physical Review B, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:10.1103/PhysRevB.108.035111. short: A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023). date_created: 2023-07-23T22:01:10Z date_published: 2023-07-15T00:00:00Z date_updated: 2023-12-13T11:58:57Z day: '15' department: - _id: KiMo doi: 10.1103/PhysRevB.108.035111 external_id: arxiv: - '2208.10038' isi: - '001062708600002' intvolume: ' 108' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2208.10038 month: '07' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Magnetotropic susceptibility type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '13972' abstract: - lang: eng text: This Special Collection is dedicated to the field of photocatalytic synthesis and contains a diverse selection of original research contributions. It includes studies on catalyst development, mechanistic investigations, method development and the use of enabling technologies, illustrating the many facets of state-of-the-art research in photocatalytic synthesis. Further, emerging topics are surveyed and discussed in three reviews and a concept article. article_number: e202300683 article_processing_charge: No article_type: letter_note author: - first_name: Line full_name: Næsborg, Line last_name: Næsborg - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Oliver S. full_name: Wenger, Oliver S. last_name: Wenger citation: ama: 'Næsborg L, Pieber B, Wenger OS. Special Collection: Photocatalytic synthesis. ChemCatChem. 2023. doi:10.1002/cctc.202300683' apa: 'Næsborg, L., Pieber, B., & Wenger, O. S. (2023). Special Collection: Photocatalytic synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202300683' chicago: 'Næsborg, Line, Bartholomäus Pieber, and Oliver S. Wenger. “Special Collection: Photocatalytic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202300683.' ieee: 'L. Næsborg, B. Pieber, and O. S. Wenger, “Special Collection: Photocatalytic synthesis,” ChemCatChem. Wiley, 2023.' ista: 'Næsborg L, Pieber B, Wenger OS. 2023. Special Collection: Photocatalytic synthesis. ChemCatChem., e202300683.' mla: 'Næsborg, Line, et al. “Special Collection: Photocatalytic Synthesis.” ChemCatChem, e202300683, Wiley, 2023, doi:10.1002/cctc.202300683.' short: L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem (2023). date_created: 2023-08-06T22:01:12Z date_published: 2023-07-27T00:00:00Z date_updated: 2023-12-13T12:02:26Z day: '27' department: - _id: BaPi doi: 10.1002/cctc.202300683 external_id: isi: - '001037859900001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/cctc.202300683 month: '07' oa: 1 oa_version: Published Version publication: ChemCatChem publication_identifier: eissn: - 1867-3899 issn: - 1867-3880 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Special Collection: Photocatalytic synthesis' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13968' abstract: - lang: eng text: The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface. acknowledged_ssus: - _id: EM-Fac acknowledgement: "This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863–BORGES. We further thank the office of the Federal Government of Lower Austria, K3-Group–Culture, Science and Education, for their financial support as part of the project “Responsive Wound Dressing”. We gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 888067).\r\nWe thank the Electron Microscopy Facility at IST Austria for their support with sputter coating the FO tips and Bernhard Pichler from AIT for software development to facilitate data evaluation." article_number: '1202132' article_processing_charge: Yes article_type: original author: - first_name: Roger full_name: Hasler, Roger last_name: Hasler - first_name: Marie Helene full_name: Steger-Polt, Marie Helene last_name: Steger-Polt - first_name: Ciril full_name: Reiner-Rozman, Ciril last_name: Reiner-Rozman - first_name: Stefan full_name: Fossati, Stefan last_name: Fossati - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Patrik full_name: Aspermair, Patrik last_name: Aspermair - first_name: Christoph full_name: Kleber, Christoph last_name: Kleber - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Jakub full_name: Dostalek, Jakub last_name: Dostalek - first_name: Wolfgang full_name: Knoll, Wolfgang last_name: Knoll citation: ama: 'Hasler R, Steger-Polt MH, Reiner-Rozman C, et al. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 2023;11. doi:10.3389/fphy.2023.1202132' apa: 'Hasler, R., Steger-Polt, M. H., Reiner-Rozman, C., Fossati, S., Lee, S., Aspermair, P., … Knoll, W. (2023). Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. Frontiers. https://doi.org/10.3389/fphy.2023.1202132' chicago: 'Hasler, Roger, Marie Helene Steger-Polt, Ciril Reiner-Rozman, Stefan Fossati, Seungho Lee, Patrik Aspermair, Christoph Kleber, Maria Ibáñez, Jakub Dostalek, and Wolfgang Knoll. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Frontiers in Physics. Frontiers, 2023. https://doi.org/10.3389/fphy.2023.1202132.' ieee: 'R. Hasler et al., “Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing,” Frontiers in Physics, vol. 11. Frontiers, 2023.' ista: 'Hasler R, Steger-Polt MH, Reiner-Rozman C, Fossati S, Lee S, Aspermair P, Kleber C, Ibáñez M, Dostalek J, Knoll W. 2023. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 11, 1202132.' mla: 'Hasler, Roger, et al. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Frontiers in Physics, vol. 11, 1202132, Frontiers, 2023, doi:10.3389/fphy.2023.1202132.' short: R. Hasler, M.H. Steger-Polt, C. Reiner-Rozman, S. Fossati, S. Lee, P. Aspermair, C. Kleber, M. Ibáñez, J. Dostalek, W. Knoll, Frontiers in Physics 11 (2023). date_created: 2023-08-06T22:01:11Z date_published: 2023-07-14T00:00:00Z date_updated: 2023-12-13T12:04:10Z day: '14' ddc: - '530' department: - _id: MaIb doi: 10.3389/fphy.2023.1202132 external_id: isi: - '001038636400001' file: - access_level: open_access checksum: fb36dda665e57bab006a000bf0faacd5 content_type: application/pdf creator: dernst date_created: 2023-08-07T07:48:11Z date_updated: 2023-08-07T07:48:11Z file_id: '13978' file_name: 2023_FrontiersPhysics_Hasler.pdf file_size: 2421758 relation: main_file success: 1 file_date_updated: 2023-08-07T07:48:11Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Frontiers in Physics publication_identifier: eissn: - 2296-424X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2023' ... --- _id: '14042' abstract: - lang: eng text: Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions. acknowledgement: "M. Bulíček and J. Málek acknowledge the support of the project No. 20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing supported by the National Technical Library in Prague." article_number: '72' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Miroslav full_name: Bulíček, Miroslav last_name: Bulíček - first_name: Josef full_name: Málek, Josef last_name: Málek - first_name: Erika full_name: Maringová, Erika id: dbabca31-66eb-11eb-963a-fb9c22c880b4 last_name: Maringová citation: ama: Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w apa: Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer Nature. https://doi.org/10.1007/s00021-023-00803-w chicago: Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics. Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w. ieee: M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer Nature, 2023. ista: Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72. mla: Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature, 2023, doi:10.1007/s00021-023-00803-w. short: M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics 25 (2023). date_created: 2023-08-13T22:01:13Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T12:08:08Z day: '01' ddc: - '510' department: - _id: JuFi doi: 10.1007/s00021-023-00803-w external_id: arxiv: - '2301.12834' isi: - '001040354900001' file: - access_level: open_access checksum: c549cd8f0dd02ed60477a05ca045f481 content_type: application/pdf creator: dernst date_created: 2023-08-14T07:24:17Z date_updated: 2023-08-14T07:24:17Z file_id: '14046' file_name: 2023_JourMathFluidMech_Bulicek.pdf file_size: 845748 relation: main_file success: 1 file_date_updated: 2023-08-14T07:24:17Z has_accepted_license: '1' intvolume: ' 25' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: Journal of Mathematical Fluid Mechanics publication_identifier: eissn: - 1422-6952 issn: - 1422-6928 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2023' ... --- _id: '14041' abstract: - lang: eng text: Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering. acknowledgement: "We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University." article_number: '817' article_processing_charge: Yes article_type: original author: - first_name: Elod full_name: Méhes, Elod last_name: Méhes - first_name: Enys full_name: Mones, Enys last_name: Mones - first_name: Máté full_name: Varga, Máté last_name: Varga - first_name: Áron full_name: Zsigmond, Áron last_name: Zsigmond - first_name: Beáta full_name: Biri-Kovács, Beáta last_name: Biri-Kovács - first_name: László full_name: Nyitray, László last_name: Nyitray - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Tamás full_name: Vicsek, Tamás last_name: Vicsek citation: ama: Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 2023;6. doi:10.1038/s42003-023-05181-7 apa: Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-023-05181-7 chicago: Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology. Springer Nature, 2023. https://doi.org/10.1038/s42003-023-05181-7. ieee: E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023. ista: Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817. mla: Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology, vol. 6, 817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7. short: E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023). date_created: 2023-08-13T22:01:13Z date_published: 2023-08-04T00:00:00Z date_updated: 2023-12-13T12:07:33Z day: '04' ddc: - '570' department: - _id: CaHe - _id: Bio doi: 10.1038/s42003-023-05181-7 external_id: isi: - '001042544100001' pmid: - '37542157' file: - access_level: open_access checksum: 1f9324f736bdbb76426b07736651c4cd content_type: application/pdf creator: dernst date_created: 2023-08-14T07:17:36Z date_updated: 2023-08-14T07:17:36Z file_id: '14045' file_name: 2023_CommBiology_Mehes.pdf file_size: 10181997 relation: main_file success: 1 file_date_updated: 2023-08-14T07:17:36Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Communications Biology publication_identifier: eissn: - 2399-3642 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2023' ... --- _id: '14039' abstract: - lang: eng text: Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them. acknowledgement: We acknowledge funding from the Austrian Science Fund (FWF F79, P32814-B, and P35061-B to S.M.; P34607-B to M.L.; and P30584-B and P33066-B to T.A.L.) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 101045340 to M.L.). We are grateful for comments on the manuscript by Justyna Sawa-Makarska, Verena Baumann, Marko Kojic, Philipp Radler, Ronja Reinhardt, and Sumire Antonioli. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Thomas A. full_name: Leonard, Thomas A. last_name: Leonard - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Sascha full_name: Martens, Sascha last_name: Martens citation: ama: Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 2023;58(15):1315-1332. doi:10.1016/j.devcel.2023.06.001 apa: Leonard, T. A., Loose, M., & Martens, S. (2023). The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.001 chicago: Leonard, Thomas A., Martin Loose, and Sascha Martens. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.001. ieee: T. A. Leonard, M. Loose, and S. Martens, “The membrane surface as a platform that organizes cellular and biochemical processes,” Developmental Cell, vol. 58, no. 15. Elsevier, pp. 1315–1332, 2023. ista: Leonard TA, Loose M, Martens S. 2023. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 58(15), 1315–1332. mla: Leonard, Thomas A., et al. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell, vol. 58, no. 15, Elsevier, 2023, pp. 1315–32, doi:10.1016/j.devcel.2023.06.001. short: T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332. date_created: 2023-08-13T22:01:12Z date_published: 2023-08-07T00:00:00Z date_updated: 2023-12-13T12:09:20Z day: '07' ddc: - '570' department: - _id: MaLo doi: 10.1016/j.devcel.2023.06.001 external_id: isi: - '001059110400001' pmid: - '37419118' file: - access_level: open_access checksum: d8c5dc97cd40c26da2ec98ae723ab368 content_type: application/pdf creator: dernst date_created: 2023-08-14T07:57:55Z date_updated: 2023-08-14T07:57:55Z file_id: '14049' file_name: 2023_DevelopmentalCell_Leonard.pdf file_size: 3184217 relation: main_file success: 1 file_date_updated: 2023-08-14T07:57:55Z has_accepted_license: '1' intvolume: ' 58' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 1315-1332 pmid: 1 project: - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: "Understanding bacterial cell division by in vitro\r\nreconstitution" - _id: bd6ae2ca-d553-11ed-ba76-a4aa239da5ee grant_number: '101045340' name: Synthetic and structural biology of Rab GTPase networks publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The membrane surface as a platform that organizes cellular and biochemical processes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2023' ... --- _id: '14040' abstract: - lang: eng text: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: ScienComp acknowledgement: P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. article_number: '4681' article_processing_charge: Yes article_type: original author: - first_name: Ziyu full_name: Zhao, Ziyu last_name: Zhao - first_name: Irene full_name: Vercellino, Irene id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87 last_name: Vercellino orcid: 0000-0001-5618-3449 - first_name: Jana full_name: Knoppová, Jana last_name: Knoppová - first_name: Roman full_name: Sobotka, Roman last_name: Sobotka - first_name: James W. full_name: Murray, James W. last_name: Murray - first_name: Peter J. full_name: Nixon, Peter J. last_name: Nixon - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Josef full_name: Komenda, Josef last_name: Komenda citation: ama: Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6 apa: Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6 chicago: Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6. ieee: Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681. mla: Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications, vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6. short: Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023). date_created: 2023-08-13T22:01:13Z date_published: 2023-08-04T00:00:00Z date_updated: 2023-12-13T12:06:56Z day: '04' ddc: - '570' department: - _id: LeSa doi: 10.1038/s41467-023-40388-6 external_id: isi: - '001042606700004' file: - access_level: open_access checksum: 3b9043df3d51c300f9be95eac3ff9d0b content_type: application/pdf creator: dernst date_created: 2023-08-14T07:01:12Z date_updated: 2023-08-14T07:01:12Z file_id: '14044' file_name: 2023_NatureComm_Zhao.pdf file_size: 2315325 relation: main_file success: 1 file_date_updated: 2023-08-14T07:01:12Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '13967' abstract: - lang: eng text: 'A classic solution technique for Markov decision processes (MDP) and stochastic games (SG) is value iteration (VI). Due to its good practical performance, this approximative approach is typically preferred over exact techniques, even though no practical bounds on the imprecision of the result could be given until recently. As a consequence, even the most used model checkers could return arbitrarily wrong results. Over the past decade, different works derived stopping criteria, indicating when the precision reaches the desired level, for various settings, in particular MDP with reachability, total reward, and mean payoff, and SG with reachability.In this paper, we provide the first stopping criteria for VI on SG with total reward and mean payoff, yielding the first anytime algorithms in these settings. To this end, we provide the solution in two flavours: First through a reduction to the MDP case and second directly on SG. The former is simpler and automatically utilizes any advances on MDP. The latter allows for more local computations, heading towards better practical efficiency.Our solution unifies the previously mentioned approaches for MDP and SG and their underlying ideas. To achieve this, we isolate objective-specific subroutines as well as identify objective-independent concepts. These structural concepts, while surprisingly simple, form the very essence of the unified solution.' acknowledgement: This research was funded in part by DFG projects 383882557 “SUV” and 427755713 “GOPro”. article_processing_charge: No author: - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 - first_name: Maximilian full_name: Weininger, Maximilian id: 02ab0197-cc70-11ed-ab61-918e71f56881 last_name: Weininger citation: ama: 'Kretinsky J, Meggendorfer T, Weininger M. Stopping criteria for value iteration on stochastic games with quantitative objectives. In: 38th Annual ACM/IEEE Symposium on Logic in Computer Science. Vol 2023. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/LICS56636.2023.10175771' apa: 'Kretinsky, J., Meggendorfer, T., & Weininger, M. (2023). Stopping criteria for value iteration on stochastic games with quantitative objectives. In 38th Annual ACM/IEEE Symposium on Logic in Computer Science (Vol. 2023). Boston, MA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS56636.2023.10175771' chicago: Kretinsky, Jan, Tobias Meggendorfer, and Maximilian Weininger. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” In 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Vol. 2023. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LICS56636.2023.10175771. ieee: J. Kretinsky, T. Meggendorfer, and M. Weininger, “Stopping criteria for value iteration on stochastic games with quantitative objectives,” in 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Boston, MA, United States, 2023, vol. 2023. ista: 'Kretinsky J, Meggendorfer T, Weininger M. 2023. Stopping criteria for value iteration on stochastic games with quantitative objectives. 38th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science vol. 2023.' mla: Kretinsky, Jan, et al. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” 38th Annual ACM/IEEE Symposium on Logic in Computer Science, vol. 2023, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/LICS56636.2023.10175771. short: J. Kretinsky, T. Meggendorfer, M. Weininger, in:, 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2023. conference: end_date: 2023-06-29 location: Boston, MA, United States name: 'LICS: Symposium on Logic in Computer Science' start_date: 2023-06-26 date_created: 2023-08-06T22:01:10Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-12-13T12:06:10Z day: '01' department: - _id: KrCh doi: 10.1109/LICS56636.2023.10175771 external_id: arxiv: - '2304.09930' isi: - '001036707700042' intvolume: ' 2023' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.09930 month: '07' oa: 1 oa_version: Preprint publication: 38th Annual ACM/IEEE Symposium on Logic in Computer Science publication_identifier: isbn: - '9798350335873' issn: - 1043-6871 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Stopping criteria for value iteration on stochastic games with quantitative objectives type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '13965' abstract: - lang: eng text: Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations. article_number: '102087' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Elizabeth full_name: Hollwey, Elizabeth id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd last_name: Hollwey - first_name: Amy full_name: Briffa, Amy last_name: Briffa - first_name: Martin full_name: Howard, Martin last_name: Howard - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 2023;81(8). doi:10.1016/j.gde.2023.102087 apa: Hollwey, E., Briffa, A., Howard, M., & Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2023.102087 chicago: Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087. ieee: E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” Current Opinion in Genetics and Development, vol. 81, no. 8. Elsevier, 2023. ista: Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 81(8), 102087. mla: Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development, vol. 81, no. 8, 102087, Elsevier, 2023, doi:10.1016/j.gde.2023.102087. short: E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023). date_created: 2023-08-06T22:01:10Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T12:05:31Z day: '01' ddc: - '570' department: - _id: DaZi doi: 10.1016/j.gde.2023.102087 external_id: isi: - '001047020200001' pmid: - '37441873' file: - access_level: open_access checksum: a294cd9506b80ed6ef218ef44ed32765 content_type: application/pdf creator: dernst date_created: 2023-08-07T08:32:26Z date_updated: 2023-08-07T08:32:26Z file_id: '13980' file_name: 2023_CurrentOpinionGenetics_Hollwey.pdf file_size: 2568632 relation: main_file success: 1 file_date_updated: 2023-08-07T08:32:26Z has_accepted_license: '1' intvolume: ' 81' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Current Opinion in Genetics and Development publication_identifier: eissn: - 1879-0380 issn: - 0959-437X publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Concepts, mechanisms and implications of long-term epigenetic inheritance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2023' ... --- _id: '14058' abstract: - lang: eng text: "Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 citation: ama: 'Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058' apa: 'Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058' chicago: 'Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058.' ieee: 'G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.' ista: 'Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.' mla: 'Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.' short: 'G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.' date_created: 2023-08-15T10:20:40Z date_published: 2023-08-15T00:00:00Z date_updated: 2023-12-13T12:15:36Z day: '15' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa - _id: BeVi doi: 10.15479/at:ista:14058 ec_funded: 1 file: - access_level: closed checksum: 4e44e169f2724ee8c9324cd60bcc2b71 content_type: application/zip creator: gpuixeus date_created: 2023-08-16T18:15:17Z date_updated: 2023-08-17T06:55:24Z file_id: '14075' file_name: Thesis_latex_forpdfa.zip file_size: 10891454 relation: source_file - access_level: open_access checksum: e10b04cd8f3fecc0d9ef6e6868b6e1e8 content_type: application/pdf creator: gpuixeus date_created: 2023-08-18T10:47:55Z date_updated: 2023-08-18T10:47:55Z file_id: '14079' file_name: PhDThesis_PuixeuG.pdf file_size: 19856686 relation: main_file success: 1 file_date_updated: 2023-08-18T10:47:55Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '230' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A grant_number: '25817' name: 'Sexual conflict: resolution, constraints and biomedical implications' publication_identifier: isbn: - 978-3-99078-035-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9803' relation: research_data status: public - id: '12933' relation: research_data status: public - id: '6831' relation: part_of_dissertation status: public - id: '14077' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: 'The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14077' abstract: - lang: eng text: "The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns." acknowledged_ssus: - _id: ScienComp acknowledgement: We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385). article_processing_charge: Yes article_type: original author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: 'Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121' apa: 'Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121' chicago: 'Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023. https://doi.org/10.1093/g3journal/jkad121.' ieee: 'G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press, 2023.' ista: 'Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).' mla: 'Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.' short: 'G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).' date_created: 2023-08-18T06:52:14Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T12:15:37Z day: '01' ddc: - '570' department: - _id: BeVi - _id: NiBa - _id: GradSch doi: 10.1093/g3journal/jkad121 ec_funded: 1 external_id: isi: - '001002997200001' file: - access_level: open_access checksum: c62e29fc7c5efbf8356f4c60cab4a2d1 content_type: application/pdf creator: dernst date_created: 2023-11-07T09:00:19Z date_updated: 2023-11-07T09:00:19Z file_id: '14498' file_name: 2023_G3_Puixeu.pdf file_size: 845642 relation: main_file success: 1 file_date_updated: 2023-11-07T09:00:19Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '8' keyword: - Genetics (clinical) - Genetics - Molecular Biology language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A grant_number: '25817' name: 'Sexual conflict: resolution, constraints and biomedical implications' publication: 'G3: Genes, Genomes, Genetics' publication_identifier: issn: - 2160-1836 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '12933' relation: research_data status: public - id: '14058' relation: dissertation_contains status: public scopus_import: '1' status: public title: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2023' ... --- _id: '14082' abstract: - lang: eng text: Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision. acknowledged_ssus: - _id: PreCl - _id: Bio acknowledgement: "The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. " article_number: jcs260668 article_processing_charge: No article_type: original author: - first_name: Tomohito full_name: Higashi, Tomohito last_name: Higashi - first_name: Rachel E. full_name: Stephenson, Rachel E. last_name: Stephenson - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 - first_name: Karla full_name: Huljev, Karla id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87 last_name: Huljev - first_name: Atsuko Y. full_name: Higashi, Atsuko Y. last_name: Higashi - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Hideki full_name: Chiba, Hideki last_name: Chiba - first_name: Ann L. full_name: Miller, Ann L. last_name: Miller citation: ama: Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 2023;136(15). doi:10.1242/jcs.260668 apa: Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260668 chicago: Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.260668. ieee: T. Higashi et al., “ZnUMBA - a live imaging method to detect local barrier breaches,” Journal of Cell Science, vol. 136, no. 15. The Company of Biologists, 2023. ista: Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668. mla: Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:10.1242/jcs.260668. short: T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023). date_created: 2023-08-20T22:01:13Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T12:11:18Z day: '01' ddc: - '570' department: - _id: CaHe - _id: EvBe doi: 10.1242/jcs.260668 ec_funded: 1 external_id: isi: - '001070149000001' file: - access_level: closed checksum: a399389b7e3d072f1788b63e612a10b3 content_type: application/pdf creator: dernst date_created: 2023-08-21T07:37:54Z date_updated: 2023-08-21T07:37:54Z embargo: 2024-08-10 embargo_to: open_access file_id: '14092' file_name: 2023_JourCellScience_Higashi.pdf file_size: 18665315 relation: main_file file_date_updated: 2023-08-21T07:37:54Z has_accepted_license: '1' intvolume: ' 136' isi: 1 issue: '15' language: - iso: eng month: '08' oa_version: None project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: ZnUMBA - a live imaging method to detect local barrier breaches type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2023' ... --- _id: '13988' abstract: - lang: eng text: Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains. acknowledgement: This work was supported in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (CAPES)—Brazil (CAPES), in part by the Fundação para a Ciência e Tecnologia (FCT) under Project UIDB/50021/2020 and Grant 2020.05270.BD, in part by the Project COSMOS (via the Orçamento de Estado (OE) with ref. PTDC/EEI-COM/29271/2017 and via the ‘‘Programa Operacional Regional de Lisboa na sua componente Fundo Europeu de Desenvolvimento Regional (FEDER)’’ with ref. Lisboa-01-0145-FEDER-029271), and in part by the project Angainor with reference LISBOA-01-0145-FEDER-031456 as well as supported by Meta Platforms for the project key Transparency at Scale. article_processing_charge: Yes article_type: original author: - first_name: Ray full_name: Neiheiser, Ray id: f09651b9-fec0-11ec-b5d8-934aff0e52a4 last_name: Neiheiser orcid: 0000-0001-7227-8309 - first_name: Gustavo full_name: Inacio, Gustavo last_name: Inacio - first_name: Luciana full_name: Rech, Luciana last_name: Rech - first_name: Carlos full_name: Montez, Carlos last_name: Montez - first_name: Miguel full_name: Matos, Miguel last_name: Matos - first_name: Luis full_name: Rodrigues, Luis last_name: Rodrigues citation: ama: Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. Practical limitations of Ethereum’s layer-2. IEEE Access. 2023;11:8651-8662. doi:10.1109/access.2023.3237897 apa: Neiheiser, R., Inacio, G., Rech, L., Montez, C., Matos, M., & Rodrigues, L. (2023). Practical limitations of Ethereum’s layer-2. IEEE Access. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/access.2023.3237897 chicago: Neiheiser, Ray, Gustavo Inacio, Luciana Rech, Carlos Montez, Miguel Matos, and Luis Rodrigues. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/access.2023.3237897. ieee: R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, and L. Rodrigues, “Practical limitations of Ethereum’s layer-2,” IEEE Access, vol. 11. Institute of Electrical and Electronics Engineers, pp. 8651–8662, 2023. ista: Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 2023. Practical limitations of Ethereum’s layer-2. IEEE Access. 11, 8651–8662. mla: Neiheiser, Ray, et al. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access, vol. 11, Institute of Electrical and Electronics Engineers, 2023, pp. 8651–62, doi:10.1109/access.2023.3237897. short: R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, L. Rodrigues, IEEE Access 11 (2023) 8651–8662. date_created: 2023-08-09T12:09:57Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T12:14:52Z day: '01' ddc: - '000' department: - _id: ElKo doi: 10.1109/access.2023.3237897 external_id: isi: - '000927831000001' file: - access_level: open_access checksum: 4b80b0ff212edf7e5842fbdd53784432 content_type: application/pdf creator: dernst date_created: 2023-08-22T06:37:48Z date_updated: 2023-08-22T06:37:48Z file_id: '14166' file_name: 2023_IEEEAccess_Neiheiser.pdf file_size: 1289285 relation: main_file success: 1 file_date_updated: 2023-08-22T06:37:48Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Engineering - General Materials Science - General Computer Science - Electrical and Electronic Engineering language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 8651-8662 publication: IEEE Access publication_identifier: issn: - 2169-3536 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Practical limitations of Ethereum’s layer-2 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2023' ... --- _id: '12933' abstract: - lang: eng text: Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster". article_processing_charge: No author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 citation: ama: 'Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933' apa: 'Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933' chicago: 'Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.' ieee: 'G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.' ista: 'Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.' mla: 'Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.' short: G. Puixeu Sala, (2023). contributor: - first_name: Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 date_created: 2023-05-10T10:00:49Z date_published: 2023-05-15T00:00:00Z date_updated: 2023-12-13T12:15:36Z day: '15' ddc: - '570' department: - _id: GradSch - _id: NiBa - _id: BeVi doi: 10.15479/AT:ISTA:12933 file: - access_level: open_access checksum: 0ba0bcd0bb8b18d84792136a4370df90 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:43Z date_updated: 2023-05-10T09:41:43Z file_id: '12934' file_name: Dataset_S1.csv file_size: 8029982 relation: main_file success: 1 - access_level: open_access checksum: a62aa9a6d4904e0fdb699cf752640863 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:43Z date_updated: 2023-05-10T09:41:43Z file_id: '12935' file_name: Dataset_S2.csv file_size: 13667640 relation: main_file success: 1 - access_level: open_access checksum: e20ea7f4f8a9bdf1b3849a44664ae58b content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:48Z date_updated: 2023-05-10T09:41:48Z file_id: '12936' file_name: Dataset_S3.csv file_size: 8369141 relation: main_file success: 1 - access_level: open_access checksum: f6156e5fc44446c907ddd0d7289d4cf8 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:50Z date_updated: 2023-05-10T09:41:50Z file_id: '12937' file_name: Dataset_S4.csv file_size: 19543247 relation: main_file success: 1 - access_level: open_access checksum: ae9f54c77a1c42b666ae6c1dfd33ac86 content_type: text/plain creator: gpuixeus date_created: 2023-05-11T12:50:18Z date_updated: 2023-05-11T12:50:18Z file_id: '12944' file_name: readme.txt file_size: 4566 relation: main_file success: 1 file_date_updated: 2023-05-11T12:50:18Z has_accepted_license: '1' month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14058' relation: used_in_publication status: public - id: '14077' relation: used_in_publication status: public status: public title: 'Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14245' abstract: - lang: eng text: We establish effective counting results for lattice points in families of domains in real, complex and quaternionic hyperbolic spaces of any dimension. The domains we focus on are defined as product sets with respect to an Iwasawa decomposition. Several natural diophantine problems can be reduced to counting lattice points in such domains. These include equidistribution of the ratio of the length of the shortest solution (x,y) to the gcd equation bx−ay=1 relative to the length of (a,b), where (a,b) ranges over primitive vectors in a disc whose radius increases, the natural analog of this problem in imaginary quadratic number fields, as well as equidistribution of integral solutions to the diophantine equation defined by an integral Lorentz form in three or more variables. We establish an effective rate of convergence for these equidistribution problems, depending on the size of the spectral gap associated with a suitable lattice subgroup in the isometry group of the relevant hyperbolic space. The main result underlying our discussion amounts to establishing effective joint equidistribution for the horospherical component and the radial component in the Iwasawa decomposition of lattice elements. acknowledgement: The authors thank the referee for important comments which led to significant improvements is the presentation of several results in the paper. They also thank Ami Paz for preparing the figures for this paper. Horesh thanks Ami Paz and Yakov Karasik for helpful discussions. Nevo thanks John Parker and Rene Rühr for providing some very useful references. Nevo is supported by ISF Grant No. 2095/15. article_processing_charge: Yes article_type: original author: - first_name: Tal full_name: Horesh, Tal id: C8B7BF48-8D81-11E9-BCA9-F536E6697425 last_name: Horesh - first_name: Amos full_name: Nevo, Amos last_name: Nevo citation: ama: 'Horesh T, Nevo A. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 2023;324(2):265-294. doi:10.2140/pjm.2023.324.265' apa: 'Horesh, T., & Nevo, A. (2023). Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.324.265' chicago: 'Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.324.265.' ieee: 'T. Horesh and A. Nevo, “Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution,” Pacific Journal of Mathematics, vol. 324, no. 2. Mathematical Sciences Publishers, pp. 265–294, 2023.' ista: 'Horesh T, Nevo A. 2023. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 324(2), 265–294.' mla: 'Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal of Mathematics, vol. 324, no. 2, Mathematical Sciences Publishers, 2023, pp. 265–94, doi:10.2140/pjm.2023.324.265.' short: T. Horesh, A. Nevo, Pacific Journal of Mathematics 324 (2023) 265–294. date_created: 2023-08-27T22:01:18Z date_published: 2023-07-26T00:00:00Z date_updated: 2023-12-13T12:19:42Z day: '26' ddc: - '510' department: - _id: TiBr doi: 10.2140/pjm.2023.324.265 external_id: arxiv: - '1612.08215' isi: - '001047690500001' file: - access_level: open_access checksum: a675b53cfb31fa46be1e879b7e77fe8c content_type: application/pdf creator: dernst date_created: 2023-09-05T07:26:17Z date_updated: 2023-09-05T07:26:17Z file_id: '14267' file_name: 2023_PacificJourMaths_Horesh.pdf file_size: 654895 relation: main_file success: 1 file_date_updated: 2023-09-05T07:26:17Z has_accepted_license: '1' intvolume: ' 324' isi: 1 issue: '2' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 265-294 publication: Pacific Journal of Mathematics publication_identifier: eissn: - 1945-5844 issn: - 0030-8730 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: 'Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 324 year: '2023' ... --- _id: '14246' abstract: - lang: eng text: The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding of a coupling between gauge potentials and matter. The typical formulation of the model is based upon a single particle picture, and should be extended when interactions with other particles become relevant. Here, we illustrate such an extension for a particle in an Aharonov-Bohm ring subject to interactions with a weakly interacting Bose gas. We show that the ground state of the system can be described using the Bose-polaron concept—a particle dressed by interactions with a bosonic environment. We connect the energy spectrum to the effective mass of the polaron, and demonstrate how to change currents in the system by tuning boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform for studying coherence and few- to many-body crossover of quasi-particles that arise from an impurity immersed in a medium. acknowledgement: "Open Access funding enabled and organized by Projekt DEAL.\r\nWe would like to thank Jonas Jager for sharing his data with us in the early stages of this project. We thank Joachim Brand and Ray Yang for sharing with us data from Yang et al.46. This work has received funding from the DFG Project no. 413495248 [VO 2437/1-1] (F.B., H.-W.H., A.G.V.). We acknowledge support from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) and the Open Access Publishing Fund of the Technical University of Darmstadt." article_number: '224' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Fabian full_name: Brauneis, Fabian last_name: Brauneis - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Hans-Werner full_name: Hammer, Hans-Werner last_name: Hammer - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 2023;6. doi:10.1038/s42005-023-01281-2 apa: Brauneis, F., Ghazaryan, A., Hammer, H.-W., & Volosniev, A. (2023). Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-023-01281-2 chicago: Brauneis, Fabian, Areg Ghazaryan, Hans-Werner Hammer, and Artem Volosniev. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” Communications Physics. Springer Nature, 2023. https://doi.org/10.1038/s42005-023-01281-2. ieee: F. Brauneis, A. Ghazaryan, H.-W. Hammer, and A. Volosniev, “Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux,” Communications Physics, vol. 6. Springer Nature, 2023. ista: Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. 2023. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 6, 224. mla: Brauneis, Fabian, et al. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” Communications Physics, vol. 6, 224, Springer Nature, 2023, doi:10.1038/s42005-023-01281-2. short: F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (2023). date_created: 2023-08-28T12:36:49Z date_published: 2023-08-22T00:00:00Z date_updated: 2023-12-13T12:21:09Z day: '22' ddc: - '530' department: - _id: MiLe doi: 10.1038/s42005-023-01281-2 external_id: arxiv: - '2301.10488' isi: - '001052577500002' file: - access_level: open_access checksum: 6edfc59b0ee7dc406d0968b05236e83d content_type: application/pdf creator: dernst date_created: 2023-09-05T08:45:49Z date_updated: 2023-09-05T08:45:49Z file_id: '14268' file_name: 2023_CommPhysics_Brauneis.pdf file_size: 855960 relation: main_file success: 1 file_date_updated: 2023-09-05T08:45:49Z has_accepted_license: '1' intvolume: ' 6' isi: 1 keyword: - General Physics and Astronomy language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: Communications Physics publication_identifier: issn: - 2399-3650 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2023' ... --- _id: '14239' abstract: - lang: eng text: "Given a resolution of rational singularities π:X~→X over a field of characteristic zero, we use a Hodge-theoretic argument to prove that the image of the functor \ Rπ∗:Db(X~)→Db(X)\r\n between bounded derived categories of coherent sheaves generates Db(X)\r\n as a triangulated category. This gives a weak version of the Bondal–Orlov localization conjecture [BO02], answering a question from [PS21]. The same result is established more generally for proper (not necessarily birational) morphisms π:X~→X , with X~\r\n smooth, satisfying Rπ∗(OX~)=OX ." acknowledgement: "We thank Agnieszka Bodzenta-Skibińska, Paolo Cascini, Wahei Hara, Sándor Kovács, Alexander Kuznetsov, Mircea Musta ă, Nebojsa Pavic, Pavel Sechin, and Michael Wemyss for discussions and e-mail correspondence. We also thank the anonymous referee for the helpful comments. M.M. was supported by the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 101034413. E.S. was partially supported by the EPSRC grant EP/T019379/1 “Derived categories and algebraic K-theory of singularities”, and by the ERC Synergy grant “Modern Aspects of Geometry: Categories, Cycles and Cohomology of Hyperkähler Varieties.”\r\n\r\n" article_number: e66 article_processing_charge: Yes article_type: original author: - first_name: Mirko full_name: Mauri, Mirko id: 2cf70c34-09c1-11ed-bd8d-c34fac206130 last_name: Mauri - first_name: Evgeny full_name: Shinder, Evgeny last_name: Shinder citation: ama: Mauri M, Shinder E. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.65 apa: Mauri, M., & Shinder, E. (2023). Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.65 chicago: Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.65. ieee: M. Mauri and E. Shinder, “Homological Bondal-Orlov localization conjecture for rational singularities,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023. ista: Mauri M, Shinder E. 2023. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 11, e66. mla: Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” Forum of Mathematics, Sigma, vol. 11, e66, Cambridge University Press, 2023, doi:10.1017/fms.2023.65. short: M. Mauri, E. Shinder, Forum of Mathematics, Sigma 11 (2023). date_created: 2023-08-27T22:01:16Z date_published: 2023-08-03T00:00:00Z date_updated: 2023-12-13T12:18:18Z day: '03' ddc: - '510' department: - _id: TaHa doi: 10.1017/fms.2023.65 ec_funded: 1 external_id: arxiv: - '2212.06786' isi: - '001041926700001' file: - access_level: open_access checksum: c36241750cc5cb06890aec0ecdfee626 content_type: application/pdf creator: dernst date_created: 2023-09-05T06:43:11Z date_updated: 2023-09-05T06:43:11Z file_id: '14266' file_name: 2023_ForumMathematics_Mauri.pdf file_size: 280865 relation: main_file success: 1 file_date_updated: 2023-09-05T06:43:11Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Forum of Mathematics, Sigma publication_identifier: eissn: - 2050-5094 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Homological Bondal-Orlov localization conjecture for rational singularities tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2023' ... --- _id: '14192' abstract: - lang: eng text: For the Fröhlich model of the large polaron, we prove that the ground state energy as a function of the total momentum has a unique global minimum at momentum zero. This implies the non-existence of a ground state of the translation invariant Fröhlich Hamiltonian and thus excludes the possibility of a localization transition at finite coupling. acknowledgement: D.M. and K.M. thank Robert Seiringer for helpful discussions. Open access funding provided by Institute of Science and Technology (IST Austria). Financial support from the Agence Nationale de la Recherche (ANR) through the projects ANR-17-CE40-0016, ANR-17-CE40-0007-01, ANR-17-EURE-0002 (J.L.) and from the European Union’s Horizon 2020 research and innovation programme under the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.) is gratefully acknowledged. article_number: '17' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jonas full_name: Lampart, Jonas last_name: Lampart - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Krzysztof full_name: Mysliwy, Krzysztof id: 316457FC-F248-11E8-B48F-1D18A9856A87 last_name: Mysliwy citation: ama: Lampart J, Mitrouskas DJ, Mysliwy K. On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. 2023;26(3). doi:10.1007/s11040-023-09460-x apa: Lampart, J., Mitrouskas, D. J., & Mysliwy, K. (2023). On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. Springer Nature. https://doi.org/10.1007/s11040-023-09460-x chicago: Lampart, Jonas, David Johannes Mitrouskas, and Krzysztof Mysliwy. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” Mathematical Physics, Analysis and Geometry. Springer Nature, 2023. https://doi.org/10.1007/s11040-023-09460-x. ieee: J. Lampart, D. J. Mitrouskas, and K. Mysliwy, “On the global minimum of the energy–momentum relation for the polaron,” Mathematical Physics, Analysis and Geometry, vol. 26, no. 3. Springer Nature, 2023. ista: Lampart J, Mitrouskas DJ, Mysliwy K. 2023. On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. 26(3), 17. mla: Lampart, Jonas, et al. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” Mathematical Physics, Analysis and Geometry, vol. 26, no. 3, 17, Springer Nature, 2023, doi:10.1007/s11040-023-09460-x. short: J. Lampart, D.J. Mitrouskas, K. Mysliwy, Mathematical Physics, Analysis and Geometry 26 (2023). date_created: 2023-08-22T14:09:47Z date_published: 2023-07-26T00:00:00Z date_updated: 2023-12-13T12:16:19Z day: '26' ddc: - '510' department: - _id: RoSe doi: 10.1007/s11040-023-09460-x external_id: arxiv: - '2206.14708' isi: - '001032992600001' file: - access_level: open_access checksum: f0941cc66cb3ed06a12ca4b7e356cfd6 content_type: application/pdf creator: dernst date_created: 2023-08-23T10:59:15Z date_updated: 2023-08-23T10:59:15Z file_id: '14225' file_name: 2023_MathPhysics_Lampart.pdf file_size: 317026 relation: main_file success: 1 file_date_updated: 2023-08-23T10:59:15Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '3' keyword: - Geometry and Topology - Mathematical Physics language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Mathematical Physics, Analysis and Geometry publication_identifier: eissn: - 1572-9656 issn: - 1385-0172 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: On the global minimum of the energy–momentum relation for the polaron tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2023' ... --- _id: '14238' abstract: - lang: eng text: We demonstrate that a sodium dimer, Na2(13Σ+u), residing on the surface of a helium nanodroplet, can be set into rotation by a nonresonant 1.0 ps infrared laser pulse. The time-dependent degree of alignment measured, exhibits a periodic, gradually decreasing structure that deviates qualitatively from that expected for gas-phase dimers. Comparison to alignment dynamics calculated from the time-dependent rotational Schrödinger equation shows that the deviation is due to the alignment dependent interaction between the dimer and the droplet surface. This interaction confines the dimer to the tangential plane of the droplet surface at the point where it resides and is the reason that the observed alignment dynamics is also well described by a 2D quantum rotor model. acknowledgement: H. S. acknowledges support from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). F. J. and R. E. Z. acknowledge support from the Centre for Scientific Computing, Aarhus and the JKU scientific computing administration, Linz, respectively. article_number: '053201' article_processing_charge: No article_type: original author: - first_name: Lorenz full_name: Kranabetter, Lorenz last_name: Kranabetter - first_name: Henrik H. full_name: Kristensen, Henrik H. last_name: Kristensen - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Constant A. full_name: Schouder, Constant A. last_name: Schouder - first_name: Adam S. full_name: Chatterley, Adam S. last_name: Chatterley - first_name: Paul full_name: Janssen, Paul last_name: Janssen - first_name: Frank full_name: Jensen, Frank last_name: Jensen - first_name: Robert E. full_name: Zillich, Robert E. last_name: Zillich - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Henrik full_name: Stapelfeldt, Henrik last_name: Stapelfeldt citation: ama: Kranabetter L, Kristensen HH, Ghazaryan A, et al. Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. 2023;131(5). doi:10.1103/PhysRevLett.131.053201 apa: Kranabetter, L., Kristensen, H. H., Ghazaryan, A., Schouder, C. A., Chatterley, A. S., Janssen, P., … Stapelfeldt, H. (2023). Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.053201 chicago: Kranabetter, Lorenz, Henrik H. Kristensen, Areg Ghazaryan, Constant A. Schouder, Adam S. Chatterley, Paul Janssen, Frank Jensen, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Nonadiabatic Laser-Induced Alignment Dynamics of Molecules on a Surface.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.053201. ieee: L. Kranabetter et al., “Nonadiabatic laser-induced alignment dynamics of molecules on a surface,” Physical Review Letters, vol. 131, no. 5. American Physical Society, 2023. ista: Kranabetter L, Kristensen HH, Ghazaryan A, Schouder CA, Chatterley AS, Janssen P, Jensen F, Zillich RE, Lemeshko M, Stapelfeldt H. 2023. Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. 131(5), 053201. mla: Kranabetter, Lorenz, et al. “Nonadiabatic Laser-Induced Alignment Dynamics of Molecules on a Surface.” Physical Review Letters, vol. 131, no. 5, 053201, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.053201. short: L. Kranabetter, H.H. Kristensen, A. Ghazaryan, C.A. Schouder, A.S. Chatterley, P. Janssen, F. Jensen, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 131 (2023). date_created: 2023-08-27T22:01:16Z date_published: 2023-08-04T00:00:00Z date_updated: 2023-12-13T12:18:54Z day: '04' department: - _id: MiLe doi: 10.1103/PhysRevLett.131.053201 ec_funded: 1 external_id: arxiv: - '2308.15247' isi: - '001101784100001' pmid: - '37595218' intvolume: ' 131' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2308.15247 month: '08' oa: 1 oa_version: Preprint pmid: 1 project: - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Nonadiabatic laser-induced alignment dynamics of molecules on a surface type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2023' ... --- _id: '14255' abstract: - lang: eng text: Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells. acknowledged_ssus: - _id: EM-Fac acknowledgement: "We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively." article_number: e1011562 article_processing_charge: Yes article_type: original author: - first_name: Jana full_name: Koch, Jana last_name: Koch - first_name: Qilin full_name: Xin, Qilin last_name: Xin - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Alicia full_name: Schäfer, Alicia last_name: Schäfer - first_name: Nina full_name: Rolfs, Nina last_name: Rolfs - first_name: Holda A. full_name: Anagho, Holda A. last_name: Anagho - first_name: Aiste full_name: Kudulyte, Aiste last_name: Kudulyte - first_name: Lea full_name: Woltereck, Lea last_name: Woltereck - first_name: Susann full_name: Kummer, Susann last_name: Kummer - first_name: Joaquin full_name: Campos, Joaquin last_name: Campos - first_name: Zina M. full_name: Uckeley, Zina M. last_name: Uckeley - first_name: Lesley full_name: Bell-Sakyi, Lesley last_name: Bell-Sakyi - first_name: Hans Georg full_name: Kräusslich, Hans Georg last_name: Kräusslich - first_name: Florian Km full_name: Schur, Florian Km id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Claudio full_name: Acuna, Claudio last_name: Acuna - first_name: Pierre Yves full_name: Lozach, Pierre Yves last_name: Lozach citation: ama: Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 2023;19(8). doi:10.1371/journal.ppat.1011562 apa: Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1011562 chicago: Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens. Public Library of Science, 2023. https://doi.org/10.1371/journal.ppat.1011562. ieee: J. Koch et al., “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” PLoS Pathogens, vol. 19, no. 8. Public Library of Science, 2023. ista: Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562. mla: Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:10.1371/journal.ppat.1011562. short: J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023). date_created: 2023-09-03T22:01:14Z date_published: 2023-08-14T00:00:00Z date_updated: 2023-12-13T12:22:22Z day: '14' ddc: - '570' department: - _id: FlSc doi: 10.1371/journal.ppat.1011562 external_id: isi: - '001050846300004' pmid: - '37578957' file: - access_level: open_access checksum: 47ca3bb54b27f28b05644be0ad064bc6 content_type: application/pdf creator: dernst date_created: 2023-09-06T06:41:52Z date_updated: 2023-09-06T06:41:52Z file_id: '14269' file_name: 2023_PloSPathogens_Koch.pdf file_size: 4458336 relation: main_file success: 1 file_date_updated: 2023-09-06T06:41:52Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: PLoS Pathogens publication_identifier: eissn: - 1553-7374 issn: - 1553-7366 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2023' ... --- _id: '14339' abstract: - lang: eng text: Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux. acknowledgement: We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: S full_name: Roychoudhry, S last_name: Roychoudhry - first_name: K full_name: Sageman-Furnas, K last_name: Sageman-Furnas - first_name: C full_name: Wolverton, C last_name: Wolverton - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: M full_name: De Angelis, M last_name: De Angelis - first_name: HL full_name: Goodman, HL last_name: Goodman - first_name: N full_name: Capstaff, N last_name: Capstaff - first_name: Lloyd full_name: JPB, Lloyd last_name: JPB - first_name: J full_name: Mullen, J last_name: Mullen - first_name: R full_name: Hangarter, R last_name: Hangarter - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: S full_name: Kepinski, S last_name: Kepinski citation: ama: Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 2023;9:1500-1513. doi:10.1038/s41477-023-01478-x apa: Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-023-01478-x chicago: Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants. Springer Nature, 2023. https://doi.org/10.1038/s41477-023-01478-x. ieee: S. Roychoudhry et al., “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” Nature Plants, vol. 9. Springer Nature, pp. 1500–1513, 2023. ista: Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513. mla: Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:10.1038/s41477-023-01478-x. short: S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513. date_created: 2023-09-15T09:56:01Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-12-13T12:23:49Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41477-023-01478-x external_id: isi: - '001069238800014' pmid: - '37666965' file: - access_level: open_access checksum: 3d6d5d5abb937c14a5f6f0afba3b8624 content_type: application/pdf creator: dernst date_created: 2023-09-20T10:51:31Z date_updated: 2023-09-20T10:51:31Z file_id: '14351' file_name: 2023_NaturePlants_Roychoudhry.pdf file_size: 9647103 relation: main_file success: 1 file_date_updated: 2023-09-20T10:51:31Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1500-1513 pmid: 1 publication: Nature Plants publication_identifier: issn: - 2055-0278 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Antigravitropic PIN polarization maintains non-vertical growth in lateral roots tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2023' ... --- _id: '14363' abstract: - lang: eng text: Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl acknowledgement: We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article. article_number: '107780' article_processing_charge: Yes article_type: original author: - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 - first_name: Florianne E full_name: Schoot Uiterkamp, Florianne E id: 3526230C-F248-11E8-B48F-1D18A9856A87 last_name: Schoot Uiterkamp - first_name: Felix full_name: Sternberg, Felix last_name: Sternberg - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Elena E. full_name: Pohl, Elena E. last_name: Pohl - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 2023;26(10). doi:10.1016/j.isci.2023.107780 apa: Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., & Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107780 chicago: Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107780. ieee: M. E. Maes et al., “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” iScience, vol. 26, no. 10. Elsevier, 2023. ista: Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780. mla: Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience, vol. 26, no. 10, 107780, Elsevier, 2023, doi:10.1016/j.isci.2023.107780. short: M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023). date_created: 2023-09-24T22:01:11Z date_published: 2023-10-20T00:00:00Z date_updated: 2023-12-13T12:27:30Z day: '20' ddc: - '570' department: - _id: SaSi doi: 10.1016/j.isci.2023.107780 external_id: isi: - '001080403500001' pmid: - '37731609' file: - access_level: open_access checksum: be1a560efdd96d20712311f4fc54aac2 content_type: application/pdf creator: dernst date_created: 2023-11-07T08:53:21Z date_updated: 2023-11-07T08:53:21Z file_id: '14497' file_name: 2023_iScience_Maes.pdf file_size: 8197935 relation: main_file success: 1 file_date_updated: 2023-11-07T08:53:21Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: iScience publication_identifier: eissn: - 2589-0042 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2023' ... --- _id: '14343' abstract: - lang: eng text: The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation. acknowledgement: "G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331." article_number: e74 article_processing_charge: Yes article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Oleksii full_name: Kolupaiev, Oleksii id: 149b70d4-896a-11ed-bdf8-8c63fd44ca61 last_name: Kolupaiev citation: ama: Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.70 apa: Cipolloni, G., Erdös, L., Henheik, S. J., & Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.70 chicago: Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.70. ieee: G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023. ista: Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74. mla: Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 11, e74, Cambridge University Press, 2023, doi:10.1017/fms.2023.70. short: G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023). date_created: 2023-09-17T22:01:09Z date_published: 2023-08-23T00:00:00Z date_updated: 2023-12-13T12:24:23Z day: '23' ddc: - '510' department: - _id: LaEr - _id: GradSch doi: 10.1017/fms.2023.70 ec_funded: 1 external_id: arxiv: - '2301.05181' isi: - '001051980200001' file: - access_level: open_access checksum: eb747420e6a88a7796fa934151957676 content_type: application/pdf creator: dernst date_created: 2023-09-20T11:09:35Z date_updated: 2023-09-20T11:09:35Z file_id: '14352' file_name: 2023_ForumMathematics_Cipolloni.pdf file_size: 852652 relation: main_file success: 1 file_date_updated: 2023-09-20T11:09:35Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Forum of Mathematics, Sigma publication_identifier: eissn: - 2050-5094 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Gaussian fluctuations in the equipartition principle for Wigner matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2023' ... --- _id: '14364' abstract: - lang: eng text: We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve -set agreement among processes or approximate agreement on a cycle of length 4 among processes in a wait-free manner in asynchronous models where processes communicate using objects that can be constructed from shared registers. However, it was unknown whether proofs based on simpler techniques were possible. We show that these impossibility results cannot be obtained by extension-based proofs in the iterated snapshot model and, hence, extension-based proofs are limited in power. acknowledgement: "We would like to thank Valerie King, Toniann Pitassi, and Michael Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research was supported by the Natural Science and Engineering Research Council of Canada under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship, and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship; the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385, CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel corporations. Some of the work on this paper was done while Faith Ellen was visiting IST Austria." article_processing_charge: No article_type: original author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Faith full_name: Ellen, Faith last_name: Ellen - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili - first_name: Leqi full_name: Zhu, Leqi id: a2117c59-cee4-11ed-b9d0-874ecf0f8ac5 last_name: Zhu citation: ama: Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. SIAM Journal on Computing. 2023;52(4):913-944. doi:10.1137/20M1375851 apa: Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2023). Why extension-based proofs fail. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1375851 chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/20M1375851. ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” SIAM Journal on Computing, vol. 52, no. 4. Society for Industrial and Applied Mathematics, pp. 913–944, 2023. ista: Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based proofs fail. SIAM Journal on Computing. 52(4), 913–944. mla: Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing, vol. 52, no. 4, Society for Industrial and Applied Mathematics, 2023, pp. 913–44, doi:10.1137/20M1375851. short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944. date_created: 2023-09-24T22:01:11Z date_published: 2023-07-25T00:00:00Z date_updated: 2023-12-13T12:28:29Z day: '25' department: - _id: DaAl doi: 10.1137/20M1375851 ec_funded: 1 external_id: arxiv: - '1811.01421' isi: - '001082972300004' intvolume: ' 52' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.01421 month: '07' oa: 1 oa_version: Preprint page: 913-944 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '6676' relation: earlier_version status: public scopus_import: '1' status: public title: Why extension-based proofs fail type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2023' ... --- _id: '14345' abstract: - lang: eng text: For a locally finite set in R2, the order-k Brillouin tessellations form an infinite sequence of convex face-to-face tilings of the plane. If the set is coarsely dense and generic, then the corresponding infinite sequences of minimum and maximum angles are both monotonic in k. As an example, a stationary Poisson point process in R2 is locally finite, coarsely dense, and generic with probability one. For such a set, the distributions of angles in the Voronoi tessellations, Delaunay mosaics, and Brillouin tessellations are independent of the order and can be derived from the formula for angles in order-1 Delaunay mosaics given by Miles (Math. Biosci. 6, 85–127 (1970)). acknowledgement: Work by all authors but A. Garber is supported by the European Research Council (ERC), Grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), Grant No. I 02979-N35. Work by A. Garber is partially supported by the Alexander von Humboldt Foundation. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Alexey full_name: Garber, Alexey last_name: Garber - first_name: Mohadese full_name: Ghafari, Mohadese last_name: Ghafari - first_name: Teresa full_name: Heiss, Teresa id: 4879BB4E-F248-11E8-B48F-1D18A9856A87 last_name: Heiss orcid: 0000-0002-1780-2689 - first_name: Morteza full_name: Saghafian, Morteza id: f86f7148-b140-11ec-9577-95435b8df824 last_name: Saghafian citation: ama: Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry. 2023. doi:10.1007/s00454-023-00566-1 apa: Edelsbrunner, H., Garber, A., Ghafari, M., Heiss, T., & Saghafian, M. (2023). On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00566-1 chicago: Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafari, Teresa Heiss, and Morteza Saghafian. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00566-1. ieee: H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, and M. Saghafian, “On angles in higher order Brillouin tessellations and related tilings in the plane,” Discrete and Computational Geometry. Springer Nature, 2023. ista: Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. 2023. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry. mla: Edelsbrunner, Herbert, et al. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” Discrete and Computational Geometry, Springer Nature, 2023, doi:10.1007/s00454-023-00566-1. short: H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, M. Saghafian, Discrete and Computational Geometry (2023). date_created: 2023-09-17T22:01:10Z date_published: 2023-09-07T00:00:00Z date_updated: 2023-12-13T12:25:06Z day: '07' department: - _id: HeEd doi: 10.1007/s00454-023-00566-1 ec_funded: 1 external_id: arxiv: - '2204.01076' isi: - '001060727600004' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00454-023-00566-1 month: '09' oa: 1 oa_version: Published Version project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: On angles in higher order Brillouin tessellations and related tilings in the plane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14378' abstract: - lang: eng text: 'Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization.' acknowledgement: "We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions. We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.), University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the support of Biocenter Finland. The AAVpreparations were produced at the Helsinki Virus (HelVi) Core." article_number: '5878' article_processing_charge: Yes article_type: original author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Emmi full_name: Tiilikainen, Emmi last_name: Tiilikainen - first_name: Inam full_name: Liaqat, Inam last_name: Liaqat - first_name: Emma full_name: Jakobsson, Emma last_name: Jakobsson - first_name: Harri full_name: Nurmi, Harri last_name: Nurmi - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 citation: ama: Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 2023;14. doi:10.1038/s41467-023-41456-7 apa: Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., & Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41456-7 chicago: Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41456-7. ieee: M. C. Ucar et al., “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. 2023. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 14, 5878. mla: Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature Communications, vol. 14, 5878, Springer Nature, 2023, doi:10.1038/s41467-023-41456-7. short: M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023). date_created: 2023-10-01T22:01:13Z date_published: 2023-09-21T00:00:00Z date_updated: 2023-12-13T12:31:05Z day: '21' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41467-023-41456-7 ec_funded: 1 external_id: isi: - '001075884500007' pmid: - '37735168' file: - access_level: open_access checksum: 4fe5423403f2531753bcd9e0fea48e05 content_type: application/pdf creator: dernst date_created: 2023-10-03T07:46:36Z date_updated: 2023-10-03T07:46:36Z file_id: '14384' file_name: 2023_NatureComm_Ucar.pdf file_size: 8143264 relation: main_file success: 1 file_date_updated: 2023-10-03T07:46:36Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14361' abstract: - lang: eng text: Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: M-Shop acknowledgement: We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. article_number: '5633' article_processing_charge: Yes article_type: original author: - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 - first_name: Isabelle D full_name: Mayer, Isabelle D id: 61763940-15b2-11ec-abd3-cfaddfbc66b4 last_name: Mayer - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 2023;14. doi:10.1038/s41467-023-41432-1 apa: Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41432-1 chicago: Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1. ieee: M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633. mla: Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature, 2023, doi:10.1038/s41467-023-41432-1. short: M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023). date_created: 2023-09-24T22:01:10Z date_published: 2023-09-13T00:00:00Z date_updated: 2023-12-13T12:29:41Z day: '13' ddc: - '530' - '570' department: - _id: MiSi - _id: NanoFab - _id: BjHo doi: 10.1038/s41467-023-41432-1 ec_funded: 1 external_id: isi: - '001087583700030' pmid: - '37704595' file: - access_level: open_access checksum: 82d2d4ad736cc8493db8ce45cd313f7b content_type: application/pdf creator: dernst date_created: 2023-09-25T08:32:37Z date_updated: 2023-09-25T08:32:37Z file_id: '14366' file_name: 2023_NatureComm_Riedl.pdf file_size: 2317272 relation: main_file success: 1 file_date_updated: 2023-09-25T08:32:37Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Synchronization in collectively moving inanimate and living active matter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14421' abstract: - lang: eng text: Only recently has it been possible to construct a self-adjoint Hamiltonian that involves the creation of Dirac particles at a point source in 3d space. Its definition makes use of an interior-boundary condition. Here, we develop for this Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously) construct a Markov jump process $(Q_t)_{t\in\mathbb{R}}$ in the configuration space of a variable number of particles that is $|\psi_t|^2$-distributed at every time t and follows Bohmian trajectories between the jumps. The jumps correspond to particle creation or annihilation events and occur either to or from a configuration with a particle located at the source. The process is the natural analog of Bell's jump process, and a central piece in its construction is the determination of the rate of particle creation. The construction requires an analysis of the asymptotic behavior of the Bohmian trajectories near the source. We find that the particle reaches the source with radial speed 0, but orbits around the source infinitely many times in finite time before absorption (or after emission). acknowledgement: J H gratefully acknowledges partial financial support by the ERC Advanced Grant 'RMTBeyond' No. 101020331. article_number: '445201' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Roderich full_name: Tumulka, Roderich last_name: Tumulka citation: ama: 'Henheik SJ, Tumulka R. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 2023;56(44). doi:10.1088/1751-8121/acfe62' apa: 'Henheik, S. J., & Tumulka, R. (2023). Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/acfe62' chicago: 'Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2023. https://doi.org/10.1088/1751-8121/acfe62.' ieee: 'S. J. Henheik and R. Tumulka, “Creation rate of Dirac particles at a point source,” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44. IOP Publishing, 2023.' ista: 'Henheik SJ, Tumulka R. 2023. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 56(44), 445201.' mla: 'Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44, 445201, IOP Publishing, 2023, doi:10.1088/1751-8121/acfe62.' short: 'S.J. Henheik, R. Tumulka, Journal of Physics A: Mathematical and Theoretical 56 (2023).' date_created: 2023-10-12T12:42:53Z date_published: 2023-10-11T00:00:00Z date_updated: 2023-12-13T13:01:25Z day: '11' ddc: - '510' department: - _id: GradSch - _id: LaEr doi: 10.1088/1751-8121/acfe62 ec_funded: 1 external_id: arxiv: - '2211.16606' isi: - '001080908000001' file: - access_level: open_access checksum: 5b68de147dd4c608b71a6e0e844d2ce9 content_type: application/pdf creator: dernst date_created: 2023-10-16T07:07:24Z date_updated: 2023-10-16T07:07:24Z file_id: '14429' file_name: 2023_JourPhysics_Henheik.pdf file_size: 721399 relation: main_file success: 1 file_date_updated: 2023-10-16T07:07:24Z has_accepted_license: '1' intvolume: ' 56' isi: 1 issue: '44' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: 'Journal of Physics A: Mathematical and Theoretical' publication_identifier: eissn: - 1751-8121 issn: - 1751-8113 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Creation rate of Dirac particles at a point source tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 56 year: '2023' ... --- _id: '14400' abstract: - lang: eng text: "We consider the problem of computing the maximal probability of satisfying an \r\n-regular specification for stochastic, continuous-state, nonlinear systems evolving in discrete time. The problem reduces, after automata-theoretic constructions, to finding the maximal probability of satisfying a parity condition on a (possibly hybrid) state space. While characterizing the exact satisfaction probability is open, we show that a lower bound on this probability can be obtained by (I) computing an under-approximation of the qualitative winning region, i.e., states from which the parity condition can be enforced almost surely, and (II) computing the maximal probability of reaching this qualitative winning region.\r\nThe heart of our approach is a technique to symbolically compute the under-approximation of the qualitative winning region in step (I) via a finite-state abstraction of the original system as a \r\n-player parity game. Our abstraction procedure uses only the support of the probabilistic evolution; it does not use precise numerical transition probabilities. We prove that the winning set in the abstract -player game induces an under-approximation of the qualitative winning region in the original synthesis problem, along with a policy to solve it. By combining these contributions with (a) a symbolic fixpoint algorithm to solve \r\n-player games and (b) existing techniques for reachability policy synthesis in stochastic nonlinear systems, we get an abstraction-based algorithm for finding a lower bound on the maximal satisfaction probability.\r\nWe have implemented the abstraction-based algorithm in Mascot-SDS, where we combined the outlined abstraction step with our tool Genie (Majumdar et al., 2023) that solves \r\n-player parity games (through a reduction to Rabin games) more efficiently than existing algorithms. We evaluated our implementation on the nonlinear model of a perturbed bistable switch from the literature. We show empirically that the lower bound on the winning region computed by our approach is precise, by comparing against an over-approximation of the qualitative winning region. Moreover, our implementation outperforms a recently proposed tool for solving this problem by a large margin." acknowledgement: "We thank Daniel Hausmann and Nir Piterman for their valuable comments on an earlier version of the manuscript of our other paper [22] where we present, among other things, the parity fixpoint for 2 1/2-player games (for a slightly more general class of games) with a different and indirect proof of correctness. Based on their comments we observed that, unlike the other fixpoints that we present in [22], the parity fixpoint does not follow the exact same structure as its counterpart for 2-player games, which we also use int his paper.\r\nWe also thank Thejaswini Raghavan for observing that our symbolic parity fixpoint algorithm can be solved in quasi-polynomial time using recent improved algorithms for solving \r\n-calculus expressions. This significantly improved the complexity bounds of our algorithm in this paper.\r\nThe work of R. Majumdar and A.-K. Schmuck are partially supported by DFG, Germany project 389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG, Germany project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802, and ERC 101089047." article_number: '101430' article_processing_charge: No article_type: original author: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 - first_name: Anne Kathrin full_name: Schmuck, Anne Kathrin last_name: Schmuck - first_name: Sadegh full_name: Soudjani, Sadegh last_name: Soudjani citation: ama: 'Majumdar R, Mallik K, Schmuck AK, Soudjani S. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 2023;51. doi:10.1016/j.nahs.2023.101430' apa: 'Majumdar, R., Mallik, K., Schmuck, A. K., & Soudjani, S. (2023). Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2023.101430' chicago: 'Majumdar, Rupak, Kaushik Mallik, Anne Kathrin Schmuck, and Sadegh Soudjani. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2023. https://doi.org/10.1016/j.nahs.2023.101430.' ieee: 'R. Majumdar, K. Mallik, A. K. Schmuck, and S. Soudjani, “Symbolic control for stochastic systems via finite parity games,” Nonlinear Analysis: Hybrid Systems, vol. 51. Elsevier, 2023.' ista: 'Majumdar R, Mallik K, Schmuck AK, Soudjani S. 2023. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 51, 101430.' mla: 'Majumdar, Rupak, et al. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems, vol. 51, 101430, Elsevier, 2023, doi:10.1016/j.nahs.2023.101430.' short: 'R. Majumdar, K. Mallik, A.K. Schmuck, S. Soudjani, Nonlinear Analysis: Hybrid Systems 51 (2023).' date_created: 2023-10-08T22:01:15Z date_published: 2023-09-27T00:00:00Z date_updated: 2023-12-13T12:58:56Z day: '27' department: - _id: ToHe doi: 10.1016/j.nahs.2023.101430 ec_funded: 1 external_id: arxiv: - '2101.00834' isi: - '001093188100001' intvolume: ' 51' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.nahs.2023.101430 month: '09' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 'Nonlinear Analysis: Hybrid Systems' publication_identifier: issn: - 1751-570X publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Symbolic control for stochastic systems via finite parity games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2023' ... --- _id: '14425' abstract: - lang: eng text: 'Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces.' acknowledgement: F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre (CSCS) for the generous allocation of CPU hours via production project s1108 at the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. article_number: '6131' article_processing_charge: Yes article_type: original author: - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng - first_name: Felix full_name: Wodaczek, Felix id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e last_name: Wodaczek orcid: 0009-0000-1457-795X - first_name: Keyang full_name: Liu, Keyang last_name: Liu - first_name: Frederick full_name: Stein, Frederick last_name: Stein - first_name: Jürg full_name: Hutter, Jürg last_name: Hutter - first_name: Ji full_name: Chen, Ji last_name: Chen - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 2023;14. doi:10.1038/s41467-023-41865-8 apa: Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., & Cheng, B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41865-8 chicago: Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter, Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41865-8. ieee: Z. Zeng et al., “Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 14, 6131. mla: Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications, vol. 14, 6131, Springer Nature, 2023, doi:10.1038/s41467-023-41865-8. short: Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature Communications 14 (2023). date_created: 2023-10-15T22:01:10Z date_published: 2023-10-02T00:00:00Z date_updated: 2023-12-13T13:02:07Z day: '02' ddc: - '540' - '000' department: - _id: BiCh - _id: GradSch doi: 10.1038/s41467-023-41865-8 ec_funded: 1 external_id: arxiv: - '2303.07433' isi: - '001084354900008' pmid: - '37783698' file: - access_level: open_access checksum: 7d1dffd36b672ec679f08f70ce79da87 content_type: application/pdf creator: dernst date_created: 2023-10-16T07:34:49Z date_updated: 2023-10-16T07:34:49Z file_id: '14432' file_name: 2023_NatureComm_Zeng.pdf file_size: 3194116 relation: main_file success: 1 file_date_updated: 2023-10-16T07:34:49Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/BingqingCheng/TiO2-water scopus_import: '1' status: public title: Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14453' abstract: - lang: eng text: Squall lines are substantially influenced by the interaction of low-level shear with cold pools associated with convective downdrafts. Beyond an optimal shear amplitude, squall lines tend to orient themselves at an angle with respect to the low-level shear. While the mechanisms behind squall line orientation seem to be increasingly well understood, uncertainties remain on the implications of this orientation. Roca and Fiolleau (2020, https://doi.org/10.1038/s43247-020-00015-4) show that long lived mesoscale convective systems, including squall lines, are disproportionately involved in rainfall extremes in the tropics. This article investigates the influence of the interaction between low-level shear and squall line outflow on squall line generated precipitation extrema in the tropics. Using a cloud resolving model, simulated squall lines in radiative convective equilibrium amid a shear-dominated regime (super optimal), a balanced regime (optimal), and an outflow dominated regime (suboptimal). Our results show that precipitation extremes in squall lines are 40% more intense in the case of optimal shear and remain 30% superior in the superoptimal regime relative to a disorganized case. With a theoretical scaling of precipitation extremes (C. Muller & Takayabu, 2020, https://doi.org/10.1088/1748-9326/ab7130), we show that the condensation rates control the amplification of precipitation extremes in tropical squall lines, mainly due to its change in vertical mass flux (dynamic component). The reduction of dilution by entrainment explains half of this change, consistent with Mulholland et al. (2021, https://doi.org/10.1175/jas-d-20-0299.1). The other half is explained by increased cloud-base velocity intensity in optimal and superoptimal squall lines. acknowledgement: The authors gratefully acknowledge funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This work is also supported by a PhD fellowship funded by the Ecole Normale Supérieure de Paris-Saclay. Authors are also grateful to Benjamin Filider, who was of great help and support in the development of ideas. Eventually, we would like to thank Martin Singh, John M. Peters and an anonymous reviewer for their valuable comments and suggestions, which greatly improved the quality of the manuscript. article_number: e2022MS003477 article_processing_charge: Yes article_type: original author: - first_name: Sophie full_name: Abramian, Sophie last_name: Abramian - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Camille full_name: Risi, Camille last_name: Risi citation: ama: Abramian S, Muller CJ, Risi C. Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. 2023;15(10). doi:10.1029/2022MS003477 apa: Abramian, S., Muller, C. J., & Risi, C. (2023). Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2022MS003477 chicago: Abramian, Sophie, Caroline J Muller, and Camille Risi. “Extreme Precipitation in Tropical Squall Lines.” Journal of Advances in Modeling Earth Systems. Wiley, 2023. https://doi.org/10.1029/2022MS003477. ieee: S. Abramian, C. J. Muller, and C. Risi, “Extreme precipitation in tropical squall lines,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 10. Wiley, 2023. ista: Abramian S, Muller CJ, Risi C. 2023. Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. 15(10), e2022MS003477. mla: Abramian, Sophie, et al. “Extreme Precipitation in Tropical Squall Lines.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 10, e2022MS003477, Wiley, 2023, doi:10.1029/2022MS003477. short: S. Abramian, C.J. Muller, C. Risi, Journal of Advances in Modeling Earth Systems 15 (2023). date_created: 2023-10-29T23:01:15Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-12-13T13:06:40Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1029/2022MS003477 ec_funded: 1 external_id: isi: - '001084933600001' file: - access_level: open_access checksum: 43e6a1a35b663843c7d3f8d0caaca1a5 content_type: application/pdf creator: dernst date_created: 2023-10-30T13:31:42Z date_updated: 2023-10-30T13:31:42Z file_id: '14470' file_name: 2023_JAMES_Abramian.pdf file_size: 1975210 relation: main_file success: 1 file_date_updated: 2023-10-30T13:31:42Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Journal of Advances in Modeling Earth Systems publication_identifier: eissn: - 1942-2466 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Extreme precipitation in tropical squall lines tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14434' abstract: - lang: eng text: High entropy alloys (HEAs) are highly suitable candidate catalysts for oxygen evolution and reduction reactions (OER/ORR) as they offer numerous parameters for optimizing the electronic structure and catalytic sites. Herein, FeCoNiMoW HEA nanoparticles are synthesized using a solution‐based low‐temperature approach. Such FeCoNiMoW nanoparticles show high entropy properties, subtle lattice distortions, and modulated electronic structure, leading to superior OER performance with an overpotential of 233 mV at 10 mA cm−2 and 276 mV at 100 mA cm−2. Density functional theory calculations reveal the electronic structures of the FeCoNiMoW active sites with an optimized d‐band center position that enables suitable adsorption of OOH* intermediates and reduces the Gibbs free energy barrier in the OER process. Aqueous zinc–air batteries (ZABs) based on this HEA demonstrate a high open circuit potential of 1.59 V, a peak power density of 116.9 mW cm−2, a specific capacity of 857 mAh gZn−1, and excellent stability for over 660 h of continuous charge–discharge cycles. Flexible and solid ZABs are also assembled and tested, displaying excellent charge–discharge performance at different bending angles. This work shows the significance of 4d/5d metal‐modulated electronic structure and optimized adsorption ability to improve the performance of OER/ORR, ZABs, and beyond. acknowledged_ssus: - _id: EM-Fac acknowledgement: The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581; the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación; the National Natural Science Foundation of China (22102002); the Anhui Provincial Natural Science Foundation (2108085QE192); Zhejiang Province key research and development project (2023C01191); the Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering (GrantNo.2022-K31); and The Key Research and Development Program of Hebei Province (20314305D). IREC is funded by the CERCA Programme from the Generalitat de Catalunya. L.L.Y. thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). This research was supported by the Scientific Service Units (SSU) of ISTA (Institute of Science and Technology Austria) through resources provided by the Electron Microscopy Facility (EMF). S.L., S.H., and M.I. acknowledge funding by ISTA and the Werner Siemens. article_number: '2303719' article_processing_charge: No article_type: original author: - first_name: Ren full_name: He, Ren last_name: He - first_name: Linlin full_name: Yang, Linlin last_name: Yang - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Daochuan full_name: Jiang, Daochuan last_name: Jiang - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Zhifu full_name: Liang, Zhifu last_name: Liang - first_name: Xuan full_name: Lu, Xuan last_name: Lu - first_name: Ahmad full_name: Ostovari Moghaddam, Ahmad last_name: Ostovari Moghaddam - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Ying full_name: Xu, Ying last_name: Xu - first_name: Yingtang full_name: Zhou, Yingtang last_name: Zhou - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: He R, Yang L, Zhang Y, et al. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. 2023. doi:10.1002/adma.202303719 apa: He, R., Yang, L., Zhang, Y., Jiang, D., Lee, S., Horta, S., … Cabot, A. (2023). A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202303719 chicago: He, Ren, Linlin Yang, Yu Zhang, Daochuan Jiang, Seungho Lee, Sharona Horta, Zhifu Liang, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202303719. ieee: R. He et al., “A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries,” Advanced Materials. Wiley, 2023. ista: He R, Yang L, Zhang Y, Jiang D, Lee S, Horta S, Liang Z, Lu X, Ostovari Moghaddam A, Li J, Ibáñez M, Xu Y, Zhou Y, Cabot A. 2023. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials., 2303719. mla: He, Ren, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials, 2303719, Wiley, 2023, doi:10.1002/adma.202303719. short: R. He, L. Yang, Y. Zhang, D. Jiang, S. Lee, S. Horta, Z. Liang, X. Lu, A. Ostovari Moghaddam, J. Li, M. Ibáñez, Y. Xu, Y. Zhou, A. Cabot, Advanced Materials (2023). date_created: 2023-10-17T10:52:23Z date_published: 2023-07-24T00:00:00Z date_updated: 2023-12-13T13:03:23Z day: '24' department: - _id: MaIb doi: 10.1002/adma.202303719 external_id: isi: - '001083876900001' pmid: - '37487245' isi: 1 keyword: - Mechanical Engineering - Mechanics of Materials - General Materials Science language: - iso: eng month: '07' oa_version: None pmid: 1 project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Advanced Materials publication_identifier: issn: - 0935-9648 - 1521-4095 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' status: public title: A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14435' abstract: - lang: eng text: Low‐cost, safe, and environmental‐friendly rechargeable aqueous zinc‐ion batteries (ZIBs) are promising as next‐generation energy storage devices for wearable electronics among other applications. However, sluggish ionic transport kinetics and the unstable electrode structure during ionic insertion/extraction hampers their deployment. Herein,  we propose a new cathode material based on a layered metal chalcogenide (LMC), bismuth telluride (Bi2Te3), coated with polypyrrole (PPy). Taking advantage of the PPy coating, the Bi2Te3@PPy composite presents strong ionic absorption affinity, high oxidation resistance, and high structural stability. The ZIBs based on Bi2Te3@PPy cathodes exhibit high capacities and ultra‐long lifespans of over 5000 cycles. They also present outstanding stability even under bending. In addition,  we analyze here the reaction mechanism using in situ X‐ray diffraction, X‐ray photoelectron spectroscopy, and computational tools and demonstrate that, in the aqueous system, Zn2+ is not inserted into the cathode as previously assumed. In contrast, proton charge storage dominates the process. Overall, this work not only shows the great potential of LMCs as ZIBs cathode materials and the advantages of PPy coating, but also clarifies the charge/discharge mechanism in rechargeable ZIBs based on LMCs. article_number: '2305128' article_processing_charge: No article_type: original author: - first_name: Guifang full_name: Zeng, Guifang last_name: Zeng - first_name: Qing full_name: Sun, Qing last_name: Sun - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Shang full_name: Wang, Shang last_name: Wang - first_name: Xuan full_name: Lu, Xuan last_name: Lu - first_name: Chaoyue full_name: Zhang, Chaoyue last_name: Zhang - first_name: Jing full_name: Li, Jing last_name: Li - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Lijie full_name: Ci, Lijie last_name: Ci - first_name: Yanhong full_name: Tian, Yanhong last_name: Tian - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Zeng G, Sun Q, Horta S, et al. A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials. doi:10.1002/adma.202305128' apa: 'Zeng, G., Sun, Q., Horta, S., Wang, S., Lu, X., Zhang, C., … Cabot, A. (n.d.). A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202305128' chicago: 'Zeng, Guifang, Qing Sun, Sharona Horta, Shang Wang, Xuan Lu, Chaoyue Zhang, Jing Li, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials. Wiley, n.d. https://doi.org/10.1002/adma.202305128.' ieee: 'G. Zeng et al., “A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries,” Advanced Materials. Wiley.' ista: 'Zeng G, Sun Q, Horta S, Wang S, Lu X, Zhang C, Li J, Li J, Ci L, Tian Y, Ibáñez M, Cabot A. A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials., 2305128.' mla: 'Zeng, Guifang, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials, 2305128, Wiley, doi:10.1002/adma.202305128.' short: G. Zeng, Q. Sun, S. Horta, S. Wang, X. Lu, C. Zhang, J. Li, J. Li, L. Ci, Y. Tian, M. Ibáñez, A. Cabot, Advanced Materials (n.d.). date_created: 2023-10-17T10:53:56Z date_published: 2023-08-09T00:00:00Z date_updated: 2023-12-13T13:03:53Z day: '09' department: - _id: MaIb doi: 10.1002/adma.202305128 external_id: isi: - '001085681000001' pmid: - '37555532' isi: 1 keyword: - Mechanical Engineering - Mechanics of Materials - General Materials Science language: - iso: eng month: '08' oa_version: None pmid: 1 publication: Advanced Materials publication_identifier: eissn: - 1521-4095 issn: - 0935-9648 publication_status: accepted publisher: Wiley quality_controlled: '1' status: public title: 'A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14463' abstract: - lang: eng text: Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin. acknowledgement: We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: James full_name: Reeve, James last_name: Reeve - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Eva L. full_name: Koch, Eva L. last_name: Koch - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Rui full_name: Faria, Rui last_name: Faria citation: ama: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 2023. doi:10.1111/mec.17160 apa: Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2023). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. Wiley. https://doi.org/10.1111/mec.17160 chicago: Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.17160. ieee: J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” Molecular Ecology. Wiley, 2023. ista: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. mla: Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology, Wiley, 2023, doi:10.1111/mec.17160. short: J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology (2023). date_created: 2023-10-29T23:01:17Z date_published: 2023-10-16T00:00:00Z date_updated: 2023-12-13T13:05:27Z day: '16' department: - _id: NiBa doi: 10.1111/mec.17160 external_id: isi: - '001085119000001' pmid: - '37843465' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/mec.17160 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14455' acknowledgement: The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work has been partially supported by Italian Ministry of Health Grant RC2023 (and the 5 × 1,000 voluntary contributions). The authors thank the children and their families with whom they work daily. article_number: '1287879' article_processing_charge: Yes article_type: letter_note author: - first_name: Antonio full_name: Narzisi, Antonio last_name: Narzisi - first_name: Alycia full_name: Halladay, Alycia last_name: Halladay - first_name: Gabriele full_name: Masi, Gabriele last_name: Masi - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Catherine full_name: Lord, Catherine last_name: Lord citation: ama: 'Narzisi A, Halladay A, Masi G, Novarino G, Lord C. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. 2023;14. doi:10.3389/fpsyt.2023.1287879' apa: 'Narzisi, A., Halladay, A., Masi, G., Novarino, G., & Lord, C. (2023). Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. Frontiers. https://doi.org/10.3389/fpsyt.2023.1287879' chicago: 'Narzisi, Antonio, Alycia Halladay, Gabriele Masi, Gaia Novarino, and Catherine Lord. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” Frontiers in Psychiatry. Frontiers, 2023. https://doi.org/10.3389/fpsyt.2023.1287879.' ieee: 'A. Narzisi, A. Halladay, G. Masi, G. Novarino, and C. Lord, “Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment,” Frontiers in Psychiatry, vol. 14. Frontiers, 2023.' ista: 'Narzisi A, Halladay A, Masi G, Novarino G, Lord C. 2023. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. 14, 1287879.' mla: 'Narzisi, Antonio, et al. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” Frontiers in Psychiatry, vol. 14, 1287879, Frontiers, 2023, doi:10.3389/fpsyt.2023.1287879.' short: A. Narzisi, A. Halladay, G. Masi, G. Novarino, C. Lord, Frontiers in Psychiatry 14 (2023). date_created: 2023-10-29T23:01:16Z date_published: 2023-10-03T00:00:00Z date_updated: 2023-12-13T13:06:07Z day: '03' ddc: - '570' department: - _id: GaNo doi: 10.3389/fpsyt.2023.1287879 external_id: isi: - '001084841700001' pmid: - '37854442' file: - access_level: open_access checksum: 0a76373e9a4c0fc199f80380de257e86 content_type: application/pdf creator: dernst date_created: 2023-10-30T12:48:40Z date_updated: 2023-10-30T12:48:40Z file_id: '14468' file_name: 2023_FrontiersPsychiatry_Narzisi.pdf file_size: 147878 relation: main_file success: 1 file_date_updated: 2023-10-30T12:48:40Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Psychiatry publication_identifier: eissn: - 1664-0640 publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14427' abstract: - lang: eng text: In the paper, we establish Squash Rigidity Theorem—the dynamical spectral rigidity for piecewise analytic Bunimovich squash-type stadia whose convex arcs are homothetic. We also establish Stadium Rigidity Theorem—the dynamical spectral rigidity for piecewise analytic Bunimovich stadia whose flat boundaries are a priori fixed. In addition, for smooth Bunimovich squash-type stadia we compute the Lyapunov exponents along the maximal period two orbit, as well as the value of the Peierls’ Barrier function from the maximal marked length spectrum associated to the rotation number 2n/4n+1. acknowledgement: 'VK acknowledges a partial support by the NSF grant DMS-1402164 and ERC Grant #885707. Discussions with Martin Leguil and Jacopo De Simoi were very useful. JC visited the University of Maryland and thanks for the hospitality. Also, JC was partially supported by the National Key Research and Development Program of China (No.2022YFA1005802), the NSFC Grant 12001392 and NSF of Jiangsu BK20200850. H.-K. Zhang is partially supported by the National Science Foundation (DMS-2220211), as well as Simons Foundation Collaboration Grants for Mathematicians (706383).' article_processing_charge: No article_type: original author: - first_name: Jianyu full_name: Chen, Jianyu last_name: Chen - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Hong Kun full_name: Zhang, Hong Kun last_name: Zhang citation: ama: Chen J, Kaloshin V, Zhang HK. Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics. 2023. doi:10.1007/s00220-023-04837-z apa: Chen, J., Kaloshin, V., & Zhang, H. K. (2023). Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04837-z chicago: Chen, Jianyu, Vadim Kaloshin, and Hong Kun Zhang. “Length Spectrum Rigidity for Piecewise Analytic Bunimovich Billiards.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04837-z. ieee: J. Chen, V. Kaloshin, and H. K. Zhang, “Length spectrum rigidity for piecewise analytic Bunimovich billiards,” Communications in Mathematical Physics. Springer Nature, 2023. ista: Chen J, Kaloshin V, Zhang HK. 2023. Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics. mla: Chen, Jianyu, et al. “Length Spectrum Rigidity for Piecewise Analytic Bunimovich Billiards.” Communications in Mathematical Physics, Springer Nature, 2023, doi:10.1007/s00220-023-04837-z. short: J. Chen, V. Kaloshin, H.K. Zhang, Communications in Mathematical Physics (2023). date_created: 2023-10-15T22:01:11Z date_published: 2023-09-29T00:00:00Z date_updated: 2023-12-13T13:02:44Z day: '29' department: - _id: VaKa doi: 10.1007/s00220-023-04837-z ec_funded: 1 external_id: arxiv: - '1902.07330' isi: - '001073177200001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07330 month: '09' oa: 1 oa_version: Preprint project: - _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '885707' name: Spectral rigidity and integrability for billiards and geodesic flows publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Length spectrum rigidity for piecewise analytic Bunimovich billiards type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14464' abstract: - lang: eng text: 'Given a triangle Δ, we study the problem of determining the smallest enclosing and largest embedded isosceles triangles of Δ with respect to area and perimeter. This problem was initially posed by Nandakumar [17, 22] and was first studied by Kiss, Pach, and Somlai [13], who showed that if Δ′ is the smallest area isosceles triangle containing Δ, then Δ′ and Δ share a side and an angle. In the present paper, we prove that for any triangle Δ, every maximum area isosceles triangle embedded in Δ and every maximum perimeter isosceles triangle embedded in Δ shares a side and an angle with Δ. Somewhat surprisingly, the case of minimum perimeter enclosing triangles is different: there are infinite families of triangles Δ whose minimum perimeter isosceles containers do not share a side and an angle with Δ.' article_processing_charge: No article_type: original author: - first_name: Áron full_name: Ambrus, Áron last_name: Ambrus - first_name: Mónika full_name: Csikós, Mónika last_name: Csikós - first_name: Gergely full_name: Kiss, Gergely last_name: Kiss - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach - first_name: Gábor full_name: Somlai, Gábor last_name: Somlai citation: ama: Ambrus Á, Csikós M, Kiss G, Pach J, Somlai G. Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. 2023;34(7):737-760. doi:10.1142/S012905412342008X apa: Ambrus, Á., Csikós, M., Kiss, G., Pach, J., & Somlai, G. (2023). Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S012905412342008X chicago: Ambrus, Áron, Mónika Csikós, Gergely Kiss, János Pach, and Gábor Somlai. “Optimal Embedded and Enclosing Isosceles Triangles.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2023. https://doi.org/10.1142/S012905412342008X. ieee: Á. Ambrus, M. Csikós, G. Kiss, J. Pach, and G. Somlai, “Optimal embedded and enclosing isosceles triangles,” International Journal of Foundations of Computer Science, vol. 34, no. 7. World Scientific Publishing, pp. 737–760, 2023. ista: Ambrus Á, Csikós M, Kiss G, Pach J, Somlai G. 2023. Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. 34(7), 737–760. mla: Ambrus, Áron, et al. “Optimal Embedded and Enclosing Isosceles Triangles.” International Journal of Foundations of Computer Science, vol. 34, no. 7, World Scientific Publishing, 2023, pp. 737–60, doi:10.1142/S012905412342008X. short: Á. Ambrus, M. Csikós, G. Kiss, J. Pach, G. Somlai, International Journal of Foundations of Computer Science 34 (2023) 737–760. date_created: 2023-10-29T23:01:18Z date_published: 2023-10-05T00:00:00Z date_updated: 2023-12-13T13:04:55Z day: '05' department: - _id: HeEd doi: 10.1142/S012905412342008X external_id: arxiv: - '2205.11637' isi: - '001080874400001' intvolume: ' 34' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2205.11637 month: '10' oa: 1 oa_version: Preprint page: 737-760 publication: International Journal of Foundations of Computer Science publication_identifier: eissn: - 1793-6373 issn: - 0129-0541 publication_status: published publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: Optimal embedded and enclosing isosceles triangles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2023' ... --- _id: '14449' abstract: - lang: eng text: The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices. acknowledgement: "This study is based upon work from COST Action ML4Microbiome “Statistical and machine learning techniques in human microbiome studies” (CA18131), supported by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain), co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131 “Statistical and machine learning techniques in human microbiome studies” members for their contribution to the COST Action objectives, and to COST (European Cooperation in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset." article_number: '1257002' article_processing_charge: Yes article_type: original author: - first_name: Domenica full_name: D’Elia, Domenica last_name: D’Elia - first_name: Jaak full_name: Truu, Jaak last_name: Truu - first_name: Leo full_name: Lahti, Leo last_name: Lahti - first_name: Magali full_name: Berland, Magali last_name: Berland - first_name: Georgios full_name: Papoutsoglou, Georgios last_name: Papoutsoglou - first_name: Michelangelo full_name: Ceci, Michelangelo last_name: Ceci - first_name: Aldert full_name: Zomer, Aldert last_name: Zomer - first_name: Marta B. full_name: Lopes, Marta B. last_name: Lopes - first_name: Eliana full_name: Ibrahimi, Eliana last_name: Ibrahimi - first_name: Aleksandra full_name: Gruca, Aleksandra last_name: Gruca - first_name: Alina full_name: Nechyporenko, Alina last_name: Nechyporenko - first_name: Marcus full_name: Frohme, Marcus last_name: Frohme - first_name: Thomas full_name: Klammsteiner, Thomas last_name: Klammsteiner - first_name: Enrique Carrillo De Santa full_name: Pau, Enrique Carrillo De Santa last_name: Pau - first_name: Laura Judith full_name: Marcos-Zambrano, Laura Judith last_name: Marcos-Zambrano - first_name: Karel full_name: Hron, Karel last_name: Hron - first_name: Gianvito full_name: Pio, Gianvito last_name: Pio - first_name: Andrea full_name: Simeon, Andrea last_name: Simeon - first_name: Ramona full_name: Suharoschi, Ramona last_name: Suharoschi - first_name: Isabel full_name: Moreno-Indias, Isabel last_name: Moreno-Indias - first_name: Andriy full_name: Temko, Andriy last_name: Temko - first_name: Miroslava full_name: Nedyalkova, Miroslava last_name: Nedyalkova - first_name: Elena Simona full_name: Apostol, Elena Simona last_name: Apostol - first_name: Ciprian Octavian full_name: Truică, Ciprian Octavian last_name: Truică - first_name: Rajesh full_name: Shigdel, Rajesh last_name: Shigdel - first_name: Jasminka Hasić full_name: Telalović, Jasminka Hasić last_name: Telalović - first_name: Erik full_name: Bongcam-Rudloff, Erik last_name: Bongcam-Rudloff - first_name: Piotr full_name: Przymus, Piotr last_name: Przymus - first_name: Naida Babić full_name: Jordamović, Naida Babić last_name: Jordamović - first_name: Laurent full_name: Falquet, Laurent last_name: Falquet - first_name: Sonia full_name: Tarazona, Sonia last_name: Tarazona - first_name: Alexia full_name: Sampri, Alexia last_name: Sampri - first_name: Gaetano full_name: Isola, Gaetano last_name: Isola - first_name: David full_name: Pérez-Serrano, David last_name: Pérez-Serrano - first_name: Vladimir full_name: Trajkovik, Vladimir last_name: Trajkovik - first_name: Lubos full_name: Klucar, Lubos last_name: Klucar - first_name: Tatjana full_name: Loncar-Turukalo, Tatjana last_name: Loncar-Turukalo - first_name: Aki S. full_name: Havulinna, Aki S. last_name: Havulinna - first_name: Christian full_name: Jansen, Christian id: 837b2259-bcc9-11ed-a196-ae55927bc6e2 last_name: Jansen - first_name: Randi J. full_name: Bertelsen, Randi J. last_name: Bertelsen - first_name: Marcus Joakim full_name: Claesson, Marcus Joakim last_name: Claesson citation: ama: 'D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1257002' apa: 'D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1257002' chicago: 'D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1257002.' ieee: 'D. D’Elia et al., “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.' ista: 'D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.' mla: 'D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology, vol. 14, 1257002, Frontiers, 2023, doi:10.3389/fmicb.2023.1257002.' short: D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023). date_created: 2023-10-22T22:01:16Z date_published: 2023-09-25T00:00:00Z date_updated: 2023-12-13T13:07:21Z day: '25' ddc: - '000' department: - _id: ScienComp doi: 10.3389/fmicb.2023.1257002 external_id: isi: - '001080536000001' pmid: - '37808321' file: - access_level: open_access checksum: 6c0acdd8fa111a699826957b8dff19d5 content_type: application/pdf creator: dernst date_created: 2023-10-30T13:38:48Z date_updated: 2023-10-30T13:38:48Z file_id: '14471' file_name: 2023_FrontiersMicrobiology_DElia.pdf file_size: 505078 relation: main_file success: 1 file_date_updated: 2023-10-30T13:38:48Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Microbiology publication_identifier: eissn: - 1664-302X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '13125' abstract: - lang: eng text: 'The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. ' acknowledgement: 'We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ' article_number: '062404' article_processing_charge: No article_type: original author: - first_name: Stefan full_name: Sack, Stefan id: dd622248-f6e0-11ea-865d-ce382a1c81a5 last_name: Sack orcid: 0000-0001-5400-8508 - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 - first_name: Richard full_name: Kueng, Richard last_name: Kueng - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404 apa: Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404 chicago: Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/physreva.107.062404. ieee: S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023. ista: Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404. mla: Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404. short: S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023). date_created: 2023-06-07T06:57:32Z date_published: 2023-06-02T00:00:00Z date_updated: 2023-12-13T14:47:25Z day: '02' ddc: - '530' department: - _id: MaSe doi: 10.1103/physreva.107.062404 ec_funded: 1 external_id: arxiv: - '2209.01159' isi: - '001016927100012' file: - access_level: open_access checksum: 0d71423888eeccaa60d8f41197f26306 content_type: application/pdf creator: dernst date_created: 2023-06-13T07:28:36Z date_updated: 2023-06-13T07:28:36Z file_id: '13131' file_name: 2023_PhysRevA_Sack.pdf file_size: 2524611 relation: main_file success: 1 file_date_updated: 2023-06-13T07:28:36Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '14622' relation: dissertation_contains status: public scopus_import: '1' status: public title: Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '14445' abstract: - lang: eng text: "We prove the following quantitative Borsuk–Ulam-type result (an equivariant analogue of Gromov’s Topological Overlap Theorem): Let X be a free ℤ/2-complex of dimension d with coboundary expansion at least ηk in dimension 0 ≤ k < d. Then for every equivariant map F: X →ℤ/2 ℝd, the fraction of d-simplices σ of X with 0 ∈ F (σ) is at least 2−d Π d−1k=0ηk.\r\n\r\nAs an application, we show that for every sufficiently thick d-dimensional spherical building Y and every map f: Y → ℝ2d, we have f(σ) ∩ f(τ) ≠ ∅ for a constant fraction μd > 0 of pairs {σ, τ} of d-simplices of Y. In particular, such complexes are non-embeddable into ℝ2d, which proves a conjecture of Tancer and Vorwerk for sufficiently thick spherical buildings.\r\n\r\nWe complement these results by upper bounds on the coboundary expansion of two families of simplicial complexes; this indicates some limitations to the bounds one can obtain by straighforward applications of the quantitative Borsuk–Ulam theorem. Specifically, we prove\r\n\r\n• an upper bound of (d + 1)/2d on the normalized (d − 1)-th coboundary expansion constant of complete (d + 1)-partite d-dimensional complexes (under a mild divisibility assumption on the sizes of the parts); and\r\n\r\n• an upper bound of (d + 1)/2d + ε on the normalized (d − 1)-th coboundary expansion of the d-dimensional spherical building associated with GLd+2(Fq) for any ε > 0 and sufficiently large q. This disproves, in a rather strong sense, a conjecture of Lubotzky, Meshulam and Mozes." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Pascal full_name: Wild, Pascal id: 4C20D868-F248-11E8-B48F-1D18A9856A87 last_name: Wild citation: ama: Wagner U, Wild P. Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. 2023;256(2):675-717. doi:10.1007/s11856-023-2521-9 apa: Wagner, U., & Wild, P. (2023). Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-023-2521-9 chicago: Wagner, Uli, and Pascal Wild. “Coboundary Expansion, Equivariant Overlap, and Crossing Numbers of Simplicial Complexes.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-023-2521-9. ieee: U. Wagner and P. Wild, “Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes,” Israel Journal of Mathematics, vol. 256, no. 2. Springer Nature, pp. 675–717, 2023. ista: Wagner U, Wild P. 2023. Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. 256(2), 675–717. mla: Wagner, Uli, and Pascal Wild. “Coboundary Expansion, Equivariant Overlap, and Crossing Numbers of Simplicial Complexes.” Israel Journal of Mathematics, vol. 256, no. 2, Springer Nature, 2023, pp. 675–717, doi:10.1007/s11856-023-2521-9. short: U. Wagner, P. Wild, Israel Journal of Mathematics 256 (2023) 675–717. date_created: 2023-10-22T22:01:14Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-12-13T13:09:07Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1007/s11856-023-2521-9 external_id: isi: - '001081646400010' file: - access_level: open_access checksum: fbb05619fe4b650f341cc730425dd9c3 content_type: application/pdf creator: dernst date_created: 2023-10-31T11:20:31Z date_updated: 2023-10-31T11:20:31Z file_id: '14475' file_name: 2023_IsraelJourMath_Wagner.pdf file_size: 623787 relation: main_file success: 1 file_date_updated: 2023-10-31T11:20:31Z has_accepted_license: '1' intvolume: ' 256' isi: 1 issue: '2' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 675-717 publication: Israel Journal of Mathematics publication_identifier: eissn: - 1565-8511 issn: - 0021-2172 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 256 year: '2023' ... --- _id: '14447' abstract: - lang: eng text: "Auxin belongs among major phytohormones and governs multiple aspects of plant growth and development. The establishment of auxin concentration gradients, determines, among other processes, plant organ positioning and growth responses to environmental stimuli.\r\nHerein we report the synthesis of new NBD- or DNS-labelled IAA derivatives and the elucidation of their biological activity, fluorescence properties and subcellular accumulation patterns in planta. These novel compounds did not show auxin-like activity, but instead antagonized physiological auxin effects. The DNS-labelled derivatives FL5 and FL6 showed strong anti-auxin activity in roots and hypocotyls, which also occurred at the level of gene transcription as confirmed by quantitative PCR analysis. The auxin antagonism of our derivatives was further demonstrated in vitro using an SPR-based binding assay. The NBD-labelled compound FL4 with the best fluorescence properties proved to be unsuitable to study auxin accumulation patterns in planta. On the other hand, the strongest anti-auxin activity possessing compounds FL5 and FL6 could be useful to study binding mechanisms to auxin receptors and for manipulations of auxin-regulated processes." acknowledgement: The authors would like to thank Karolína Kubiasová and Iñigo Saiz-Fernández for valuable scientific discussions. Open access publishing supported by the National Technical Library in Prague. This work was supported by the Palacký University Olomouc Young Researcher Grant Competition (JG_2020_002), by the Internal Grant Agency of Palacký University Olomouc (IGA_PrF_2023_016, IGA_PrF_2023_031), by the Ministry of Education, Youth and Sports of the Czech Republic through the European Regional Development Fund-Project Plants as a tool for sustainable global development (CZ.02.1.01/0.0/0.0/16_019/0000827) and the project Support of mobility at Palacký University Olomouc II. (CZ.02.2.69/0.0/0.0/18_053/0016919). The Biacore T200 SPR instrument was provided by the WISB Research Technology Facility within the School of Life Sciences, University of Warwick. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Kristýna full_name: Bieleszová, Kristýna last_name: Bieleszová - first_name: Pavel full_name: Hladík, Pavel last_name: Hladík - first_name: Martin full_name: Kubala, Martin last_name: Kubala - first_name: Richard full_name: Napier, Richard last_name: Napier - first_name: Federica full_name: Brunoni, Federica last_name: Brunoni - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Karel full_name: Doležal, Karel last_name: Doležal - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Asta full_name: Žukauskaitė, Asta last_name: Žukauskaitė citation: ama: 'Bieleszová K, Hladík P, Kubala M, et al. New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. 2023. doi:10.1007/s10725-023-01083-0' apa: 'Bieleszová, K., Hladík, P., Kubala, M., Napier, R., Brunoni, F., Gelová, Z., … Žukauskaitė, A. (2023). New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. Springer Nature. https://doi.org/10.1007/s10725-023-01083-0' chicago: 'Bieleszová, Kristýna, Pavel Hladík, Martin Kubala, Richard Napier, Federica Brunoni, Zuzana Gelová, Lukas Fiedler, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” Plant Growth Regulation. Springer Nature, 2023. https://doi.org/10.1007/s10725-023-01083-0.' ieee: 'K. Bieleszová et al., “New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana,” Plant Growth Regulation. Springer Nature, 2023.' ista: 'Bieleszová K, Hladík P, Kubala M, Napier R, Brunoni F, Gelová Z, Fiedler L, Kulich I, Strnad M, Doležal K, Novák O, Friml J, Žukauskaitė A. 2023. New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation.' mla: 'Bieleszová, Kristýna, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” Plant Growth Regulation, Springer Nature, 2023, doi:10.1007/s10725-023-01083-0.' short: K. Bieleszová, P. Hladík, M. Kubala, R. Napier, F. Brunoni, Z. Gelová, L. Fiedler, I. Kulich, M. Strnad, K. Doležal, O. Novák, J. Friml, A. Žukauskaitė, Plant Growth Regulation (2023). date_created: 2023-10-22T22:01:15Z date_published: 2023-10-13T00:00:00Z date_updated: 2023-12-13T13:08:25Z day: '13' department: - _id: JiFr doi: 10.1007/s10725-023-01083-0 external_id: isi: - '001084334300001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10725-023-01083-0 month: '10' oa: 1 oa_version: Published Version publication: Plant Growth Regulation publication_identifier: eissn: - 1573-5087 issn: - 0167-6903 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14622' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefan full_name: Sack, Stefan id: dd622248-f6e0-11ea-865d-ce382a1c81a5 last_name: Sack orcid: 0000-0001-5400-8508 citation: ama: 'Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622' apa: 'Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622' chicago: 'Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.' ieee: 'S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.' ista: 'Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.' mla: 'Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.' short: 'S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.' date_created: 2023-11-28T10:58:13Z date_published: 2023-11-30T00:00:00Z date_updated: 2023-12-13T14:47:25Z day: '30' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:14622 ec_funded: 1 file: - access_level: closed checksum: 068fd3570506ec42b2faa390de784bc4 content_type: application/pdf creator: ssack date_created: 2023-11-30T15:53:10Z date_updated: 2023-12-01T11:10:46Z embargo: 2024-11-30 embargo_to: open_access file_id: '14635' file_name: PhD_Thesis.pdf file_size: 11947523 relation: main_file - access_level: closed checksum: 0fa3bc0d108aed0ac59d2c6beef2220a content_type: application/zip creator: ssack date_created: 2023-11-30T15:54:11Z date_updated: 2023-12-01T11:10:46Z file_id: '14636' file_name: PhD Thesis (1).zip file_size: 18422964 relation: source_file file_date_updated: 2023-12-01T11:10:46Z has_accepted_license: '1' language: - iso: eng month: '11' oa_version: Published Version page: '142' project: - _id: bd660c93-d553-11ed-ba76-fb0fb6f49c0d name: Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11471' relation: part_of_dissertation status: public - id: '13125' relation: part_of_dissertation status: public - id: '9760' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: 'Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14683' abstract: - lang: eng text: "Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1" acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H. article_number: '102771' article_processing_charge: No article_type: review author: - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 2023;5(1). doi:10.1016/j.xpro.2023.102771 apa: Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2023). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771 chicago: Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols. Elsevier, 2023. https://doi.org/10.1016/j.xpro.2023.102771. ieee: N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” STAR Protocols, vol. 5, no. 1. Elsevier, 2023. ista: Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771. mla: Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols, vol. 5, no. 1, 102771, Elsevier, 2023, doi:10.1016/j.xpro.2023.102771. short: N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023). date_created: 2023-12-13T11:48:05Z date_published: 2023-12-08T00:00:00Z date_updated: 2023-12-18T08:06:14Z day: '08' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2023.102771 ec_funded: 1 external_id: pmid: - '38070137' intvolume: ' 5' issue: '1' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.xpro.2023.102771 month: '12' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T0101031 name: Role of Eed in neural stem cell lineage progression - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F07805 name: Molecular Mechanisms of Neural Stem Cell Lineage Progression - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: STAR Protocols publication_identifier: issn: - 2666-1667 publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2023' ... --- _id: '12486' abstract: - lang: eng text: This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas. acknowledgement: "The author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).\r\nThe author thanks Lorenzo Dello Schiavo, Lucio Galeati and Mark Veraar for helpful comments. The author acknowledges Caterina Balzotti for her support in creating the picture. The author\r\nthanks the anonymous referee for helpful comments. " article_processing_charge: No article_type: original author: - first_name: Antonio full_name: Agresti, Antonio id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72 last_name: Agresti orcid: 0000-0002-9573-2962 citation: ama: 'Agresti A. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. 2023. doi:10.1007/s40072-023-00319-4' apa: 'Agresti, A. (2023). Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-023-00319-4' chicago: 'Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-023-00319-4.' ieee: 'A. Agresti, “Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations,” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023.' ista: 'Agresti A. 2023. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations.' mla: 'Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations, Springer Nature, 2023, doi:10.1007/s40072-023-00319-4.' short: 'A. Agresti, Stochastics and Partial Differential Equations: Analysis and Computations (2023).' date_created: 2023-02-02T10:45:47Z date_published: 2023-11-28T00:00:00Z date_updated: 2023-12-18T07:53:45Z day: '28' ddc: - '510' department: - _id: JuFi doi: 10.1007/s40072-023-00319-4 ec_funded: 1 external_id: arxiv: - '2207.08293' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s40072-023-00319-4 month: '11' oa: 1 oa_version: Submitted Version project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication: 'Stochastics and Partial Differential Equations: Analysis and Computations' publication_identifier: eissn: - 2194-041X issn: - 2194-0401 publication_status: epub_ahead publisher: Springer Nature scopus_import: '1' status: public title: Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14665' abstract: - lang: eng text: We derive lower bounds on the maximal rates for multiple packings in high-dimensional Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L - 1 balls of radius √ nN around points in C . This is a natural generalization of the sphere packing problem. We study the multiple packing problem for both bounded point sets whose points have norm at most √ nP for some constant P > 0, and unbounded point sets whose points are allowed to be anywhere in R n . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied over finite fields. We derive the best known lower bounds on the optimal multiple packing density. This is accomplished by establishing an inequality which relates the list-decoding error exponent for additive white Gaussian noise channels, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We also derive novel bounds on the list-decoding error exponent for infinite constellations and closed-form expressions for the list-decoding error exponents for the power-constrained AWGN channel, which may be of independent interest beyond multiple packing. article_processing_charge: No article_type: original author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 - first_name: Shashank full_name: Vatedka, Shashank last_name: Vatedka citation: ama: 'Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 2023. doi:10.1109/TIT.2023.3334032' apa: 'Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3334032' chicago: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory. IEEE, 2023. https://doi.org/10.1109/TIT.2023.3334032.' ieee: 'Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,” IEEE Transactions on Information Theory. IEEE, 2023.' ista: 'Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory.' mla: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory, IEEE, 2023, doi:10.1109/TIT.2023.3334032.' short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory (2023). date_created: 2023-12-10T23:01:00Z date_published: 2023-11-16T00:00:00Z date_updated: 2023-12-18T07:46:45Z day: '16' department: - _id: MaMo doi: 10.1109/TIT.2023.3334032 external_id: arxiv: - '2211.04408' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2211.04408 month: '11' oa: 1 oa_version: Preprint publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: epub_ahead publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Multiple packing: Lower bounds via error exponents' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14693' abstract: - lang: eng text: "Lucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field." acknowledgement: "Home Theory of Cryptography Conference paper\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nDownload book PDF\r\nDownload book EPUB\r\nSimilar content being viewed by others\r\n\r\nSlider with three content items shown per slide. Use the Previous and Next buttons to navigate the slides or the slide controller buttons at the end to navigate through each slide.\r\nPrevious slide\r\nGeneric-Group Delay Functions Require Hidden-Order Groups\r\nChapter© 2020\r\n\r\nShifted powers in Lucas–Lehmer sequences\r\nArticle30 January 2019\r\n\r\nA New Class of Trapdoor Verifiable Delay Functions\r\nChapter© 2023\r\n\r\nWeak Pseudoprimality Associated with the Generalized Lucas Sequences\r\nChapter© 2022\r\n\r\nOn the Security of Time-Lock Puzzles and Timed Commitments\r\nChapter© 2020\r\n\r\nGeneration of full cycles by a composition of NLFSRs\r\nArticle08 March 2014\r\n\r\nCryptographically Strong de Bruijn Sequences with Large Periods\r\nChapter© 2013\r\n\r\nOpen Problems on With-Carry Sequence Generators\r\nChapter© 2014\r\n\r\nGenerically Speeding-Up Repeated Squaring Is Equivalent to Factoring: Sharp Thresholds for All Generic-Ring Delay Functions\r\nChapter© 2020\r\n\r\nNext slide\r\nGo to slide 1\r\nGo to slide 2\r\nGo to slide 3\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nCharlotte Hoffmann, Pavel Hubáček, Chethan Kamath & Tomáš Krňák \r\nConference paper\r\nFirst Online: 27 November 2023\r\n83 Accesses\r\n\r\nPart of the Lecture Notes in Computer Science book series (LNCS,volume 14372)\r\n\r\nAbstract\r\nLucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\n\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\n\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.\r\n\r\nKeywords\r\nDelay functions\r\nVerifiable delay functions\r\nLucas sequences\r\nDownload conference paper PDF\r\n\r\n1 Introduction\r\nA verifiable delay function (VDF) \r\n is a function that satisfies two properties. First, it is a delay function, which means it must take a prescribed (wall) time T to compute f, irrespective of the amount of parallelism available. Second, it should be possible for anyone to quickly verify – say, given a short proof \r\n – the value of the function (even without resorting to parallelism), where by quickly we mean that the verification time should be independent of or significantly smaller than T (e.g., logarithmic in T). If we drop either of the two requirements, then the primitive turns out trivial to construct. For instance, for an appropriately chosen hash function h, the delay function \r\n defined by T-times iterated hashing of the input is a natural heuristic for an inherently sequential task which, however, seems hard to verify more efficiently than by recomputing. On the other hand, the identity function \r\n is trivial to verify but also easily computable. Designing a simple function satisfying the two properties simultaneously proved to be a nontrivial task.\r\n\r\nThe notion of VDFs was introduced in [31] and later formalised in [9]. In principle, since the task of constructing a VDF reduces to the task of incrementally-verifiable computation [9, 53], constructions of VDFs could leverage succinct non-interactive arguments of knowledge (SNARKs): take any sequentially-hard function f (for instance, iterated hashing) as the delay function and then use the SNARK on top of it as the mechanism for verifying the computation of the delay function. However, as discussed in [9], the resulting construction is not quite practical since we would rely on a general-purpose machinery of SNARKs with significant overhead.\r\n\r\nEfficient VDFs via Algebraic Delay Functions. VDFs have recently found interesting applications in design of blockchains [17], randomness beacons [43, 51], proofs of data replication [9], or short-lived zero-knowledge proofs and signatures [3]. Since efficiency is an important factor there, this has resulted in a flurry of constructions of VDFs that are tailored with application and practicality in mind. They rely on more algebraic, structured delay functions that often involve iterating an atomic operation so that one can resort to custom proof systems to achieve verifiability. These constructions involve a range of algebraic settings like the RSA or class groups [5, 8, 25, 42, 55], permutation polynomials over finite fields [9], isogenies of elliptic curves [21, 52] and, very recently, lattices [15, 28]. The constructions in [42, 55] are arguably the most practical and the mechanism that underlies their delay function is the same: carry out iterated squaring in groups of unknown order, like RSA groups [47] or class groups [12]. What distinguishes these two proposals is the way verification is carried out, i.e., how the underlying “proof of exponentiation” works: while Pietrzak [42] resorts to an LFKN-style recursive proof system [35], Wesolowski [55] uses a clever linear decomposition of the exponent.\r\n\r\nIterated Modular Squaring and Sequentiality. The delay function that underlies the VDFs in [5, 25, 42, 55] is the same, and its security relies on the conjectured sequential hardness of iterated squaring in a group of unknown order (suggested in the context of time-lock puzzles by Rivest, Shamir, and Wagner [48]). Given that the practically efficient VDFs all rely on the above single delay function, an immediate open problem is to identify additional sources of sequential hardness that are structured enough to support practically efficient verifiability.\r\n\r\n1.1 Our Approach to (Verifiable) Delay Functions\r\nIn this work, we study an alternative source of sequential hardness in the algebraic setting and use it to construct efficient verifiable delay functions. The sequentiality of our delay function relies on an atomic operation that is related to the computation of so-called Lucas sequences [29, 34, 57], explained next.\r\n\r\nLucas Sequences. A Lucas sequence is a constant-recursive integer sequence that satisfies the recurrence relation\r\n\r\nfor integers P and Q.Footnote1 Specifically, the Lucas sequences of integers \r\n and \r\n of the first and second type (respectively) are defined recursively as\r\n\r\nwith \r\n, and\r\n\r\nwith \r\n.\r\n\r\nThese sequences can be alternatively defined by the characteristic polynomial \r\n. Specifically, given the discriminant \r\n of the characteristic polynomial, one can alternatively compute the above sequences by performing operations in the extension field\r\n\r\nusing the identities\r\n\r\nwhere \r\n and its conjugate \r\n are roots of the characteristic polynomial. Since conjugation and exponentiation commute in the extension field (i.e., \r\n), computing the i-th terms of the two Lucas sequences over integers reduces to computing \r\n in the extension field, and vice versa.\r\n\r\nThe intrinsic connection between computing the terms in the Lucas sequences and that of exponentiation in the extension has been leveraged to provide alternative instantiations of public-key encryption schemes like RSA and ElGamal in terms of Lucas sequences [7, 30]. However, as we explain later, the corresponding underlying computational hardness assumptions are not necessarily equivalent.\r\n\r\nOverview of Our Delay Function. The delay function in [5, 25, 42, 55] is defined as the iterated squaring base x in a (safe) RSA groupFootnote2 modulo N:\r\n\r\nOur delay function is its analogue in the setting of Lucas sequences:\r\n\r\nAs mentioned above, computing \r\n can be carried out equivalently in the extension field \r\n using the known relationship to roots of the characteristic polynomial of the Lucas sequence. Thus, the delay function can be alternatively defined as\r\n\r\nNote that the atomic operation of our delay function is “doubling” the index of an element of the Lucas sequence modulo N (i.e., \r\n) or, equivalently, squaring in the extension field \r\n (as opposed to squaring in \r\n). Using the representation of \r\n as \r\n, squaring in \r\n can be expressed as a combination of squaring, multiplication and addition modulo N, since\r\n\r\n(1)\r\nSince \r\n is a group of unknown order (provided the factorization of N is kept secret), iterated squaring remains hard here. In fact, we show in Sect. 3.2 that iterated squaring in \r\n is at least as hard as iterated squaring for RSA moduli N. Moreover, we conjecture in Conjecture 1 that it is, in fact, strictly harder (also see discussion below on advantages of our approach).\r\n\r\nVerifying Modular Lucas Sequence. To obtain a VDF, we need to show how to efficiently verify our delay function. To this end, we show how to adapt the interactive proof of exponentiation from [42] to our setting, which then – via the Fiat-Shamir Transform [22] – yields the non-interactive verification algorithm.Footnote3 Thus, our main result is stated informally below.\r\n\r\nTheorem 1\r\n(Informally stated, see Theorem 2). Assuming sequential hardness of modular Lucas sequence, there exists statistically-sound VDF in the random-oracle model.\r\n\r\nHowever, the modification of Pietrzak’s protocol is not trivial and we have to overcome several hurdles that we face in this task, which we elaborate on in Sect. 1.2. We conclude this section with discussions about our results.\r\n\r\nAdvantage of Our Approach. Our main advantage is the reliance on a potentially weaker (sequential) hardness assumption while maintaining efficiency: we show in Sect. 3.2 that modular Lucas sequences are at least as sequentially-hard as the classical delay function given by iterated modular squaring [48]. Despite the linear recursive structure of Lucas sequences, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring (Conjecture 1). In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring. Even though both assumptions need the group order to be hidden, we believe that there is need for a nuanced analysis of sequential hardness assumptions in hidden order groups, especially because all current delay functions that provide sufficient structure for applications are based on iterated modular squaring. If the iterated modular squaring assumption is broken, our delay function is currently the only practical alternative in the RSA group.\r\n\r\nDelay Functions in Idealised Models. Recent works studied the relationship of group-theoretic (verifiable) delay functions to the hardness of factoring in idealised models such as the algebraic group model and the generic ring model [27, 50]. In the generic ring model, Rotem and Segev [50] showed the equivalence of straight-line delay functions in the RSA setting and factoring. Our construction gives rise to a straight-line delay function and, by their result, its sequentiality is equivalent to factoring for generic algorithms. However, their result holds only in the generic ring model and leaves the relationship between the two assumptions unresolved in the standard model.\r\n\r\nCompare this with the status of the RSA assumption and factoring. On one hand, we know that in the generic ring model, RSA and factoring are equivalent [2]. Yet, it is possible to rule out certain classes of reductions from factoring to RSA in the standard model [11]. Most importantly, despite the equivalence in the generic ring model, there is currently no reduction from factoring to RSA in the standard model and it remains one of the major open problems in number theory related to cryptography since the introduction of the RSA assumption.\r\n\r\nIn summary, speeding up iterated squaring by a non-generic algorithm could be possible (necessarily exploiting the representations of ring elements modulo N), while such an algorithm may not lead to a speed-up in the computation of modular Lucas sequences despite the result of Rotem and Segev [50].\r\n\r\n1.2 Technical Overview\r\nPietrzak’s VDF. Let \r\n be an RSA modulus where p and q are safe primes and let x be a random element from \r\n. At its core, Pietrzak’s VDF relies on the interactive protocol for the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and, in a round-by-round fashion, reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round, the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued till \r\n is obtained at which point the verifier simply checks whether \r\n using a single modular squaring.\r\n\r\nSince the challenges r are public, the protocol can be compiled into a non-interactive one using the Fiat-Shamir transform [22] and this yields a means to verify the delay function\r\n\r\nIt is worth pointing out that the choice of safe primes is crucial for proving soundness: in case the group has easy-to-find elements of small order then it becomes easy to break soundness (see, e.g., [10]).\r\n\r\nAdapting Pietrzak’s Protocol to Lucas Sequences. For a modulus \r\n and integers \r\n, recall that our delay function is defined as\r\n\r\nor equivalently\r\n\r\nfor the discriminant \r\n of the characteristic polynomial \r\n. Towards building a verification algorithm for this delay function, the natural first step is to design an interactive protocol for the statement\r\n\r\n“(N, P, Q, y, T) satisfies \r\n.”\r\n\r\nIt turns out that the interactive protocol from [42] can be adapted for this purpose. However, we encounter two technicalities in this process.\r\n\r\nDealing with elements of small order. The main problem that we face while designing our protocol is avoiding elements of small order. In the case of [42], this was accomplished by moving to the setting of signed quadratic residues [26] in which the sub-groups are all of large order. It is not clear whether a corresponding object exists for our algebraic setting. However, in an earlier draft of Pietrzak’s protocol [41], this problem was dealt with in a different manner: the prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by squaring it) with a guarantee that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nIn our setting, we cannot simply ask for the square root of the midpoint as the subgroup of \r\n we effectively work in has a different structure. Nevertheless, we can use a similar approach: for an appropriately chosen small a, we provide an a-th root of \r\n (instead of \r\n itself) to the prover in the beginning of the protocol. The prover then computes the whole sequence for \r\n. In the end, he has the a-th root of every term of the original sequence and he can recover any element of the original sequence by raising to the a-th power.\r\n\r\nSampling strong modulus. The second technicality is related to the first one. In order to ensure that we can use the above trick, we require a modulus where the small subgroups are reasonably small not only in the group \r\n but also in the extension \r\n. Thus the traditional sampling algorithms that are used to sample strong primes (e.g., [46]) are not sufficient for our purposes. However, sampling strong primes that suit our criteria can still be carried out efficiently as we show in the full version.\r\n\r\nComparing Our Technique with [8, 25]. The VDFs in [8, 25] are also inspired by [42] and, hence, faced the same problem of low-order elements. In [8], this is dealt with by amplifying the soundness at the cost of parallel repetition and hence larger proofs and extra computation. In [25], the number of repetitions of [8] is reduced significantly by introducing the following technique: The exponent of the initial instance is reduced by some parameter \r\n and at the end of an interactive phase, the verifier performs final exponentiation with \r\n, thereby weeding out potential false low-order elements in the claim. This technique differs from the approach taken in our work in the following ways: The technique from [25] works in arbitrary groups but it requires the parameter \r\n to be large and of a specific form. In particular, the VDF becomes more efficient when \r\n is larger than \r\n. In our protocol, we work in RSA groups whose modulus is the product of primes that satisfy certain conditions depending on a. This enables us to choose a parameter a that is smaller than a statistical security parameter and thereby makes the final exponentiation performed by the verifier much more efficient. Further, a can be any natural number, while \r\n must be set as powers of all small prime numbers up a certain bound in [25].\r\n\r\n1.3 More Related Work\r\nTimed Primitives. The notion of VDFs was introduced in [31] and later formalised in [9]. VDFs are closely related to the notions of time-lock puzzles [48] and proofs of sequential work [36]. Roughly speaking, a time-lock puzzle is a delay function that additionally allows efficient sampling of the output via a trapdoor. A proof of sequential work, on the other hand, is a delay “multi-function”, in the sense that the output is not necessarily unique. Constructions of time-lock puzzles are rare [6, 38, 48], and there are known limitations: e.g., that it cannot exist in the random-oracle model [36]. However, we know how to construct proofs of sequential work in the random-oracle model [1, 16, 19, 36].\r\n\r\nSince VDFs have found several applications, e.g., in the design of resource-efficient blockchains [17], randomness beacons [43, 51] and proof of data replication [9], there have been several constructions. Among them, the most notable are the iterated-squaring based construction from [8, 25, 42, 55], the permutation-polynomial based construction from [9], the isogenies-based construction from [13, 21, 52] and the construction from lattice problems [15, 28]. The constructions in [42, 55] are quite practical (see the survey [10]) and the VDF deployed in the cryptocurrency Chia is basically their construction adapted to the algebraic setting of class groups [17]. This is arguably the closest work to ours. On the other hand, the constructions from [21, 52], which work in the algebraic setting of isogenies of elliptic curves where no analogue of square and multiply is known, simply rely on “exponentiation”. Although, these constructions provide a certain form of quantum resistance, they are presently far from efficient. Freitag et al. [23] constructed VDFs from any sequentially hard function and polynomial hardness of learning with errors, the first from standard assumptions. The works of Cini, Lai, and Malavolta [15, 28] constructed the first VDF from lattice-based assumptions and conjectured it to be post-quantum secure.\r\n\r\nSeveral variants of VDFs have also been proposed. A VDF is said to be unique if the proof that is used for verification is unique [42]. Recently, Choudhuri et al. [5] constructed unique VDFs from the sequential hardness of iterated squaring in any RSA group and polynomial hardness of LWE. A VDF is tight [18] if the gap between simply computing the function and computing it with a proof is small. Yet another extension is a continuous VDF [20]. The feasibility of time-lock puzzles and proofs of sequential works were recently extended to VDFs. It was shown [50] that the latter requirement, i.e., working in a group of unknown order, is inherent in a black-box sense. It was shown in [18, 37] that there are barriers to constructing tight VDFs in the random-oracle model.\r\n\r\nVDFs also have surprising connection to complexity theory [14, 20, 33].\r\n\r\nWork Related to Lucas Sequences. Lucas sequences have long been studied in the context of number theory: see for example [45] or [44] for a survey of its applications to number theory. Its earliest application to cryptography can be traced to the \r\n factoring algorithm [56]. Constructive applications were found later thanks to the parallels with exponentiation. Several encryption and signature schemes were proposed, most notably the LUC family of encryption and signatures [30, 39]. It was later shown that some of these schemes can be broken or that the advantages it claimed were not present [7]. Other applications can be found in [32].\r\n\r\n2 Preliminaries\r\n2.1 Interactive Proof Systems\r\nInteractive Protocols. An interactive protocol consists of a pair \r\n of interactive Turing machines that are run on a common input \r\n. The first machine \r\n is the prover and is computationally unbounded. The second machine \r\n is the verifier and is probabilistic polynomial-time.\r\n\r\nIn an \r\n-round (i.e., \r\n-message) interactive protocol, in each round \r\n, first \r\n sends a message \r\n to \r\n and then \r\n sends a message \r\n to \r\n, where \r\n is a finite alphabet. At the end of the interaction, \r\n runs a (deterministic) Turing machine on input \r\n. The interactive protocol is public-coin if \r\n is a uniformly distributed random string in \r\n.\r\n\r\nInteractive Proof Systems. The notion of an interactive proof for a language L is due to Goldwasser, Micali and Rackoff [24].\r\n\r\nDefinition 1\r\nFor a function \r\n, an interactive protocol \r\n is an \r\n-statistically-sound interactive proof system for L if:\r\n\r\nCompleteness: For every \r\n, if \r\n interacts with \r\n on common input \r\n, then \r\n accepts with probability 1.\r\n\r\nSoundness: For every \r\n and every (computationally-unbounded) cheating prover strategy \r\n, the verifier \r\n accepts when interacting with \r\n with probability less than \r\n, where \r\n is called the soundness error.\r\n\r\n2.2 Verifiable Delay Functions\r\nWe adapt the definition of verifiable delay functions from [9] but we decouple the verifiability and sequentiality properties for clarity of exposition of our results. First, we present the definition of a delay function.\r\n\r\nDefinition 2\r\nA delay function \r\n consists of a triple of algorithms with the following syntax:\r\n\r\n:\r\n\r\nOn input a security parameter \r\n, the algorithm \r\n outputs public parameters \r\n.\r\n\r\n:\r\n\r\nOn input public parameters \r\n and a time parameter \r\n, the algorithm \r\n outputs a challenge x.\r\n\r\n:\r\n\r\nOn input a challenge pair (x, T), the (deterministic) algorithm \r\n outputs the value y of the delay function in time T.\r\n\r\nThe security property required of a delay function is sequential hardness as defined below.\r\n\r\nDefinition 3\r\n(Sequentiality). We say that a delay function \r\n satisfies the sequentiality property, if there exists an \r\n such that for all \r\n and for every adversary \r\n, where \r\n uses \r\n processors and runs in time \r\n, there exists a negligible function \r\n such that\r\n\r\nfigure a\r\nA few remarks about our definition of sequentiality are in order:\r\n\r\n1.\r\nWe require computing \r\n to be hard in less than T sequential steps even using any polynomially-bounded amount of parallelism and precomputation. Note that it is necessary to bound the amount of parallelism, as an adversary could otherwise break the underlying hardness assumption (e.g. hardness of factorization). Analogously, T should be polynomial in \r\n as, otherwise, breaking the underlying hardness assumptions becomes easier than computing \r\n itself for large values of T.\r\n\r\n2.\r\nAnother issue is what bound on the number of sequential steps of the adversary should one impose. For example, the delay function based on T repeated modular squarings can be computed in sequential time \r\n using polynomial parallelism [4]. Thus, one cannot simply bound the sequential time of the adversary by o(T). Similarly to [38], we adapt the \r\n bound for \r\n which, in particular, is asymptotically smaller than \r\n.\r\n\r\n3.\r\nWithout loss of generality, we assume that the size of \r\n is at least linear in n and the adversary A does not have to get the unary representation of the security parameter \r\n as its input.\r\n\r\nThe definition of verifiable delay function extends a delay function with the possibility to compute publicly-verifiable proofs of correctness of the output value.\r\n\r\nDefinition 4\r\nA delay function \r\n is a verifiable delay function if it is equipped with two additional algorithms \r\n and \r\n with the following syntax:\r\n\r\n:\r\n\r\nOn input public parameters and a challenge pair (x, T), the \r\n algorithm outputs \r\n, where \r\n is a proof that the output y is the output of \r\n.\r\n\r\n:\r\n\r\nOn input public parameters, a challenge pair (x, T), and an output/proof pair \r\n, the (deterministic) algorithm \r\n outputs either \r\n or \r\n.\r\n\r\nIn addition to sequentiality (inherited from the underlying delay function), the \r\n and \r\n algorithms must together satisfy correctness and (statistical) soundness as defined below.\r\n\r\nDefinition 5\r\n(Correctness). A verifiable delay function \r\n is correct if for all \r\n\r\nfigure b\r\nDefinition 6\r\n(Statistical soundness). A verifiable delay function \r\n is statistically sound if for every (computationally unbounded) malicious prover \r\n there exists a negligible function \r\n such that for all \r\n\r\nfigure c\r\n3 Delay Functions from Lucas Sequences\r\nIn this section, we propose a delay function based on Lucas sequences and prove its sequentiality assuming that iterated squaring in a group of unknown order is sequential (Sect. 3.1). Further, we conjecture (Sect. 3.2) that our delay function candidate is even more robust than its predecessor proposed by Rivest, Shamir, and Wagner [48]. Finally, we turn our delay function candidate into a verifiable delay function (Sect. 4).\r\n\r\n3.1 The Atomic Operation\r\nOur delay function is based on subsequences of Lucas sequences, whose indexes are powers of two. Below, we use \r\n to denote the set of non-negative integers.\r\n\r\nDefinition 7\r\nFor integers \r\n, the Lucas sequences \r\n and \r\n are defined for all \r\n as\r\n\r\nwith \r\n and \r\n, and\r\n\r\nwith \r\n and \r\n.\r\n\r\nWe define subsequences \r\n, respectively \r\n, of \r\n, respectively \r\n for all \r\n as\r\n\r\n(2)\r\nAlthough the value of \r\n depends on parameters (P, Q), we omit (P, Q) from the notation because these parameters will be always obvious from the context.\r\n\r\nThe underlying atomic operation for our delay function is\r\n\r\nThere are several ways to compute \r\n in T sequential steps, and we describe two of them below.\r\n\r\nAn Approach Based on Squaring in a Suitable Extension Ring. To compute the value \r\n, we can use the extension ring \r\n, where \r\n is the discriminant of the characteristic polynomial \r\n of the Lucas sequence. The characteristic polynomial f(z) has a root \r\n, and it is known that, for all \r\n, it holds that\r\n\r\nThus, by iterated squaring of \r\n, we can compute terms of our target subsequences. To get a better understanding of squaring in the extension ring, consider the representation of the root \r\n for some \r\n. Then,\r\n\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(3)\r\nAn Approach Based on Known Identities. Many useful identities for members of modular Lucas sequences are known, such as\r\n\r\n(4)\r\nSetting \r\n we get\r\n\r\n(5)\r\nThe above identities are not hard to derive (see, e.g., Lemma 12.5 in [40]). Indexes are doubled on each of application of the identities in Eq. (5), and, thus, for \r\n, we define an auxiliary sequence \r\n by \r\n. Using the identities in Eq. (5), we get recursive equations\r\n\r\n(6)\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(7)\r\nAfter a closer inspection, the reader may have an intuition that an auxiliary sequence \r\n, which introduces a third state variable, is redundant. This intuition is indeed right. In fact, there is another easily derivable identity\r\n\r\n(8)\r\nwhich can be found, e.g., as Lemma 12.2 in [40]. On the other hand, Eq. (8) is quite interesting because it allows us to compute large powers of an element \r\n using two Lucas sequences. We use this fact in the security reduction in Sect. 3.2. Our construction of a delay function, denoted \r\n, is given in Fig. 1.\r\n\r\nFig. 1.\r\nfigure 1\r\nOur delay function candidate \r\n based on a modular Lucas sequence.\r\n\r\nFull size image\r\nOn the Discriminant D. Notice that whenever D is a quadratic residue modulo N, the value \r\n is an element of \r\n and hence \r\n. By definition, LCS.Gen generates a parameter D that is a quadratic residue with probability 1/4, so it might seem that in one fourth of the cases there is another approach to compute \r\n: find the element \r\n and then perform n sequential squarings in the group \r\n. However, it is well known that finding square roots of uniform elements in \r\n is equivalent to factoring the modulus N, so this approach is not feasible. We can therefore omit any restrictions on the discriminant D in the definition of our delay function LCS.\r\n\r\n3.2 Reduction from RSW Delay Function\r\nIn order to prove the sequentiality property (Definition 3) of our candidate \r\n, we rely on the standard conjecture of the sequentiality of the \r\n time-lock puzzles, implicitly stated in [48] as the underlying hardness assumption.\r\n\r\nDefinition 8\r\n(\r\n delay function). The \r\n delay function is defined as follows:\r\n\r\n: Samples two n-bit primes p and q and outputs \r\n.\r\n\r\n: Outputs an x sampled from the uniform distribution on \r\n.\r\n\r\n: Outputs \r\n.\r\n\r\nTheorem 2\r\nIf the \r\n delay function has the sequentiality property, then the \r\n delay function has the sequentiality property.\r\n\r\nProof\r\nSuppose there exists an adversary \r\n who contradicts the sequentiality of \r\n, where \r\n is a precomputation algorithm and \r\n is an online algorithm. We construct an adversary \r\n who contradicts the sequentiality of \r\n as follows:\r\n\r\nThe algorithm \r\n is defined identically to the algorithm \r\n.\r\n\r\nOn input \r\n, \r\n picks a P from the uniform distribution on \r\n, sets\r\n\r\nand it runs \r\n to compute \r\n. The algorithm \r\n computes \r\n using the identity in Eq. (8).\r\n\r\nNote that the input distribution for the algorithm \r\n produced by \r\n differs from the one produced by \r\n, because the \r\n generator samples Q from the uniform distribution on \r\n (instead of \r\n). However, this is not a problem since the size of \r\n is negligible compared to the size of \r\n, so the statistical distance between the distribution of D produced by \r\n and the distribution of D sampled by \r\n is negligible in the security parameter. Thus, except for a negligible multiplicative loss, the adversary \r\n attains the same success probability of breaking the sequentiality of \r\n as the probability of \r\n breaking the sequentiality of \r\n – a contradiction to the assumption of the theorem. \r\n\r\nWe believe that the converse implication to Theorem 2 is not true, i.e., that breaking the sequentiality of \r\n does not necessarily imply breaking the sequentiality of \r\n. Below, we state it as a conjecture.\r\n\r\nConjecture 1\r\nSequentiality of \r\n cannot be reduced to sequentiality of \r\n.\r\n\r\nOne reason why the above conjecture might be true is that, while the \r\n delay function is based solely only on multiplication in the group \r\n, our \r\n delay function uses the full arithmetic (addition and multiplication) of the commutative ring \r\n.\r\n\r\nOne way to support the conjecture would be to construct an algorithm that speeds up iterated squaring but is not immediately applicable to Lucas sequences. By [49] we know that this cannot be achieved by a generic algorithm. A non-generic algorithm that solves iterated squaring in time \r\n is presented in [4]. The main tool of their construction is the Explicit Chinese Remainder Theorem modulo N. However, a similiar theorem exists also for univariate polynomial rings, which suggests that a similar speed-up can be obtained for our delay function by adapting the techniques in [4] to our setting.\r\n\r\n4 VDF from Lucas Sequences\r\nIn Sect. 3.1 we saw different ways of computing the atomic operation of the delay function. Computing \r\n in the extension field seems to be the more natural and time and space effective approach. Furthermore, writing the atomic operation \r\n as \r\n is very clear, and, thus, we follow this approach throughout the rest of the paper.\r\n\r\n4.1 Structure of \r\nTo construct a VDF based on Lucas sequences, we use an algebraic extension\r\n\r\n(9)\r\nwhere N is an RSA modulus and \r\n. In this section, we describe the structure of the algebraic extension given in Expression (9). Based on our understanding of the structure of the above algebraic extension, we can conclude that using modulus N composed of safe primes (i.e., for all prime factors p of N, \r\n has a large prime divisor) is necessary but not sufficient condition for security of our construction. We specify some sufficient conditions on factors of N in the subsequent Sect. 4.2.\r\n\r\nFirst, we introduce some simplifying notation for quotient rings.\r\n\r\nDefinition 9\r\nFor \r\n and \r\n, we denote by \r\n the quotient ring \r\n, where (m, f(x)) denotes the ideal of the ring \r\n generated by m and f(x).\r\n\r\nObservation 1, below, allows us to restrict our analysis only to the structure of \r\n for prime \r\n.\r\n\r\nObservation 1\r\nLet \r\n be distinct primes, \r\n and \r\n. Then\r\n\r\nProof\r\nUsing the Chinese reminder theorem, we get\r\n\r\nas claimed. \r\n\r\nThe following lemma characterizes the structure of \r\n with respect to the discriminant of f. We use \r\n to denote the standard Legendre symbol.\r\n\r\nLemma 1\r\nLet \r\n and \r\n be a polynomial of degree 2 with the discriminant D. Then\r\n\r\nProof\r\nWe consider each case separately:\r\n\r\nIf \r\n, then f(x) is irreducible over \r\n and \r\n is a field with \r\n elements. Since \r\n is a finite field, \r\n is cyclic and contains \r\n elements.\r\n\r\nIf \r\n, then \r\n and f has some double root \r\n and it can be written as \r\n for some \r\n. Since the ring \r\n is isomorphic to the ring \r\n (consider the isomorphism \r\n), we can restrict ourselves to describing the structure of \r\n.\r\n\r\nWe will prove that the function \r\n,\r\n\r\nis an isomorphism. First, the polynomial \r\n is invertible if and only if \r\n (inverse is \r\n). For the choice \r\n, we have\r\n\r\nThus \r\n is onto. Second, \r\n is, in fact, a bijection, because\r\n\r\n(10)\r\nFinally, \r\n is a homomorphism, because\r\n\r\nIf \r\n, then f(x) has two roots \r\n. We have an isomorphism\r\n\r\nand \r\n. \r\n\r\n4.2 Strong Groups and Strong Primes\r\nTo achieve the verifiability property of our construction, we need \r\n to contain a strong subgroup (defined next) of order asymptotically linear in p. We remark that our definition of strong primes is stronger than the one by Rivest and Silverman [46].\r\n\r\nDefinition 10\r\n(Strong groups). For \r\n, we say that a non-trivial group \r\n is \r\n-strong, if the order of each non-trivial subgroup of \r\n is greater than \r\n.\r\n\r\nObservation 2\r\nIf \r\n and \r\n are \r\n-strong groups, then \r\n is a \r\n-strong group.\r\n\r\nIt can be seen from Lemma 1 that \r\n always contains groups of small order (e.g. \r\n). To avoid these, we descend into the subgroup of a-th powers of elements of \r\n. Below, we introduce the corresponding notation.\r\n\r\nDefinition 11\r\nFor an Abelian group \r\n and \r\n, we define the subgroup \r\n of \r\n in the multiplicative notation and \r\n in the additive notation.\r\n\r\nFurther, we show in Lemma 2 below that \r\n-strong primality (defined next) is a sufficient condition for \r\n to be a \r\n-strong group.\r\n\r\nDefinition 12\r\n(Strong primes). Let \r\n and \r\n. We say that p is a \r\n-strong prime, if \r\n and there exists \r\n, \r\n, such that \r\n and every prime factor of W is greater than \r\n.\r\n\r\nSince a is a public parameter in our setup, super-polynomial a could reveal partial information about the factorization of N. However, we could allow a to be polynomial in \r\n while maintaining hardness of factoring N.Footnote4 For the sake of simplicity of Definition 12, we rather use stronger condition \r\n. The following simple observation will be useful for proving Lemma 2.\r\n\r\nObservation 3\r\nFor \r\n.\r\n\r\nLemma 2\r\nLet p be a \r\n-strong prime and \r\n be a quadratic polynomial. Then, \r\n is a \r\n-strong group.\r\n\r\nProof\r\nFrom definition of the strong primes, there exists \r\n, whose factors are bigger than \r\n and \r\n. We denote \r\n a factor of W. Applying Observation 3 to Lemma 1, we get\r\n\r\nIn particular, we used above the fact that Observation 2 implies that \r\n as explained next. Since \r\n, all divisors of \r\n are divisors of aW. By definition of a and W in Definition 12, we also have that \r\n, which implies that any factor of \r\n divides either a or W, but not both. When we divide \r\n by all the common divisors with a, only the common divisors with W are left, which implies \r\n. The proof of the lemma is now completed by Observation 2.\r\n\r\nCorollary 1\r\nLet p be a \r\n-strong prime, q be a \r\n-strong prime, \r\n, \r\n, \r\n and \r\n. Then \r\n is \r\n-strong.\r\n\r\n4.3 Our Interactive Protocol\r\nOur interactive protocol is formally described in Fig. 3. To understand this protocol, we first recall the outline of Pietrzak’s interactive protocol from Sect. 1.2 and then highlight the hurdles. Let \r\n be an RSA modulus where p and q are strong primes and let x be a random element from \r\n. The interactive protocol in [42] allows a prover to convince the verifier of the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and in a round-by-round fashion reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued until \r\n is obtained at which point the verifier simply checks whether \r\n.\r\n\r\nThe main problem, we face while designing our protocol is ensuring that the verifier can check whether \r\n sent by prover lies in an appropriate subgroup of \r\n. In the first draft of Pietrzak’s protocol [41], prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by simply squaring it) with a guarantee, that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nUsing Pietrzak’s protocol directly for our delay function would require computing a-th roots in RSA group for some arbitrary a. Since this is a computationally hard problem, we cannot use the same trick. In fact, the VDF construction of Wesolowski [54] is based on similar hardness assumption.\r\n\r\nWhile Pietrzak shifted from \r\n to the group of signed quadratic residues \r\n in his following paper [42] to get unique proofs, we resort to his old idea of ‘squaring a square root’ and generalise it.\r\n\r\nThe high level idea is simple. First, on input \r\n, prover computes the sequence \r\n. Next, during the protocol, verifier maps all elements sent by the prover by homomorphism\r\n\r\n(11)\r\ninto the target strong group \r\n. This process is illustrated in Fig. 2. Notice that the equality \r\n for the original sequence implies the equality \r\n for the mapped sequence \r\n.\r\n\r\nFig. 2.\r\nfigure 2\r\nIllustration of our computation of the iterated squaring using the a-th root of \r\n. Horizontal arrows are \r\n and diagonal arrows are \r\n.\r\n\r\nFull size image\r\nRestriction to Elements of \r\n. Mapping Eq. (11) introduces a new technical difficulty. Since \r\n is not injective, we narrow the domain inputs, for which the output of our VDF is verifiable, from \r\n to \r\n. Furthermore, the only way to verify that a certain x is an element of \r\n is to get an a-th root of x and raise it to the ath power. So we have to represent elements of \r\n by elements of \r\n anyway. To resolve these two issues, we introduce a non-unique representation of elements of \r\n.\r\n\r\nDefinition 13\r\nFor \r\n and \r\n, we denote \r\n (an element of \r\n) by [x]. Since this representation of \r\n is not unique, we define an equality relation by\r\n\r\nWe will denote by tilde () the elements that were already powered to the a by a verifier (i.e. ). Thus tilded variables verifiably belong to the target group \r\n.\r\n\r\nIn the following text, the goal of the brackets notation in Definition 13 is to distinguish places where the equality means the equality of elements of \r\n from those places, where the equality holds up to \r\n. A reader can also see the notation in Definition 13 as a concrete representation of elements of a factor group \r\n.\r\n\r\nOur security reduction 2 required the delay function to operate everywhere on \r\n. This is not a problem if the \r\n algorithm is modified to output the set \r\n.\r\n\r\nFig. 3.\r\nfigure 3\r\nOur Interactive Protocol for \r\n.\r\n\r\nFull size image\r\n4.4 Security\r\nRecall here that \r\n is \r\n-strong group, so there exist\r\n\r\n and \r\n such that\r\n\r\n(12)\r\nDefinition 14\r\nFor \r\n and \r\n, we define \r\n as i-th coordinate of \r\n, where \r\n is the isomorphism given by Eq. (12).\r\n\r\nLemma 3\r\nLet \r\n and \r\n. If \r\n, then\r\n\r\n\t(13)\r\nProof\r\nFix \r\n, \r\n and y. Let some \r\n satisfy\r\n\r\n(14)\r\nUsing notation from Definition 14, we rewrite Eq. (14) as a set of equations\r\n\r\nFor every \r\n, by reordering the terms, the j-th equation becomes\r\n\r\n(15)\r\nIf \r\n, then \r\n. Further for every \r\n. It follows that \r\n. Putting these two equations together gives us \r\n, which contradicts our assumption \r\n.\r\n\r\nIt follows that there exists \r\n such that\r\n\r\n(16)\r\nThereafter there exists \r\n such that \r\n divides \r\n and\r\n\r\n(17)\r\nFurthermore, from Eq. (15), \r\n divides \r\n. Finally, dividing eq. Eq. (15) by \r\n, we get that r is determined uniquely (\r\n),\r\n\r\nUsing the fact that \r\n, this uniqueness of r upper bounds number of \r\n, such that Eq. (14) holds, to one. It follows that the probability that Eq. (14) holds for r chosen randomly from the uniform distribution over \r\n is less than \r\n. \r\n\r\nCorollary 2\r\nThe halving protocol will turn an invalid input tuple (i.e. \r\n) into a valid output tuple (i.e. \r\n) with probability less than \r\n.\r\n\r\nTheorem 3\r\nFor any computationally unbounded prover who submits anything other than \r\n such that \r\n in phase 2 of the protocol, the soundness error is upper-bounded by \r\n\r\nProof\r\nIn each round of the protocol, T decreases to \r\n. It follows that the number of rounds of the halving protocol before reaching \r\n is upper bounded by \r\n.\r\n\r\nIf the verifier accepts the solution tuple \r\n in the last round, then the equality \r\n must hold. It follows that the initial inequality must have turned into equality in some round of the halving protocol. By Lemma 3, the probability of this event is bounded by \r\n. Finally, using the union bound for all rounds, we obtain the upper bound (\r\n. \ \r\n\r\n4.5 Our VDF\r\nAnalogously to the VDF of Pietrzak [42], we compile our public-coin interactive proof given in Fig. 3 into a VDF using the Fiat-Shamir heuristic. The complete construction is given in Fig. 4. For ease of exposition, we assume that the time parameter T is always a power of two.\r\n\r\nFig. 4.\r\nfigure 4\r\n based on Lucas sequences\r\n\r\nFull size image\r\nAs discussed in Sect. 4.3, it is crucial for the security of the protocol that the prover computes a sequence of powers of the a-th root of the challenge and the resulting value (as well as the intermediate values) received from the prover is lifted to the appropriate group by raising it to the a-th power. We use the tilde notation in Fig. 4 in order to denote elements on the sequence relative to the a-th root.\r\n\r\nNote that, by the construction, the output of our VDF is the \r\n-th power of the root of the characteristic polynomial for Lucas sequence with parameters P and Q. Therefore, the value of the delay function implicitly corresponds to the \r\n-th term of the Lucas sequence.\r\n\r\nTheorem 4\r\nLet \r\n be the statistical security parameter. The \r\n VDF defined in Fig. 4 is correct and statistically-sound with a negligible soundness error if \r\n is modelled as a random oracle, against any adversary that makes \r\n oracle queries.\r\n\r\nProof\r\nThe correctness follows directly by construction.\r\n\r\nTo prove its statistical soundness, we proceed in a similar way to [42]. We cannot apply Fiat-Shamir transformation directly, because our protocol does not have constant number of rounds, thus we use Fiat-Shamir heuristic to each round separately.\r\n\r\nFirst, we use a random oracle as the \r\n function. Second, if a malicious prover computed a proof accepted by verifier for some tuple \r\n such that\r\n\r\n(19)\r\nthen he must have succeeded in turning inequality from Eq. (19) into equality in some round. By Lemma 3, probability of such a flipping is bounded by \r\n. Every such an attempt requires one query to random oracle. Using a union bound, it follows that the probability that a malicious prover who made q queries to random oracle succeeds in flipping initial inequality into equality in some round is upper-bounded by \r\n.\r\n\r\nSince q is \r\n, \r\n is a negligible function and thus the soundness error is negligible. \ \r\n\r\nNotes\r\n1.\r\nNote that integer sequences like Fibonacci numbers and Mersenne numbers are special cases of Lucas sequences.\r\n\r\n2.\r\nThe choice of modulus N is said to be safe if \r\n for safe primes \r\n and \r\n, where \r\n and \r\n are also prime.\r\n\r\n3.\r\nFurther, using the ideas from [14, 20], it is possible to construct so-called continuous VDFs from Lucas sequences.\r\n\r\n4.\r\nSince we set a to be at most polynomial in \r\n, its is possible to go over all possible candidate values for a in time polynomial in \r\n. 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Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, by the European Research Council (ERC) under the European Union’s Horizon Europe research and innovation programme (grant agreement No. 101042417, acronym SPP), and by ISF grant 1789/19." alternative_title: - LNCS article_processing_charge: No author: - first_name: Charlotte full_name: Hoffmann, Charlotte id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7 last_name: Hoffmann orcid: 0000-0003-2027-5549 - first_name: Pavel full_name: Hubáček, Pavel last_name: Hubáček - first_name: Chethan full_name: Kamath, Chethan last_name: Kamath - first_name: Tomáš full_name: Krňák, Tomáš last_name: Krňák citation: ama: 'Hoffmann C, Hubáček P, Kamath C, Krňák T. (Verifiable) delay functions from Lucas sequences. In: 21st International Conference on Theory of Cryptography. Vol 14372. Springer Nature; 2023:336-362. doi:10.1007/978-3-031-48624-1_13' apa: 'Hoffmann, C., Hubáček, P., Kamath, C., & Krňák, T. (2023). (Verifiable) delay functions from Lucas sequences. In 21st International Conference on Theory of Cryptography (Vol. 14372, pp. 336–362). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48624-1_13' chicago: Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Tomáš Krňák. “(Verifiable) Delay Functions from Lucas Sequences.” In 21st International Conference on Theory of Cryptography, 14372:336–62. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48624-1_13. ieee: C. Hoffmann, P. Hubáček, C. Kamath, and T. Krňák, “(Verifiable) delay functions from Lucas sequences,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14372, pp. 336–362. ista: 'Hoffmann C, Hubáček P, Kamath C, Krňák T. 2023. (Verifiable) delay functions from Lucas sequences. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14372, 336–362.' mla: Hoffmann, Charlotte, et al. “(Verifiable) Delay Functions from Lucas Sequences.” 21st International Conference on Theory of Cryptography, vol. 14372, Springer Nature, 2023, pp. 336–62, doi:10.1007/978-3-031-48624-1_13. short: C. Hoffmann, P. Hubáček, C. Kamath, T. Krňák, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 336–362. conference: end_date: 2023-12-02 location: Taipei, Taiwan name: 'TCC: Theory of Cryptography' start_date: 2023-11-29 date_created: 2023-12-17T23:00:54Z date_published: 2023-11-27T00:00:00Z date_updated: 2023-12-18T09:00:00Z day: '27' department: - _id: KrPi doi: 10.1007/978-3-031-48624-1_13 intvolume: ' 14372' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/1404 month: '11' oa: 1 oa_version: Preprint page: 336-362 publication: 21st International Conference on Theory of Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783031486234' issn: - 0302-9743 publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: (Verifiable) delay functions from Lucas sequences type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14372 year: '2023' ... --- _id: '14691' abstract: - lang: eng text: "Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20].\r\nThe recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting.\r\nIn this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k.\r\nWe prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al.\r\nOur lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper." alternative_title: - LNCS article_processing_charge: No author: - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Miguel full_name: Cueto Noval, Miguel id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc last_name: Cueto Noval - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:271-300. doi:10.1007/978-3-031-48621-0_10' apa: 'Auerbach, B., Cueto Noval, M., Pascual Perez, G., & Pietrzak, K. Z. (2023). On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 271–300). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_10' chicago: Auerbach, Benedikt, Miguel Cueto Noval, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” In 21st International Conference on Theory of Cryptography, 14371:271–300. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_10. ieee: B. Auerbach, M. Cueto Noval, G. Pascual Perez, and K. Z. Pietrzak, “On the cost of post-compromise security in concurrent Continuous Group-Key Agreement,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14371, pp. 271–300. ista: 'Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. 2023. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14371, 271–300.' mla: Auerbach, Benedikt, et al. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 271–300, doi:10.1007/978-3-031-48621-0_10. short: B. Auerbach, M. Cueto Noval, G. Pascual Perez, K.Z. Pietrzak, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 271–300. conference: end_date: 2023-12-02 location: Taipei, Taiwan name: 'TCC: Theory of Cryptography' start_date: 2023-11-29 date_created: 2023-12-17T23:00:53Z date_published: 2023-11-27T00:00:00Z date_updated: 2023-12-18T08:36:51Z day: '27' department: - _id: KrPi doi: 10.1007/978-3-031-48621-0_10 intvolume: ' 14371' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/1123 month: '11' oa: 1 oa_version: Preprint page: 271-300 publication: 21st International Conference on Theory of Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783031486203' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: On the cost of post-compromise security in concurrent Continuous Group-Key Agreement type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14371 year: '2023' ... --- _id: '14692' abstract: - lang: eng text: "The generic-group model (GGM) aims to capture algorithms working over groups of prime order that only rely on the group operation, but do not exploit any additional structure given by the concrete implementation of the group. In it, it is possible to prove information-theoretic lower bounds on the hardness of problems like the discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its introduction, it has served as a valuable tool to assess the concrete security provided by cryptographic schemes based on such problems. A work on the related algebraic-group model (AGM) introduced a method, used by many subsequent works, to adapt GGM lower bounds for one problem to another, by means of conceptually simple reductions.\r\nIn this work, we propose an alternative approach to extend GGM bounds from one problem to another. Following an idea by Yun [EC15], we show that, in the GGM, the security of a large class of problems can be reduced to that of geometric search-problems. By reducing the security of the resulting geometric-search problems to variants of the search-by-hypersurface problem, for which information theoretic lower bounds exist, we give alternative proofs of several results that used the AGM approach.\r\nThe main advantage of our approach is that our reduction from geometric search-problems works, as well, for the GGM with preprocessing (more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]). As a consequence, this opens up the possibility of transferring preprocessing GGM bounds from one problem to another, also by means of simple reductions. Concretely, we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm, the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s GGM without additional restrictions on the query behavior of the adversary, while the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight that this is not the case for the AGM approach." alternative_title: - LNCS article_processing_charge: No author: - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Charlotte full_name: Hoffmann, Charlotte id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7 last_name: Hoffmann orcid: 0000-0003-2027-5549 - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X citation: ama: 'Auerbach B, Hoffmann C, Pascual Perez G. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:301-330. doi:10.1007/978-3-031-48621-0_11' apa: 'Auerbach, B., Hoffmann, C., & Pascual Perez, G. (2023). Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 301–330). Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_11' chicago: 'Auerbach, Benedikt, Charlotte Hoffmann, and Guillermo Pascual Perez. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” In 21st International Conference on Theory of Cryptography, 14371:301–30. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_11.' ieee: 'B. Auerbach, C. Hoffmann, and G. Pascual Perez, “Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing,” in 21st International Conference on Theory of Cryptography, 2023, vol. 14371, pp. 301–330.' ista: 'Auerbach B, Hoffmann C, Pascual Perez G. 2023. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. 21st International Conference on Theory of Cryptography. , LNCS, vol. 14371, 301–330.' mla: 'Auerbach, Benedikt, et al. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 301–30, doi:10.1007/978-3-031-48621-0_11.' short: B. Auerbach, C. Hoffmann, G. Pascual Perez, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 301–330. date_created: 2023-12-17T23:00:54Z date_published: 2023-11-27T00:00:00Z date_updated: 2023-12-18T09:17:03Z day: '27' department: - _id: KrPi doi: 10.1007/978-3-031-48621-0_11 intvolume: ' 14371' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/808 month: '11' oa: 1 oa_version: Preprint page: 301-330 publication: 21st International Conference on Theory of Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783031486203' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14371 year: '2023' ... --- _id: '14690' abstract: - lang: eng text: Generalized multifractality characterizes system size dependence of pure scaling local observables at Anderson transitions in all 10 symmetry classes of disordered systems. Recently, the concept of generalized multifractality has been extended to boundaries of critical disordered noninteracting systems. Here we study the generalized boundary multifractality in the presence of electron-electron interaction, focusing on the spin quantum Hall symmetry class (class C). Employing the two-loop renormalization group analysis within the Finkel'stein nonlinear sigma model, we compute the anomalous dimensions of the pure scaling operators located at the boundary of the system. We find that generalized boundary multifractal exponents are twice larger than their bulk counterparts. Exact symmetry relations between generalized boundary multifractal exponents in the case of noninteracting systems are explicitly broken by the interaction. acknowledgement: The authors are grateful to J. Karcher and A. Mirlin for collaboration on the related project. We thank I. Gruzberg and A. Mirlin for useful discussions and comments. I.S.B. is grateful to M. Parfenov and P. Ostrovsky for collaboration on the related project. The research was supported by Russian Science Foundation (Grant No. 22-42-04416). article_number: '205429' article_processing_charge: No article_type: original author: - first_name: Serafim full_name: Babkin, Serafim id: 41e64307-6672-11ee-b9ad-cc7a0075a479 last_name: Babkin orcid: 0009-0003-7382-8036 - first_name: I full_name: Burmistrov, I last_name: Burmistrov citation: ama: Babkin S, Burmistrov I. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 2023;108(20). doi:10.1103/PhysRevB.108.205429 apa: Babkin, S., & Burmistrov, I. (2023). Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.205429 chicago: Babkin, Serafim, and I Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.205429. ieee: S. Babkin and I. Burmistrov, “Boundary multifractality in the spin quantum Hall symmetry class with interaction,” Physical Review B, vol. 108, no. 20. American Physical Society, 2023. ista: Babkin S, Burmistrov I. 2023. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 108(20), 205429. mla: Babkin, Serafim, and I. Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B, vol. 108, no. 20, 205429, American Physical Society, 2023, doi:10.1103/PhysRevB.108.205429. short: S. Babkin, I. Burmistrov, Physical Review B 108 (2023). date_created: 2023-12-17T23:00:53Z date_published: 2023-11-15T00:00:00Z date_updated: 2023-12-18T08:45:28Z day: '15' department: - _id: MaSe doi: 10.1103/PhysRevB.108.205429 external_id: arxiv: - '2308.16852' intvolume: ' 108' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2308.16852' month: '11' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Boundary multifractality in the spin quantum Hall symmetry class with interaction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '14689' article_processing_charge: No article_type: letter_note author: - first_name: Elizabeth full_name: Ing-Simmons, Elizabeth last_name: Ing-Simmons - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik orcid: 0000-0001-6617-9742 - first_name: Juan M. full_name: Vaquerizas, Juan M. last_name: Vaquerizas citation: ama: 'Ing-Simmons E, Machnik NN, Vaquerizas JM. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 2023;55(12):2053-2055. doi:10.1038/s41588-023-01595-5' apa: 'Ing-Simmons, E., Machnik, N. N., & Vaquerizas, J. M. (2023). Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-023-01595-5' chicago: 'Ing-Simmons, Elizabeth, Nick N Machnik, and Juan M. Vaquerizas. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-023-01595-5.' ieee: 'E. Ing-Simmons, N. N. Machnik, and J. M. Vaquerizas, “Reply to: Revisiting the use of structural similarity index in Hi-C,” Nature Genetics, vol. 55, no. 12. Springer Nature, pp. 2053–2055, 2023.' ista: 'Ing-Simmons E, Machnik NN, Vaquerizas JM. 2023. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 55(12), 2053–2055.' mla: 'Ing-Simmons, Elizabeth, et al. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” Nature Genetics, vol. 55, no. 12, Springer Nature, 2023, pp. 2053–55, doi:10.1038/s41588-023-01595-5.' short: E. Ing-Simmons, N.N. Machnik, J.M. Vaquerizas, Nature Genetics 55 (2023) 2053–2055. date_created: 2023-12-17T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2023-12-18T08:51:38Z day: '01' department: - _id: MaRo doi: 10.1038/s41588-023-01595-5 external_id: pmid: - '38052961' intvolume: ' 55' issue: '12' language: - iso: eng month: '12' oa_version: None page: 2053-2055 pmid: 1 publication: Nature Genetics publication_identifier: eissn: - 1546-1718 issn: - 1061-4036 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Reply to: Revisiting the use of structural similarity index in Hi-C' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2023' ... --- _id: '14701' article_processing_charge: No article_type: review author: - first_name: Lynden A. full_name: Archer, Lynden A. last_name: Archer - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce - first_name: Ernesto J. full_name: Calvo, Ernesto J. last_name: Calvo - first_name: Daniel full_name: Dewar, Daniel last_name: Dewar - first_name: James H. J. full_name: Ellison, James H. J. last_name: Ellison - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Xiangwen full_name: Gao, Xiangwen last_name: Gao - first_name: Laurence J. full_name: Hardwick, Laurence J. last_name: Hardwick - first_name: Gabriela full_name: Horwitz, Gabriela last_name: Horwitz - first_name: Jürgen full_name: Janek, Jürgen last_name: Janek - first_name: Lee R. full_name: Johnson, Lee R. last_name: Johnson - first_name: Jack W. full_name: Jordan, Jack W. last_name: Jordan - first_name: Shoichi full_name: Matsuda, Shoichi last_name: Matsuda - first_name: Svetlana full_name: Menkin, Svetlana last_name: Menkin - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Qianyuan full_name: Qiu, Qianyuan last_name: Qiu - first_name: Thukshan full_name: Samarakoon, Thukshan last_name: Samarakoon - first_name: Israel full_name: Temprano, Israel last_name: Temprano - first_name: Kohei full_name: Uosaki, Kohei last_name: Uosaki - first_name: Ganesh full_name: Vailaya, Ganesh last_name: Vailaya - first_name: Eric D. full_name: Wachsman, Eric D. last_name: Wachsman - first_name: Yiying full_name: Wu, Yiying last_name: Wu - first_name: Shen full_name: Ye, Shen last_name: Ye citation: ama: 'Archer LA, Bruce PG, Calvo EJ, et al. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. 2023. doi:10.1039/d3fd90062b' apa: 'Archer, L. A., Bruce, P. G., Calvo, E. J., Dewar, D., Ellison, J. H. J., Freunberger, S. A., … Ye, S. (2023). Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90062b' chicago: 'Archer, Lynden A., Peter G. Bruce, Ernesto J. Calvo, Daniel Dewar, James H. J. Ellison, Stefan Alexander Freunberger, Xiangwen Gao, et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd90062b.' ieee: 'L. A. Archer et al., “Towards practical metal–oxygen batteries: General discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.' ista: 'Archer LA, Bruce PG, Calvo EJ, Dewar D, Ellison JHJ, Freunberger SA, Gao X, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Menkin S, Mondal S, Qiu Q, Samarakoon T, Temprano I, Uosaki K, Vailaya G, Wachsman ED, Wu Y, Ye S. 2023. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions.' mla: 'Archer, Lynden A., et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90062b.' short: L.A. Archer, P.G. Bruce, E.J. Calvo, D. Dewar, J.H.J. Ellison, S.A. Freunberger, X. Gao, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Menkin, S. Mondal, Q. Qiu, T. Samarakoon, I. Temprano, K. Uosaki, G. Vailaya, E.D. Wachsman, Y. Wu, S. Ye, Faraday Discussions (2023). date_created: 2023-12-20T10:48:09Z date_published: 2023-12-19T00:00:00Z date_updated: 2023-12-20T11:54:06Z day: '19' department: - _id: StFr doi: 10.1039/d3fd90062b keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '12' oa_version: None publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: epub_ahead publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Towards practical metal–oxygen batteries: General discussion' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14702' article_processing_charge: No article_type: review author: - first_name: Gary A. full_name: Attard, Gary A. last_name: Attard - first_name: Ernesto J. full_name: Calvo, Ernesto J. last_name: Calvo - first_name: Larry A. full_name: Curtiss, Larry A. last_name: Curtiss - first_name: Daniel full_name: Dewar, Daniel last_name: Dewar - first_name: James H. J. full_name: Ellison, James H. J. last_name: Ellison - first_name: Xiangwen full_name: Gao, Xiangwen last_name: Gao - first_name: Clare P. full_name: Grey, Clare P. last_name: Grey - first_name: Laurence J. full_name: Hardwick, Laurence J. last_name: Hardwick - first_name: Gabriela full_name: Horwitz, Gabriela last_name: Horwitz - first_name: Juergen full_name: Janek, Juergen last_name: Janek - first_name: Lee R. full_name: Johnson, Lee R. last_name: Johnson - first_name: Jack W. full_name: Jordan, Jack W. last_name: Jordan - first_name: Shoichi full_name: Matsuda, Shoichi last_name: Matsuda - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Alex R. full_name: Neale, Alex R. last_name: Neale - first_name: Nagore full_name: Ortiz-Vitoriano, Nagore last_name: Ortiz-Vitoriano - first_name: Israel full_name: Temprano, Israel last_name: Temprano - first_name: Ganesh full_name: Vailaya, Ganesh last_name: Vailaya - first_name: Eric D. full_name: Wachsman, Eric D. last_name: Wachsman - first_name: Hsien-Hau full_name: Wang, Hsien-Hau last_name: Wang - first_name: Yiying full_name: Wu, Yiying last_name: Wu - first_name: Shen full_name: Ye, Shen last_name: Ye citation: ama: 'Attard GA, Calvo EJ, Curtiss LA, et al. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. 2023. doi:10.1039/d3fd90059b' apa: 'Attard, G. A., Calvo, E. J., Curtiss, L. A., Dewar, D., Ellison, J. H. J., Gao, X., … Ye, S. (2023). Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90059b' chicago: 'Attard, Gary A., Ernesto J. Calvo, Larry A. Curtiss, Daniel Dewar, James H. J. Ellison, Xiangwen Gao, Clare P. Grey, et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd90059b.' ieee: 'G. A. Attard et al., “Materials for stable metal–oxygen battery cathodes: general discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.' ista: 'Attard GA, Calvo EJ, Curtiss LA, Dewar D, Ellison JHJ, Gao X, Grey CP, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Mondal S, Neale AR, Ortiz-Vitoriano N, Temprano I, Vailaya G, Wachsman ED, Wang H-H, Wu Y, Ye S. 2023. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions.' mla: 'Attard, Gary A., et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90059b.' short: G.A. Attard, E.J. Calvo, L.A. Curtiss, D. Dewar, J.H.J. Ellison, X. Gao, C.P. Grey, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Mondal, A.R. Neale, N. Ortiz-Vitoriano, I. Temprano, G. Vailaya, E.D. Wachsman, H.-H. Wang, Y. Wu, S. Ye, Faraday Discussions (2023). date_created: 2023-12-20T10:49:43Z date_published: 2023-12-18T00:00:00Z date_updated: 2023-12-20T11:58:12Z day: '18' department: - _id: StFr doi: 10.1039/d3fd90059b keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '12' oa_version: None publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: epub_ahead publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Materials for stable metal–oxygen battery cathodes: general discussion' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14360' abstract: - lang: eng text: To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment. acknowledgement: "We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL." article_number: '5644' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Ewa full_name: Sitarska, Ewa last_name: Sitarska - first_name: Silvia Dias full_name: Almeida, Silvia Dias last_name: Almeida - first_name: Marianne Sandvold full_name: Beckwith, Marianne Sandvold last_name: Beckwith - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp - first_name: Jakub full_name: Czuchnowski, Jakub last_name: Czuchnowski - first_name: Marc full_name: Siggel, Marc last_name: Siggel - first_name: Rita full_name: Roessner, Rita last_name: Roessner - first_name: Aline full_name: Tschanz, Aline last_name: Tschanz - first_name: Christer full_name: Ejsing, Christer last_name: Ejsing - first_name: Yannick full_name: Schwab, Yannick last_name: Schwab - first_name: Jan full_name: Kosinski, Jan last_name: Kosinski - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Anna full_name: Kreshuk, Anna last_name: Kreshuk - first_name: Anna full_name: Erzberger, Anna last_name: Erzberger - first_name: Alba full_name: Diz-Muñoz, Alba last_name: Diz-Muñoz citation: ama: Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 2023;14. doi:10.1038/s41467-023-41173-1 apa: Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41173-1 chicago: Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41173-1. ieee: E. Sitarska et al., “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644. mla: Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications, vol. 14, 5644, Springer Nature, 2023, doi:10.1038/s41467-023-41173-1. short: E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023). date_created: 2023-09-24T22:01:10Z date_published: 2023-09-13T00:00:00Z date_updated: 2023-12-21T14:30:01Z day: '13' ddc: - '570' department: - _id: MiSi doi: 10.1038/s41467-023-41173-1 external_id: isi: - '001087583700008' pmid: - '37704612' file: - access_level: open_access checksum: ad670e3b3c64fc585675948370f6b149 content_type: application/pdf creator: dernst date_created: 2023-09-25T08:22:58Z date_updated: 2023-09-25T08:22:58Z file_id: '14365' file_name: 2023_NatureComm_Sitarska.pdf file_size: 2725421 relation: main_file success: 1 file_date_updated: 2023-09-25T08:22:58Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14697' relation: dissertation_contains status: public scopus_import: '1' status: public title: Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14274' abstract: - lang: eng text: Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization. acknowledgement: "We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411." article_number: adc9584 article_processing_charge: No article_type: original author: - first_name: Jonna H full_name: Alanko, Jonna H id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87 last_name: Alanko orcid: 0000-0002-7698-3061 - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Nikola full_name: Canigova, Nikola id: 3795523E-F248-11E8-B48F-1D18A9856A87 last_name: Canigova orcid: 0000-0002-8518-5926 - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584 apa: Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584 chicago: Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584. ieee: J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023. ista: Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584. mla: Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584. short: J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023). date_created: 2023-09-06T08:07:51Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-12-21T14:30:01Z day: '01' department: - _id: MiSi - _id: EdHa - _id: NanoFab doi: 10.1126/sciimmunol.adc9584 ec_funded: 1 external_id: isi: - '001062110600003' pmid: - '37656776' intvolume: ' 8' isi: 1 issue: '87' keyword: - General Medicine - Immunology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/sciimmunol.adc9584 month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis - _id: 265E2996-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01250-B20 name: Nano-Analytics of Cellular Systems - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Science Immunology publication_identifier: issn: - 2470-9468 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: record: - id: '14279' relation: research_data status: public - id: '14697' relation: dissertation_contains status: public scopus_import: '1' status: public title: CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2023' ... --- _id: '14697' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp citation: ama: 'Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697' apa: 'Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697' chicago: 'Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.' ieee: 'J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.' ista: 'Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.' mla: 'Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697.' short: 'J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.' date_created: 2023-12-18T19:14:28Z date_published: 2023-12-20T00:00:00Z date_updated: 2023-12-21T14:30:02Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/at:ista:14697 ec_funded: 1 file: - access_level: closed checksum: 457927165d5d556305d3086f6b83e5c7 content_type: application/pdf creator: jstopp date_created: 2023-12-20T09:35:34Z date_updated: 2023-12-20T09:35:34Z embargo: 2024-12-20 embargo_to: open_access file_id: '14699' file_name: Thesis.pdf file_size: 51585778 relation: main_file - access_level: closed checksum: e8d26449ac461f5e8478a62c9507506f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jstopp date_created: 2023-12-20T09:35:35Z date_updated: 2023-12-20T10:41:42Z file_id: '14700' file_name: Thesis.docx file_size: 69625950 relation: source_file file_date_updated: 2023-12-20T10:41:42Z has_accepted_license: '1' language: - iso: eng month: '12' oa_version: Published Version page: '226' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-038-1 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6328' relation: part_of_dissertation status: public - id: '7885' relation: part_of_dissertation status: public - id: '12272' relation: part_of_dissertation status: public - id: '14274' relation: part_of_dissertation status: public - id: '14360' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: 'Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14651' abstract: - lang: eng text: 'For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.' acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651 apa: Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651 chicago: Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651. ieee: L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023. ista: Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. mla: Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651. short: L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023. date_created: 2023-12-11T19:30:37Z date_published: 2023-12-12T00:00:00Z date_updated: 2023-12-22T11:04:45Z day: '12' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:14651 ec_funded: 1 file: - access_level: open_access checksum: 520bdb61e95e66070e02824947d2c5fa content_type: application/pdf creator: larathoo date_created: 2023-12-13T15:37:55Z date_updated: 2023-12-13T15:37:55Z file_id: '14684' file_name: Phd_Thesis_LA.pdf file_size: 34101468 relation: main_file success: 1 - access_level: closed checksum: d8e59afd0817c98fba2564a264508e5c content_type: application/zip creator: larathoo date_created: 2023-12-13T15:42:23Z date_updated: 2023-12-14T08:58:18Z file_id: '14685' file_name: Phd_Thesis_LA.zip file_size: 31052872 relation: source_file - access_level: closed checksum: 9a778c949932286f4519e1f1fca2820d content_type: application/zip creator: larathoo date_created: 2023-12-11T19:24:59Z date_updated: 2023-12-14T08:58:18Z file_id: '14681' file_name: Supplementary_Materials.zip file_size: 10713896 relation: supplementary_material file_date_updated: 2023-12-14T08:58:18Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '96' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14703' abstract: - lang: eng text: We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation. acknowledgement: "The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council." article_number: '2312.12213' article_processing_charge: No author: - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida - first_name: Hugo full_name: Lavenant, Hugo last_name: Lavenant citation: ama: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. doi:10.48550/arXiv.2312.12213 apa: Ishida, S., & Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. https://doi.org/10.48550/arXiv.2312.12213 chicago: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2312.12213. ieee: S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. . ista: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213. mla: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, 2312.12213, doi:10.48550/arXiv.2312.12213. short: S. Ishida, H. Lavenant, ArXiv (n.d.). date_created: 2023-12-21T10:14:37Z date_published: 2023-12-19T00:00:00Z date_updated: 2023-12-27T13:44:33Z day: '19' department: - _id: GradSch - _id: ChWo doi: 10.48550/arXiv.2312.12213 external_id: arxiv: - '2312.12213' keyword: - Optimal transport - Hamilton-Jacobi equation - convex optimization language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2312.12213 month: '12' oa: 1 oa_version: Preprint project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: arXiv publication_status: submitted status: public title: Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation type: preprint user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14716' abstract: - lang: eng text: "Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.\r\n\r\nResults: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.\r\n\r\nConclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers." acknowledgement: Open Access funding enabled and organized by Projekt DEAL. A.Y. and O.V.K. acknowledge financial support from the Klaus Faber Foundation. A.A.A. was funded by the Helmholtz AI project AMR-XAI. The work of O.O.B. is funded by Fonds zur Förderung der Wissenschaftlichen Forschung (FWF), Grant ESP 253-B. article_number: '404' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Alper full_name: Yurtseven, Alper last_name: Yurtseven - first_name: Sofia full_name: Buyanova, Sofia id: 2F54A7BC-3902-11EA-AC87-BC9F3DDC885E last_name: Buyanova - first_name: Amay Ajaykumar A. full_name: Agrawal, Amay Ajaykumar A. last_name: Agrawal - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Olga V V. full_name: Kalinina, Olga V V. last_name: Kalinina citation: ama: Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023;23(1). doi:10.1186/s12866-023-03147-7 apa: Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., & Kalinina, O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. Springer Nature. https://doi.org/10.1186/s12866-023-03147-7 chicago: Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva, and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology. Springer Nature, 2023. https://doi.org/10.1186/s12866-023-03147-7. ieee: A. Yurtseven, S. Buyanova, A. A. A. Agrawal, O. Bochkareva, and O. V. V. Kalinina, “Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis,” BMC Microbiology, vol. 23, no. 1. Springer Nature, 2023. ista: Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. 2023. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 23(1), 404. mla: Yurtseven, Alper, et al. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology, vol. 23, no. 1, 404, Springer Nature, 2023, doi:10.1186/s12866-023-03147-7. short: A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (2023). date_created: 2023-12-31T23:01:02Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T09:20:57Z day: '01' ddc: - '570' department: - _id: FyKo doi: 10.1186/s12866-023-03147-7 external_id: pmid: - '38124060' file: - access_level: open_access checksum: 7ff5e95f3496ff663301eb4a13a316d5 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:09:32Z date_updated: 2024-01-02T09:09:32Z file_id: '14723' file_name: 2023_BMCMicrobiology_Yurtseven.pdf file_size: 1979922 relation: main_file success: 1 file_date_updated: 2024-01-02T09:09:32Z has_accepted_license: '1' intvolume: ' 23' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Microbiology publication_identifier: eissn: - 1471-2180 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2023' ... --- _id: '14718' abstract: - lang: eng text: 'Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. ' acknowledgement: "This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413 and the\r\n“VAMOS” grant ERC-2020-AdG 101020093." article_processing_charge: No author: - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Pastva S, Henzinger TA. Binary decision diagrams on modern hardware. In: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. TU Vienna Academic Press; 2023:122-131. doi:10.34727/2023/isbn.978-3-85448-060-0_20' apa: 'Pastva, S., & Henzinger, T. A. (2023). Binary decision diagrams on modern hardware. In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design (pp. 122–131). Ames, IA, United States: TU Vienna Academic Press. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20' chicago: Pastva, Samuel, and Thomas A Henzinger. “Binary Decision Diagrams on Modern Hardware.” In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, 122–31. TU Vienna Academic Press, 2023. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20. ieee: S. Pastva and T. A. Henzinger, “Binary decision diagrams on modern hardware,” in Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, Ames, IA, United States, 2023, pp. 122–131. ista: 'Pastva S, Henzinger TA. 2023. Binary decision diagrams on modern hardware. Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. FMCAD: Conference on Formal Methods in Computer-aided design, 122–131.' mla: Pastva, Samuel, and Thomas A. Henzinger. “Binary Decision Diagrams on Modern Hardware.” Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–31, doi:10.34727/2023/isbn.978-3-85448-060-0_20. short: S. Pastva, T.A. Henzinger, in:, Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–131. conference: end_date: 2023-10-27 location: Ames, IA, United States name: 'FMCAD: Conference on Formal Methods in Computer-aided design' start_date: 2023-10-25 date_created: 2023-12-31T23:01:03Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-02T08:16:28Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.34727/2023/isbn.978-3-85448-060-0_20 ec_funded: 1 file: - access_level: open_access checksum: 818d6e13dd508f3a04f0941081022e5d content_type: application/pdf creator: dernst date_created: 2024-01-02T08:14:23Z date_updated: 2024-01-02T08:14:23Z file_id: '14721' file_name: 2023_FMCAD_Pastva.pdf file_size: 524321 relation: main_file success: 1 file_date_updated: 2024-01-02T08:14:23Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 122-131 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design publication_identifier: isbn: - '9783854480600' publication_status: published publisher: TU Vienna Academic Press quality_controlled: '1' scopus_import: '1' status: public title: Binary decision diagrams on modern hardware tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14717' abstract: - lang: eng text: We count primitive lattices of rank d inside Zn as their covolume tends to infinity, with respect to certain parameters of such lattices. These parameters include, for example, the subspace that a lattice spans, namely its projection to the Grassmannian; its homothety class and its equivalence class modulo rescaling and rotation, often referred to as a shape. We add to a prior work of Schmidt by allowing sets in the spaces of parameters that are general enough to conclude the joint equidistribution of these parameters. In addition to the primitive d-lattices Λ themselves, we also consider their orthogonal complements in Zn⁠, A1⁠, and show that the equidistribution occurs jointly for Λ and A1⁠. Finally, our asymptotic formulas for the number of primitive lattices include an explicit bound on the error term. acknowledgement: This work was done when both authors were visiting Institute of Science and Technology (IST) Austria. T.H. was being supported by Engineering and Physical Sciences Research Council grant EP/P026710/1. Y.K. had a great time there and is grateful for the hospitality. The appendix to this paper is largely based on a mini course T.H. had given at IST in February 2020. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Tal full_name: Horesh, Tal id: C8B7BF48-8D81-11E9-BCA9-F536E6697425 last_name: Horesh - first_name: Yakov full_name: Karasik, Yakov last_name: Karasik citation: ama: Horesh T, Karasik Y. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 2023;74(4):1253-1294. doi:10.1093/qmath/haad008 apa: Horesh, T., & Karasik, Y. (2023). Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haad008 chicago: Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics. Oxford University Press, 2023. https://doi.org/10.1093/qmath/haad008. ieee: T. Horesh and Y. Karasik, “Equidistribution of primitive lattices in ℝn,” Quarterly Journal of Mathematics, vol. 74, no. 4. Oxford University Press, pp. 1253–1294, 2023. ista: Horesh T, Karasik Y. 2023. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 74(4), 1253–1294. mla: Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics, vol. 74, no. 4, Oxford University Press, 2023, pp. 1253–94, doi:10.1093/qmath/haad008. short: T. Horesh, Y. Karasik, Quarterly Journal of Mathematics 74 (2023) 1253–1294. date_created: 2023-12-31T23:01:03Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T07:39:55Z day: '01' ddc: - '510' department: - _id: TiBr doi: 10.1093/qmath/haad008 external_id: arxiv: - '2012.04508' file: - access_level: open_access checksum: bf29baa9eae8500f3374dbcb80712687 content_type: application/pdf creator: dernst date_created: 2024-01-02T07:37:09Z date_updated: 2024-01-02T07:37:09Z file_id: '14720' file_name: 2023_QuarterlyJourMath_Horesh.pdf file_size: 724748 relation: main_file success: 1 file_date_updated: 2024-01-02T07:37:09Z has_accepted_license: '1' intvolume: ' 74' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1253-1294 project: - _id: 26A8D266-B435-11E9-9278-68D0E5697425 grant_number: EP-P026710-2 name: Between rational and integral points publication: Quarterly Journal of Mathematics publication_identifier: eissn: - 1464-3847 issn: - 0033-5606 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Equidistribution of primitive lattices in ℝn tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2023' ... --- _id: '14719' abstract: - lang: eng text: Lithium–sulfur batteries are regarded as an advantageous option for meeting the growing demand for high-energy-density storage, but their commercialization relies on solving the current limitations of both sulfur cathodes and lithium metal anodes. In this scenario, the implementation of lithium sulfide (Li2S) cathodes compatible with alternative anode materials such as silicon has the potential to alleviate the safety concerns associated with lithium metal. In this direction, here, we report a sulfur cathode based on Li2S nanocrystals grown on a catalytic host consisting of CoFeP nanoparticles supported on tubular carbon nitride. Nanosized Li2S is incorporated into the host by a scalable liquid infiltration–evaporation method. Theoretical calculations and experimental results demonstrate that the CoFeP–CN composite can boost the polysulfide adsorption/conversion reaction kinetics and strongly reduce the initial overpotential activation barrier by stretching the Li–S bonds of Li2S. Besides, the ultrasmall size of the Li2S particles in the Li2S–CoFeP–CN composite cathode facilitates the initial activation. Overall, the Li2S–CoFeP–CN electrodes exhibit a low activation barrier of 2.56 V, a high initial capacity of 991 mA h gLi2S–1, and outstanding cyclability with a small fading rate of 0.029% per cycle over 800 cycles. Moreover, Si/Li2S full cells are assembled using the nanostructured Li2S–CoFeP–CN cathode and a prelithiated anode based on graphite-supported silicon nanowires. These Si/Li2S cells demonstrate high initial discharge capacities above 900 mA h gLi2S–1 and good cyclability with a capacity fading rate of 0.28% per cycle over 150 cycles. acknowledged_ssus: - _id: EM-Fac - _id: NanoFab acknowledgement: The authors acknowledge the support from the 2BoSS project of the ERA-MIN3 program with the Spanish grant number PCI2022-132985/AEI/10.13039/501100011033 and the French grant number ANR-22-MIN3-0003-01. J.L. acknowledges the support from the Natural Science Foundation of Sichuan Province 2022NSFSC1229. The authors acknowledge the funding from Generalitat de Catalunya 2021 SGR 01581 and European Union NextGenerationEU/PRTR. This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). article_processing_charge: No article_type: original author: - first_name: Hamid full_name: Mollania, Hamid last_name: Mollania - first_name: Chaoqi full_name: Zhang, Chaoqi last_name: Zhang - first_name: Ruifeng full_name: Du, Ruifeng last_name: Du - first_name: Xueqiang full_name: Qi, Xueqiang last_name: Qi - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Caroline full_name: Keller, Caroline last_name: Keller - first_name: Pascale full_name: Chenevier, Pascale last_name: Chenevier - first_name: Majid full_name: Oloomi-Buygi, Majid last_name: Oloomi-Buygi - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Mollania H, Zhang C, Du R, et al. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 2023;15(50):58462–58475. doi:10.1021/acsami.3c14072 apa: Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c14072 chicago: Mollania, Hamid, Chaoqi Zhang, Ruifeng Du, Xueqiang Qi, Junshan Li, Sharona Horta, Maria Ibáñez, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c14072. ieee: H. Mollania et al., “Nanostructured Li₂S cathodes for silicon-sulfur batteries,” ACS Applied Materials and Interfaces, vol. 15, no. 50. American Chemical Society, pp. 58462–58475, 2023. ista: Mollania H, Zhang C, Du R, Qi X, Li J, Horta S, Ibáñez M, Keller C, Chenevier P, Oloomi-Buygi M, Cabot A. 2023. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 15(50), 58462–58475. mla: Mollania, Hamid, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces, vol. 15, no. 50, American Chemical Society, 2023, pp. 58462–58475, doi:10.1021/acsami.3c14072. short: H. Mollania, C. Zhang, R. Du, X. Qi, J. Li, S. Horta, M. Ibáñez, C. Keller, P. Chenevier, M. Oloomi-Buygi, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 58462–58475. date_created: 2023-12-31T23:01:03Z date_published: 2023-12-05T00:00:00Z date_updated: 2024-01-02T08:35:06Z day: '05' department: - _id: MaIb doi: 10.1021/acsami.3c14072 intvolume: ' 15' issue: '50' language: - iso: eng month: '12' oa_version: None page: 58462–58475 publication: ACS Applied Materials and Interfaces publication_identifier: eissn: - 1944-8252 issn: - 1944-8244 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Nanostructured Li₂S cathodes for silicon-sulfur batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14715' abstract: - lang: eng text: We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ. acknowledgement: We thank Lea Boßmann, Phan Thành Nam and Simone Rademacher for helpful remarks. P.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Grant No. SFB/TRR 352 “Mathematics of Many-Body Quantum Systems and Their Collective Phenomena.” article_number: '121901' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Peter full_name: Pickl, Peter last_name: Pickl citation: ama: Mitrouskas DJ, Pickl P. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 2023;64(12). doi:10.1063/5.0172199 apa: Mitrouskas, D. J., & Pickl, P. (2023). Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0172199 chicago: Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0172199. ieee: D. J. Mitrouskas and P. Pickl, “Exponential decay of the number of excitations in the weakly interacting Bose gas,” Journal of Mathematical Physics, vol. 64, no. 12. AIP Publishing, 2023. ista: Mitrouskas DJ, Pickl P. 2023. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 64(12), 121901. mla: Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics, vol. 64, no. 12, 121901, AIP Publishing, 2023, doi:10.1063/5.0172199. short: D.J. Mitrouskas, P. Pickl, Journal of Mathematical Physics 64 (2023). date_created: 2023-12-31T23:01:02Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T08:51:28Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1063/5.0172199 external_id: arxiv: - '2307.11062' file: - access_level: open_access checksum: 66572f718a36465576cf0d6b3f7e01fc content_type: application/pdf creator: dernst date_created: 2024-01-02T08:45:07Z date_updated: 2024-01-02T08:45:07Z file_id: '14722' file_name: 2023_JourMathPhysics_Mitrouskas.pdf file_size: 4346922 relation: main_file success: 1 file_date_updated: 2024-01-02T08:45:07Z has_accepted_license: '1' intvolume: ' 64' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Journal of Mathematical Physics publication_identifier: eissn: - 1089-7658 issn: - 0022-2488 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Exponential decay of the number of excitations in the weakly interacting Bose gas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2023' ... --- _id: '14240' abstract: - lang: eng text: This paper introduces a novel method for simulating large bodies of water as a height field. At the start of each time step, we partition the waves into a bulk flow (which approximately satisfies the assumptions of the shallow water equations) and surface waves (which approximately satisfy the assumptions of Airy wave theory). We then solve the two wave regimes separately using appropriate state-of-the-art techniques, and re-combine the resulting wave velocities at the end of each step. This strategy leads to the first heightfield wave model capable of simulating complex interactions between both deep and shallow water effects, like the waves from a boat wake sloshing up onto a beach, or a dam break producing wave interference patterns and eddies. We also analyze the numerical dispersion created by our method and derive an exact correction factor for waves at a constant water depth, giving us a numerically perfect re-creation of theoretical water wave dispersion patterns. acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank Georg Sperl for helping with early research for this paper, Mickael Ly and Yi-Lu Chen for proofreading, and members of the ISTA Visual Computing Group for general feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).\r\nThe motorboat and sailboat were modeled by Sergei and the palmtrees by YadroGames. The environment map was created by Emil Persson." article_number: '83' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 2023;42(4). doi:10.1145/3592098 apa: Jeschke, S., & Wojtan, C. (2023). Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3592098 chicago: Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592098. ieee: S. Jeschke and C. Wojtan, “Generalizing shallow water simulations with dispersive surface waves,” ACM Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023. ista: Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 42(4), 83. mla: Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics, vol. 42, no. 4, 83, Association for Computing Machinery, 2023, doi:10.1145/3592098. short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023). date_created: 2023-08-27T22:01:17Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-01-02T09:35:55Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/3592098 external_id: isi: - '001044671300049' file: - access_level: open_access checksum: 1d178bb2f8011d9f5aedda6427e18c7a content_type: video/mp4 creator: sjeschke date_created: 2023-12-21T12:26:40Z date_updated: 2023-12-21T12:26:40Z file_id: '14704' file_name: PaperVideo_final.mp4 file_size: 511572575 relation: main_file success: 1 - access_level: open_access checksum: a49b2e744d5cd1276bb8b2e0ce6dc638 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:34:27Z date_updated: 2024-01-02T09:34:27Z file_id: '14725' file_name: 2023_ACMToG_Jeschke.pdf file_size: 7469177 relation: main_file success: 1 file_date_updated: 2024-01-02T09:34:27Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Generalizing shallow water simulations with dispersive surface waves tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '14710' abstract: - lang: eng text: The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells. acknowledgement: 'We thank Lucy Colwell for suggesting that we use covariance based methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker for collaborations on designed protein complexes. We also thank Ned Wingreen for suggesting the alternative derivation of (11). This research was supported by the Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University, and the National Science Foundation through the Center for the Physics of Biological Function (PHY-1734030).' article_number: '8328' article_processing_charge: Yes article_type: original author: - first_name: Agnese I. full_name: Curatolo, Agnese I. last_name: Curatolo - first_name: Ofer full_name: Kimchi, Ofer last_name: Kimchi - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Ryan K. full_name: Krueger, Ryan K. last_name: Krueger - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner citation: ama: Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. doi:10.1038/s41467-023-43168-4 apa: Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4 chicago: Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger, and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-43168-4. ieee: A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner, “A computational toolbox for the assembly yield of complex and heterogeneous structures,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328. mla: Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications, vol. 14, 8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4. short: A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023). date_created: 2023-12-24T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T11:36:46Z day: '01' ddc: - '530' department: - _id: CaGo doi: 10.1038/s41467-023-43168-4 file: - access_level: open_access checksum: fd9e9d527c2691f03fbc24031a75a3b3 content_type: application/pdf creator: kschuh date_created: 2023-12-27T08:40:43Z date_updated: 2023-12-27T08:40:43Z file_id: '14714' file_name: 2023_NatureComm_Curatolo.pdf file_size: 1342319 relation: main_file success: 1 file_date_updated: 2023-12-27T08:40:43Z has_accepted_license: '1' intvolume: ' 14' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A computational toolbox for the assembly yield of complex and heterogeneous structures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14709' abstract: - lang: eng text: Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Marta full_name: Del Bianco, Marta last_name: Del Bianco - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Lucia full_name: Strader, Lucia last_name: Strader - first_name: Stefan full_name: Kepinski, Stefan last_name: Kepinski citation: ama: 'Del Bianco M, Friml J, Strader L, Kepinski S. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 2023;74(22):6889-6892. doi:10.1093/jxb/erad420' apa: 'Del Bianco, M., Friml, J., Strader, L., & Kepinski, S. (2023). Auxin research: Creating tools for a greener future. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erad420' chicago: 'Del Bianco, Marta, Jiří Friml, Lucia Strader, and Stefan Kepinski. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany. Oxford University Press, 2023. https://doi.org/10.1093/jxb/erad420.' ieee: 'M. Del Bianco, J. Friml, L. Strader, and S. Kepinski, “Auxin research: Creating tools for a greener future,” Journal of Experimental Botany, vol. 74, no. 22. Oxford University Press, pp. 6889–6892, 2023.' ista: 'Del Bianco M, Friml J, Strader L, Kepinski S. 2023. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 74(22), 6889–6892.' mla: 'Del Bianco, Marta, et al. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany, vol. 74, no. 22, Oxford University Press, 2023, pp. 6889–92, doi:10.1093/jxb/erad420.' short: M. Del Bianco, J. Friml, L. Strader, S. Kepinski, Journal of Experimental Botany 74 (2023) 6889–6892. date_created: 2023-12-24T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T09:29:24Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/jxb/erad420 external_id: pmid: - '38038239' file: - access_level: open_access checksum: f66fb960fd791dea53fd0e087f2fbbe8 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:23:57Z date_updated: 2024-01-02T09:23:57Z file_id: '14724' file_name: 2023_JourExperimentalBotany_DelBianco.pdf file_size: 425194 relation: main_file success: 1 file_date_updated: 2024-01-02T09:23:57Z has_accepted_license: '1' intvolume: ' 74' issue: '22' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 6889-6892 pmid: 1 publication: Journal of Experimental Botany publication_identifier: eissn: - 1460-2431 issn: - 0022-0957 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Auxin research: Creating tools for a greener future' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2023' ... --- _id: '14726' abstract: - lang: eng text: Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants. article_number: koad324 article_processing_charge: No article_type: original author: - first_name: Liang-Zi full_name: Zhou, Liang-Zi last_name: Zhou - first_name: Lele full_name: Wang, Lele last_name: Wang - first_name: Xia full_name: Chen, Xia last_name: Chen - first_name: Zengxiang full_name: Ge, Zengxiang id: f43371a3-09ff-11eb-8013-bd0c6a2f6de8 last_name: Ge orcid: 0000-0001-9381-3577 - first_name: Julia full_name: Mergner, Julia last_name: Mergner - first_name: Xingli full_name: Li, Xingli last_name: Li - first_name: Bernhard full_name: Küster, Bernhard last_name: Küster - first_name: Gernot full_name: Längst, Gernot last_name: Längst - first_name: Li-Jia full_name: Qu, Li-Jia last_name: Qu - first_name: Thomas full_name: Dresselhaus, Thomas last_name: Dresselhaus citation: ama: Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. 2023. doi:10.1093/plcell/koad324 apa: Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2023). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koad324 chicago: Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell. Oxford University Press, 2023. https://doi.org/10.1093/plcell/koad324. ieee: L.-Z. Zhou et al., “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” The Plant Cell. Oxford University Press, 2023. ista: Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2023. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell., koad324. mla: Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell, koad324, Oxford University Press, 2023, doi:10.1093/plcell/koad324. short: L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell (2023). date_created: 2024-01-02T11:19:37Z date_published: 2023-12-23T00:00:00Z date_updated: 2024-01-03T12:43:41Z day: '23' ddc: - '580' doi: 10.1093/plcell/koad324 extern: '1' has_accepted_license: '1' keyword: - Cell Biology - Plant Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/plcell/koad324 month: '12' oa: 1 oa_version: Published Version publication: The Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: epub_ahead publisher: Oxford University Press quality_controlled: '1' status: public title: The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12833' abstract: - lang: eng text: 'The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.' acknowledgement: "This work was begun at the University of Waterloo and was partially supported by the Natural Sciences and Engineering Council of Canada (NSERC).\r\n" article_number: '9' article_processing_charge: No article_type: original author: - first_name: Ahmad full_name: Biniaz, Ahmad last_name: Biniaz - first_name: Kshitij full_name: Jain, Kshitij last_name: Jain - first_name: Anna full_name: Lubiw, Anna last_name: Lubiw - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Tillmann full_name: Miltzow, Tillmann last_name: Miltzow - first_name: Debajyoti full_name: Mondal, Debajyoti last_name: Mondal - first_name: Anurag Murty full_name: Naredla, Anurag Murty last_name: Naredla - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Alexi full_name: Turcotte, Alexi last_name: Turcotte citation: ama: Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 2023;24(2). doi:10.46298/DMTCS.8383 apa: Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (2023). Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. EPI Sciences. https://doi.org/10.46298/DMTCS.8383 chicago: Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science. EPI Sciences, 2023. https://doi.org/10.46298/DMTCS.8383. ieee: A. Biniaz et al., “Token swapping on trees,” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2. EPI Sciences, 2023. ista: Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. 2023. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 24(2), 9. mla: Biniaz, Ahmad, et al. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2, 9, EPI Sciences, 2023, doi:10.46298/DMTCS.8383. short: A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, Discrete Mathematics and Theoretical Computer Science 24 (2023). date_created: 2023-04-16T22:01:08Z date_published: 2023-01-18T00:00:00Z date_updated: 2024-01-04T12:42:09Z day: '18' ddc: - '000' department: - _id: KrCh - _id: HeEd - _id: UlWa doi: 10.46298/DMTCS.8383 external_id: arxiv: - '1903.06981' file: - access_level: open_access checksum: 439102ea4f6e2aeefd7107dfb9ccf532 content_type: application/pdf creator: dernst date_created: 2023-04-17T08:10:28Z date_updated: 2023-04-17T08:10:28Z file_id: '12844' file_name: 2022_DMTCS_Biniaz.pdf file_size: 2072197 relation: main_file success: 1 file_date_updated: 2023-04-17T08:10:28Z has_accepted_license: '1' intvolume: ' 24' issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Discrete Mathematics and Theoretical Computer Science publication_identifier: eissn: - 1365-8050 issn: - 1462-7264 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '7950' relation: earlier_version status: public scopus_import: '1' status: public title: Token swapping on trees tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2023' ... --- _id: '14735' abstract: - lang: eng text: "Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs." acknowledgement: 'Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Christos full_name: Stefo, Christos id: a20e8902-32b0-11ee-9fa8-b23fa638b793 last_name: Stefo - first_name: Zhuolun full_name: Xiang, Zhuolun last_name: Xiang - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: 'Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1' apa: 'Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1' chicago: Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1. ieee: C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20. ista: 'Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.' mla: Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1. short: C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-08T09:17:38Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:28:14Z day: '01' department: - _id: ElKo - _id: GradSch doi: 10.1007/978-3-031-47754-6_1 intvolume: ' 13950' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2022/1554 month: '12' oa: 1 oa_version: Preprint page: 3-20 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Secure Network and Hardware for Efficient Blockchains publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 0302-9743 isbn: - '9783031477539' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Executing and proving over dirty ledgers type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13950 year: '2023' ... --- _id: '14733' abstract: - lang: eng text: Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Rajesh B full_name: Jethwa, Rajesh B id: 4cc538d5-803f-11ed-ab7e-8139573aad8f last_name: Jethwa orcid: 0000-0002-0404-4356 - first_name: Dominic full_name: Hey, Dominic last_name: Hey - first_name: Rachel N. full_name: Kerber, Rachel N. last_name: Kerber - first_name: Andrew D. full_name: Bond, Andrew D. last_name: Bond - first_name: Dominic S. full_name: Wright, Dominic S. last_name: Wright - first_name: Clare P. full_name: Grey, Clare P. last_name: Grey citation: ama: Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. 2023. doi:10.1021/acsaem.3c02223 apa: Jethwa, R. B., Hey, D., Kerber, R. N., Bond, A. D., Wright, D. S., & Grey, C. P. (2023). Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.3c02223 chicago: Jethwa, Rajesh B, Dominic Hey, Rachel N. Kerber, Andrew D. Bond, Dominic S. Wright, and Clare P. Grey. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaem.3c02223. ieee: R. B. Jethwa, D. Hey, R. N. Kerber, A. D. Bond, D. S. Wright, and C. P. Grey, “Exploring the landscape of heterocyclic quinones for redox flow batteries,” ACS Applied Energy Materials. American Chemical Society, 2023. ista: Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. 2023. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. mla: Jethwa, Rajesh B., et al. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials, American Chemical Society, 2023, doi:10.1021/acsaem.3c02223. short: R.B. Jethwa, D. Hey, R.N. Kerber, A.D. Bond, D.S. Wright, C.P. Grey, ACS Applied Energy Materials (2023). date_created: 2024-01-05T09:20:48Z date_published: 2023-12-28T00:00:00Z date_updated: 2024-01-08T09:03:01Z day: '28' ddc: - '540' department: - _id: StFr doi: 10.1021/acsaem.3c02223 ec_funded: 1 has_accepted_license: '1' keyword: - Electrical and Electronic Engineering - Materials Chemistry - Electrochemistry - Energy Engineering and Power Technology - Chemical Engineering (miscellaneous) language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acsaem.3c02223 month: '12' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: ACS Applied Energy Materials publication_identifier: eissn: - 2574-0962 publication_status: epub_ahead publisher: American Chemical Society quality_controlled: '1' status: public title: Exploring the landscape of heterocyclic quinones for redox flow batteries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14734' abstract: - lang: eng text: Developing cost-effective and high-performance thermoelectric (TE) materials to assemble efficient TE devices presents a multitude of challenges and opportunities. Cu3SbSe4 is a promising p-type TE material based on relatively earth abundant elements. However, the challenge lies in its poor electrical conductivity. Herein, an efficient and scalable solution-based approach is developed to synthesize high-quality Cu3SbSe4 nanocrystals doped with Pb at the Sb site. After ligand displacement and annealing treatments, the dried powders are consolidated into dense pellets, and their TE properties are investigated. Pb doping effectively increases the charge carrier concentration, resulting in a significant increase in electrical conductivity, while the Seebeck coefficients remain consistently high. The calculated band structure shows that Pb doping induces band convergence, thereby increasing the effective mass. Furthermore, the large ionic radius of Pb2+ results in the generation of additional point and plane defects and interphases, dramatically enhancing phonon scattering, which significantly decreases the lattice thermal conductivity at high temperatures. Overall, a maximum figure of merit (zTmax) ≈ 0.85 at 653 K is obtained in Cu3Sb0.97Pb0.03Se4. This represents a 1.6-fold increase compared to the undoped sample and exceeds most doped Cu3SbSe4-based materials produced by solid-state, demonstrating advantages of versatility and cost-effectiveness using a solution-based technology. acknowledgement: Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation. article_processing_charge: No article_type: original author: - first_name: Shanhong full_name: Wan, Shanhong last_name: Wan - first_name: Shanshan full_name: Xiao, Shanshan last_name: Xiao - first_name: Mingquan full_name: Li, Mingquan last_name: Li - first_name: Xin full_name: Wang, Xin last_name: Wang - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - first_name: Min full_name: Hong, Min last_name: Hong - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 citation: ama: Wan S, Xiao S, Li M, et al. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. 2023. doi:10.1002/smtd.202301377 apa: Wan, S., Xiao, S., Li, M., Wang, X., Lim, K. H., Hong, M., … Liu, Y. (2023). Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. Wiley. https://doi.org/10.1002/smtd.202301377 chicago: Wan, Shanhong, Shanshan Xiao, Mingquan Li, Xin Wang, Khak Ho Lim, Min Hong, Maria Ibáñez, Andreu Cabot, and Yu Liu. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods. Wiley, 2023. https://doi.org/10.1002/smtd.202301377. ieee: S. Wan et al., “Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4,” Small Methods. Wiley, 2023. ista: Wan S, Xiao S, Li M, Wang X, Lim KH, Hong M, Ibáñez M, Cabot A, Liu Y. 2023. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. mla: Wan, Shanhong, et al. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods, Wiley, 2023, doi:10.1002/smtd.202301377. short: S. Wan, S. Xiao, M. Li, X. Wang, K.H. Lim, M. Hong, M. Ibáñez, A. Cabot, Y. Liu, Small Methods (2023). date_created: 2024-01-07T23:00:51Z date_published: 2023-12-28T00:00:00Z date_updated: 2024-01-08T09:17:04Z day: '28' department: - _id: MaIb doi: 10.1002/smtd.202301377 external_id: pmid: - '38152986' language: - iso: eng month: '12' oa_version: None pmid: 1 project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Small Methods publication_identifier: eissn: - 2366-9608 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14737' abstract: - lang: eng text: 'John’s fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\mathbb{R}^{d}$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\mathbb{R}^{d}$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called Löwner’s ellipsoid, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the Löwner problems is more intricate than it is in the setting of convex bodies.' acknowledgement: "We thank Alexander Litvak for the many discussions on Theorem 1.1. Igor Tsiutsiurupa participated in the early stage of this project. To our deep regret, Igor chose another road for his life and stopped working with us.\r\nThis work was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences [to M.N.]; the National Research, Development, and Innovation Fund (NRDI) [K119670 and K131529 to M.N.]; and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovation and Technology from the source of the NRDI [to M.N.]." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Márton full_name: Naszódi, Márton last_name: Naszódi citation: ama: Ivanov G, Naszódi M. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023;2023(23):20613-20669. doi:10.1093/imrn/rnad210 apa: Ivanov, G., & Naszódi, M. (2023). Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnad210 chicago: Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices. Oxford University Press, 2023. https://doi.org/10.1093/imrn/rnad210. ieee: G. Ivanov and M. Naszódi, “Functional John and Löwner conditions for pairs of log-concave functions,” International Mathematics Research Notices, vol. 2023, no. 23. Oxford University Press, pp. 20613–20669, 2023. ista: Ivanov G, Naszódi M. 2023. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023(23), 20613–20669. mla: Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices, vol. 2023, no. 23, Oxford University Press, 2023, pp. 20613–69, doi:10.1093/imrn/rnad210. short: G. Ivanov, M. Naszódi, International Mathematics Research Notices 2023 (2023) 20613–20669. date_created: 2024-01-08T09:48:56Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:57:25Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1093/imrn/rnad210 external_id: arxiv: - '2212.11781' file: - access_level: open_access checksum: 353666cea80633beb0f1ffd342dff6d4 content_type: application/pdf creator: dernst date_created: 2024-01-08T09:53:09Z date_updated: 2024-01-08T09:53:09Z file_id: '14738' file_name: 2023_IMRN_Ivanov.pdf file_size: 815777 relation: main_file success: 1 file_date_updated: 2024-01-08T09:53:09Z has_accepted_license: '1' intvolume: ' 2023' issue: '23' keyword: - General Mathematics language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 20613-20669 publication: International Mathematics Research Notices publication_identifier: eissn: - 1687-0247 issn: - 1073-7928 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Functional John and Löwner conditions for pairs of log-concave functions tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '14736' abstract: - lang: eng text: Payment channel networks (PCNs) are a promising technology to improve the scalability of cryptocurrencies. PCNs, however, face the challenge that the frequent usage of certain routes may deplete channels in one direction, and hence prevent further transactions. In order to reap the full potential of PCNs, recharging and rebalancing mechanisms are required to provision channels, as well as an admission control logic to decide which transactions to reject in case capacity is insufficient. This paper presents a formal model of this optimisation problem. In particular, we consider an online algorithms perspective, where transactions arrive over time in an unpredictable manner. Our main contributions are competitive online algorithms which come with provable guarantees over time. We empirically evaluate our algorithms on randomly generated transactions to compare the average performance of our algorithms to our theoretical bounds. We also show how this model and approach differs from related problems in classic communication networks. acknowledgement: Supported by the German Federal Ministry of Education and Research (BMBF), grant 16KISK020K (6G-RIC), 2021–2025, and ERC CoG 863818 (ForM-SMArt). alternative_title: - LNCS article_processing_charge: No author: - first_name: Mahsa full_name: Bastankhah, Mahsa last_name: Bastankhah - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Mohammad Ali full_name: Maddah-Ali, Mohammad Ali last_name: Maddah-Ali - first_name: Stefan full_name: Schmid, Stefan last_name: Schmid - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: ama: 'Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. R2: Boosting liquidity in payment channel networks with online admission control. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:309-325. doi:10.1007/978-3-031-47754-6_18' apa: 'Bastankhah, M., Chatterjee, K., Maddah-Ali, M. A., Schmid, S., Svoboda, J., & Yeo, M. X. (2023). R2: Boosting liquidity in payment channel networks with online admission control. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 309–325). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_18' chicago: 'Bastankhah, Mahsa, Krishnendu Chatterjee, Mohammad Ali Maddah-Ali, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” In 27th International Conference on Financial Cryptography and Data Security, 13950:309–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_18.' ieee: 'M. Bastankhah, K. Chatterjee, M. A. Maddah-Ali, S. Schmid, J. Svoboda, and M. X. Yeo, “R2: Boosting liquidity in payment channel networks with online admission control,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 309–325.' ista: 'Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. 2023. R2: Boosting liquidity in payment channel networks with online admission control. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 309–325.' mla: 'Bastankhah, Mahsa, et al. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 309–25, doi:10.1007/978-3-031-47754-6_18.' short: M. Bastankhah, K. Chatterjee, M.A. Maddah-Ali, S. Schmid, J. Svoboda, M.X. Yeo, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 309–325. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-08T09:30:22Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:36:36Z day: '01' department: - _id: KrCh - _id: KrPi doi: 10.1007/978-3-031-47754-6_18 ec_funded: 1 intvolume: ' 13950' language: - iso: eng month: '12' oa_version: None page: 309-325 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 1611-3349 isbn: - '9783031477539' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'R2: Boosting liquidity in payment channel networks with online admission control' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13950 year: '2023' ... --- _id: '14739' abstract: - lang: eng text: Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods. acknowledgement: "The work of Maria-Jose Jimenez, Eduardo Paluzo-Hidalgo and Manuel Soriano-Trigueros was supported in part by the Spanish grant Ministerio de Ciencia e Innovacion under Grants TED2021-129438B-I00 and PID2019-107339GB-I00, and in part by REXASI-PRO H-EU project, call HORIZON-CL4-2021-HUMAN-01-01 under Grant 101070028. The work of\r\nMaria-Jose Jimenez was supported by a grant of Convocatoria de la Universidad de Sevilla para la recualificacion del sistema universitario español, 2021-23, funded by the European Union, NextGenerationEU. The work of Vidit Nanda was supported in part by EPSRC under Grant EP/R018472/1 and in part by US AFOSR under Grant FA9550-22-1-0462. \r\nWe are grateful to the team of GUDHI and TEASPOON developers, for their work and their support. We are also grateful to Streamlit for providing extra resources to deploy the web app\r\nonline on Streamlit community cloud. We thank the anonymous referees for their helpful suggestions." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Dashti full_name: Ali, Dashti last_name: Ali - first_name: Aras full_name: Asaad, Aras last_name: Asaad - first_name: Maria-Jose full_name: Jimenez, Maria-Jose last_name: Jimenez - first_name: Vidit full_name: Nanda, Vidit last_name: Nanda - first_name: Eduardo full_name: Paluzo-Hidalgo, Eduardo last_name: Paluzo-Hidalgo - first_name: Manuel full_name: Soriano Trigueros, Manuel id: 15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8 last_name: Soriano Trigueros orcid: 0000-0003-2449-1433 citation: ama: Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2023;45(12):14069-14080. doi:10.1109/tpami.2023.3308391 apa: Ali, D., Asaad, A., Jimenez, M.-J., Nanda, V., Paluzo-Hidalgo, E., & Soriano Trigueros, M. (2023). A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/tpami.2023.3308391 chicago: Ali, Dashti, Aras Asaad, Maria-Jose Jimenez, Vidit Nanda, Eduardo Paluzo-Hidalgo, and Manuel Soriano Trigueros. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2023. https://doi.org/10.1109/tpami.2023.3308391. ieee: D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, and M. Soriano Trigueros, “A survey of vectorization methods in topological data analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12. IEEE, pp. 14069–14080, 2023. ista: Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. 2023. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 45(12), 14069–14080. mla: Ali, Dashti, et al. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12, IEEE, 2023, pp. 14069–80, doi:10.1109/tpami.2023.3308391. short: D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, M. Soriano Trigueros, IEEE Transactions on Pattern Analysis and Machine Intelligence 45 (2023) 14069–14080. date_created: 2024-01-08T09:59:46Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T10:11:46Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1109/tpami.2023.3308391 file: - access_level: open_access checksum: 465c28ef0b151b4b1fb47977ed5581ab content_type: application/pdf creator: dernst date_created: 2024-01-08T10:09:14Z date_updated: 2024-01-08T10:09:14Z file_id: '14740' file_name: 2023_IEEEToP_Ali.pdf file_size: 2370988 relation: main_file success: 1 file_date_updated: 2024-01-08T10:09:14Z has_accepted_license: '1' intvolume: ' 45' issue: '12' keyword: - Applied Mathematics - Artificial Intelligence - Computational Theory and Mathematics - Computer Vision and Pattern Recognition - Software language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 14069-14080 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: eissn: - 1939-3539 issn: - 0162-8828 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: A survey of vectorization methods in topological data analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2023' ... --- _id: '14742' abstract: - lang: eng text: "Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life." acknowledgement: "K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper." article_number: a041447 article_processing_charge: No article_type: original author: - first_name: Kay full_name: Lucek, Kay last_name: Lucek - first_name: Mabel D. full_name: Giménez, Mabel D. last_name: Giménez - first_name: Mathieu full_name: Joron, Mathieu last_name: Joron - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Jeremy B. full_name: Searle, Jeremy B. last_name: Searle - first_name: Nora full_name: Walden, Nora last_name: Walden - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria citation: ama: 'Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447' apa: 'Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447' chicago: 'Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.' ieee: 'K. Lucek et al., “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.' ista: 'Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.' mla: 'Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.' short: K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023). date_created: 2024-01-08T12:43:48Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-08T12:52:29Z day: '01' department: - _id: NiBa - _id: BeVi doi: 10.1101/cshperspect.a041447 external_id: pmid: - '37604585' intvolume: ' 15' issue: '11' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/cshperspect.a041447 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Cold Spring Harbor Perspectives in Biology publication_identifier: issn: - 1943-0264 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: 'The impact of chromosomal rearrangements in speciation: From micro- to macroevolution' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14744' abstract: - lang: eng text: "Sharding distributed ledgers is a promising on-chain solution for scaling blockchains but lacks formal grounds, nurturing skepticism on whether such complex systems can scale blockchains securely. We fill this gap by introducing the first formal framework as well as a roadmap to robust sharding. In particular, we first define the properties sharded distributed ledgers should fulfill. We build upon and extend the Bitcoin backbone protocol by defining consistency and scalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system.\r\nUsing our model, we explore the limitations of sharding. We show that a sharded ledger with n participants cannot scale under a fully adaptive adversary, but it can scale up to m shards where n=c'm log m, under an epoch-adaptive adversary; the constant c' encompasses the trade-off between security and scalability. This is possible only if the sharded ledgers create succinct proofs of the valid state updates at every epoch. We leverage our results to identify the sufficient components for robust sharding, which we incorporate in a protocol abstraction termed Divide & Scale. To demonstrate the power of our framework, we analyze the most prominent sharded blockchains (Elastico, Monoxide, OmniLedger, RapidChain) and pinpoint where they fail to meet the desired properties." acknowledgement: The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant agreement 2020388). alternative_title: - LNCS article_processing_charge: No author: - first_name: Zeta full_name: Avarikioti, Zeta last_name: Avarikioti - first_name: Antoine full_name: Desjardins, Antoine id: 06d0c166-aec1-11ee-a7c0-b96e840a602b last_name: Desjardins - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer citation: ama: 'Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. Divide & Scale: Formalization and roadmap to robust sharding. In: 30th International Colloquium on Structural Information and Communication Complexity. Vol 13892. Springer Nature; 2023:199-245. doi:10.1007/978-3-031-32733-9_10' apa: 'Avarikioti, Z., Desjardins, A., Kokoris Kogias, E., & Wattenhofer, R. (2023). Divide & Scale: Formalization and roadmap to robust sharding. In 30th International Colloquium on Structural Information and Communication Complexity (Vol. 13892, pp. 199–245). Alcalá de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_10' chicago: 'Avarikioti, Zeta, Antoine Desjardins, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” In 30th International Colloquium on Structural Information and Communication Complexity, 13892:199–245. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_10.' ieee: 'Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, and R. Wattenhofer, “Divide & Scale: Formalization and roadmap to robust sharding,” in 30th International Colloquium on Structural Information and Communication Complexity, Alcalá de Henares, Spain, 2023, vol. 13892, pp. 199–245.' ista: 'Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. 2023. Divide & Scale: Formalization and roadmap to robust sharding. 30th International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 199–245.' mla: 'Avarikioti, Zeta, et al. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” 30th International Colloquium on Structural Information and Communication Complexity, vol. 13892, Springer Nature, 2023, pp. 199–245, doi:10.1007/978-3-031-32733-9_10.' short: Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, R. Wattenhofer, in:, 30th International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2023, pp. 199–245. conference: end_date: 2023-06-09 location: Alcalá de Henares, Spain name: 'SIROCCO: Structural Information and Communication Complexity' start_date: 2023-06-06 date_created: 2024-01-08T12:56:46Z date_published: 2023-06-01T00:00:00Z date_updated: 2024-01-09T07:40:57Z day: '01' department: - _id: ElKo doi: 10.1007/978-3-031-32733-9_10 intvolume: ' 13892' language: - iso: eng month: '06' oa_version: None page: 199-245 publication: 30th International Colloquium on Structural Information and Communication Complexity publication_identifier: eisbn: - '9783031327339' eissn: - 1611-3349 isbn: - '9783031327322' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Divide & Scale: Formalization and roadmap to robust sharding' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13892 year: '2023' ... --- _id: '14749' abstract: - lang: eng text: We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry. article_processing_charge: No article_type: original author: - first_name: Umang full_name: Mishra, Umang id: 4328fa4c-f128-11eb-9611-c107b0fe4d51 last_name: Mishra - first_name: Vyacheslav full_name: Li, Vyacheslav id: 3A4FAA92-F248-11E8-B48F-1D18A9856A87 last_name: Li - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald - first_name: Sofya full_name: Agafonova, Sofya id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80 last_name: Agafonova orcid: 0000-0003-0582-2946 - first_name: Fritz R full_name: Diorico, Fritz R id: 2E054C4C-F248-11E8-B48F-1D18A9856A87 last_name: Diorico - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X citation: ama: Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 2023;48(15):3973-3976. doi:10.1364/ol.495553 apa: Mishra, U., Li, V., Wald, S., Agafonova, S., Diorico, F. R., & Hosten, O. (2023). Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/ol.495553 chicago: Mishra, Umang, Vyacheslav Li, Sebastian Wald, Sofya Agafonova, Fritz R Diorico, and Onur Hosten. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters. Optica Publishing Group, 2023. https://doi.org/10.1364/ol.495553. ieee: U. Mishra, V. Li, S. Wald, S. Agafonova, F. R. Diorico, and O. Hosten, “Monitoring and active stabilization of laser injection locking using beam ellipticity,” Optics Letters, vol. 48, no. 15. Optica Publishing Group, pp. 3973–3976, 2023. ista: Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. 2023. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 48(15), 3973–3976. mla: Mishra, Umang, et al. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters, vol. 48, no. 15, Optica Publishing Group, 2023, pp. 3973–76, doi:10.1364/ol.495553. short: U. Mishra, V. Li, S. Wald, S. Agafonova, F.R. Diorico, O. Hosten, Optics Letters 48 (2023) 3973–3976. date_created: 2024-01-08T13:01:46Z date_published: 2023-07-21T00:00:00Z date_updated: 2024-01-09T08:09:32Z day: '21' department: - _id: OnHo doi: 10.1364/ol.495553 external_id: arxiv: - '2212.01266' intvolume: ' 48' issue: '15' keyword: - Atomic and Molecular Physics - and Optics language: - iso: eng month: '07' oa_version: Preprint page: 3973-3976 publication: Optics Letters publication_identifier: eissn: - 1539-4794 issn: - 0146-9592 publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Monitoring and active stabilization of laser injection locking using beam ellipticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2023' ... --- _id: '14752' abstract: - lang: eng text: 'Radiative cooling of the lowest atmospheric levels is of strong importance for modulating atmospheric circulations and organizing convection, but detailed observations and a robust theoretical understanding are lacking. Here we use unprecedented observational constraints from subsidence regimes in the tropical Atlantic to develop a theory for the shape and magnitude of low‐level longwave radiative cooling in clear‐sky, showing peaks larger than 5–10 K/day at the top of the boundary layer. A suite of novel scaling approximations is first developed from simplified spectral theory, in close agreement with the measurements. The radiative cooling peak height is set by the maximum lapse rate in water vapor path, and its magnitude is mainly controlled by the ratio of column relative humidity above and below the peak. We emphasize how elevated intrusions of moist air can reduce low‐level cooling, by sporadically shading the spectral range which effectively cools to space. The efficiency of this spectral shading depends both on water content and altitude of moist intrusions; its height dependence cannot be explained by the temperature difference between the emitting and absorbing layers, but by the decrease of water vapor extinction with altitude. This analytical work can help to narrow the search for low‐level cloud patterns sensitive to radiative‐convective feedbacks: the most organized patterns with largest cloud fractions occur in atmospheres below 10% relative humidity and feel the strongest low‐level cooling. This motivates further assessment of favorable conditions for radiative‐convective feedbacks and a robust quantification of corresponding shallow cloud dynamics in current and warmer climates.' acknowledgement: The authors would like to thank two anonymous reviews and gratefully acknowledge diverse funding agencies and resources used for this work. B.F. and C.M. thank funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041), and the EUREC4A campaign organizers for giving the opportunity to take part to the campaign and use the data early on. R. P. was supported by the US National Science Foundation (award AGS 19–16908), by the National Oceanic and Atmospheric Administration (award NA200AR4310375), and the Vetlesen Foundation. article_number: e2023AV000880 article_processing_charge: Yes article_type: original author: - first_name: B. full_name: Fildier, B. last_name: Fildier - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: R. full_name: Pincus, R. last_name: Pincus - first_name: S. full_name: Fueglistaler, S. last_name: Fueglistaler citation: ama: Fildier B, Muller CJ, Pincus R, Fueglistaler S. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 2023;4(3). doi:10.1029/2023av000880 apa: Fildier, B., Muller, C. J., Pincus, R., & Fueglistaler, S. (2023). How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. American Geophysical Union. https://doi.org/10.1029/2023av000880 chicago: Fildier, B., Caroline J Muller, R. Pincus, and S. Fueglistaler. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances. American Geophysical Union, 2023. https://doi.org/10.1029/2023av000880. ieee: B. Fildier, C. J. Muller, R. Pincus, and S. Fueglistaler, “How moisture shapes low‐level radiative cooling in subsidence regimes,” AGU Advances, vol. 4, no. 3. American Geophysical Union, 2023. ista: Fildier B, Muller CJ, Pincus R, Fueglistaler S. 2023. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 4(3), e2023AV000880. mla: Fildier, B., et al. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances, vol. 4, no. 3, e2023AV000880, American Geophysical Union, 2023, doi:10.1029/2023av000880. short: B. Fildier, C.J. Muller, R. Pincus, S. Fueglistaler, AGU Advances 4 (2023). date_created: 2024-01-08T13:07:49Z date_published: 2023-06-01T00:00:00Z date_updated: 2024-01-09T08:54:03Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1029/2023av000880 ec_funded: 1 file: - access_level: open_access checksum: af773220a9fa194c61a8dc2fae092c16 content_type: application/pdf creator: dernst date_created: 2024-01-09T08:51:25Z date_updated: 2024-01-09T08:51:25Z file_id: '14761' file_name: 2023_AGUAdvances_Fildier.pdf file_size: 24149551 relation: main_file success: 1 file_date_updated: 2024-01-09T08:51:25Z has_accepted_license: '1' intvolume: ' 4' issue: '3' keyword: - General Earth and Planetary Sciences language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: AGU Advances publication_identifier: eissn: - 2576-604X publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: How moisture shapes low‐level radiative cooling in subsidence regimes tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2023' ... --- _id: '14754' abstract: - lang: eng text: The large-scale laminar/turbulent spiral patterns that appear in the linearly unstable regime of counter-rotating Taylor–Couette flow are investigated from a statistical perspective by means of direct numerical simulation. Unlike the vast majority of previous numerical studies, we analyse the flow in periodic parallelogram-annular domains, following a coordinate change that aligns one of the parallelogram sides with the spiral pattern. The domain size, shape and spatial resolution have been varied and the results compared with those in a sufficiently large computational orthogonal domain with natural axial and azimuthal periodicity. We find that a minimal parallelogram of the right tilt significantly reduces the computational cost without notably compromising the statistical properties of the supercritical turbulent spiral. Its mean structure, obtained from extremely long time integrations in a co-rotating reference frame using the method of slices, bears remarkable similarity with the turbulent stripes observed in plane Couette flow, the centrifugal instability playing only a secondary role. acknowledgement: K.D.’s research was supported by Australian Research Council Discovery Early Career Researcher Award (DE170100171). B.W., R.A., F.M. and A.M. research was supported by the Spanish Ministerio de Economía y Competitividad (grant nos. FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación (grant no. PID2020-114043GB-I00) and the Generalitat de Catalunya (grant no. 2017-SGR-785). B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC no. 201806440152). F.M. is a Serra-Húnter Fellow. article_number: '0112' article_processing_charge: No article_type: original author: - first_name: B. full_name: Wang, B. last_name: Wang - first_name: F. full_name: Mellibovsky, F. last_name: Mellibovsky - first_name: Roger full_name: Ayats López, Roger id: ab77522d-073b-11ed-8aff-e71b39258362 last_name: Ayats López orcid: 0000-0001-6572-0621 - first_name: K. full_name: Deguchi, K. last_name: Deguchi - first_name: A. full_name: Meseguer, A. last_name: Meseguer citation: ama: Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 2023;381(2246). doi:10.1098/rsta.2022.0112 apa: Wang, B., Mellibovsky, F., Ayats López, R., Deguchi, K., & Meseguer, A. (2023). Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. The Royal Society. https://doi.org/10.1098/rsta.2022.0112 chicago: Wang, B., F. Mellibovsky, Roger Ayats López, K. Deguchi, and A. Meseguer. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A. The Royal Society, 2023. https://doi.org/10.1098/rsta.2022.0112. ieee: B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, and A. Meseguer, “Mean structure of the supercritical turbulent spiral in Taylor–Couette flow,” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246. The Royal Society, 2023. ista: Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. 2023. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 381(2246), 0112. mla: Wang, B., et al. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246, 0112, The Royal Society, 2023, doi:10.1098/rsta.2022.0112. short: B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, A. Meseguer, Philosophical Transactions of the Royal Society A 381 (2023). date_created: 2024-01-08T13:11:45Z date_published: 2023-05-01T00:00:00Z date_updated: 2024-01-09T09:15:29Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.1098/rsta.2022.0112 external_id: pmid: - '36907214' file: - access_level: open_access checksum: 1978d126c0ce2f47c22ac20107cc0106 content_type: application/pdf creator: dernst date_created: 2024-01-09T09:13:53Z date_updated: 2024-01-09T09:13:53Z file_id: '14763' file_name: 2023_PhilTransactionsA_Wang_accepted.pdf file_size: 6421086 relation: main_file success: 1 file_date_updated: 2024-01-09T09:13:53Z has_accepted_license: '1' intvolume: ' 381' issue: '2246' keyword: - General Physics and Astronomy - General Engineering - General Mathematics language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version pmid: 1 publication: Philosophical Transactions of the Royal Society A publication_identifier: eissn: - 1471-2962 issn: - 1364-503X publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: Mean structure of the supercritical turbulent spiral in Taylor–Couette flow tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 381 year: '2023' ... --- _id: '14753' abstract: - lang: eng text: "Several fixed-target experiments reported J/ψ and ϒ polarizations, as functions of Feynman x (xF) and transverse momentum (PT), in three different frames, using different combinations of beam particles, target nuclei, and collision energies. Despite the diverse and heterogeneous picture formed by these measurements, a detailed look allows us to discern qualitative physical patterns that inspire a simple empirical model. This data-driven scenario offers a good quantitative description of the J/ψ and ϒ(1S) polarizations measured in proton- and pion-nucleus collisions, in the xF 0.5 domain: more than 80 data points (not statistically independent) are well reproduced with only one free parameter. This study sets the context for future low-PT\r\n quarkonium polarization measurements in proton- and pion-nucleus collisions, such as those to be made by the AMBER experiment, and shows that such measurements provide significant constraints on the poorly-known parton distribution functions of the pion." acknowledgement: "P.F. and C.L. acknowledge support from Fundação para a Ciência e a Tecnologia, Portugal, under contract CERN/FIS-PAR/0010/2019.\r\nOpen Access funded by SCOAP3." article_number: '137871' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Pietro full_name: Faccioli, Pietro last_name: Faccioli - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Carlos full_name: Lourenço, Carlos last_name: Lourenço citation: ama: 'Faccioli P, Krätschmer I, Lourenço C. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 2023;840. doi:10.1016/j.physletb.2023.137871' apa: 'Faccioli, P., Krätschmer, I., & Lourenço, C. (2023). Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2023.137871' chicago: 'Faccioli, Pietro, Ilse Krätschmer, and Carlos Lourenço. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B. Elsevier, 2023. https://doi.org/10.1016/j.physletb.2023.137871.' ieee: 'P. Faccioli, I. Krätschmer, and C. Lourenço, “Low-pT quarkonium polarization measurements: Challenges and opportunities,” Physics Letters B, vol. 840. Elsevier, 2023.' ista: 'Faccioli P, Krätschmer I, Lourenço C. 2023. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 840, 137871.' mla: 'Faccioli, Pietro, et al. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B, vol. 840, 137871, Elsevier, 2023, doi:10.1016/j.physletb.2023.137871.' short: P. Faccioli, I. Krätschmer, C. Lourenço, Physics Letters B 840 (2023). date_created: 2024-01-08T13:09:17Z date_published: 2023-05-10T00:00:00Z date_updated: 2024-01-09T09:02:22Z day: '10' ddc: - '530' department: - _id: MaRo doi: 10.1016/j.physletb.2023.137871 file: - access_level: open_access checksum: 02dec160dbc81d95985e755869d8afbf content_type: application/pdf creator: dernst date_created: 2024-01-09T08:59:24Z date_updated: 2024-01-09T08:59:24Z file_id: '14762' file_name: 2023_PhysicsLettersB_Faccioli.pdf file_size: 855494 relation: main_file success: 1 file_date_updated: 2024-01-09T08:59:24Z has_accepted_license: '1' intvolume: ' 840' keyword: - Nuclear and High Energy Physics language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physics Letters B publication_identifier: eissn: - 1873-2445 issn: - 0370-2693 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Low-pT quarkonium polarization measurements: Challenges and opportunities' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 840 year: '2023' ... --- _id: '14750' abstract: - lang: eng text: "Consider the random matrix model A1/2UBU∗A1/2, where A and B are two N × N deterministic matrices and U is either an N × N Haar unitary or orthogonal random matrix. It is well known that on the macroscopic scale (Invent. Math. 104 (1991) 201–220), the limiting empirical spectral distribution (ESD) of the above model is given by the free multiplicative convolution\r\nof the limiting ESDs of A and B, denoted as μα \x02 μβ, where μα and μβ are the limiting ESDs of A and B, respectively. In this paper, we study the asymptotic microscopic behavior of the edge eigenvalues and eigenvectors statistics. We prove that both the density of μA \x02μB, where μA and μB are the ESDs of A and B, respectively and the associated subordination functions\r\nhave a regular behavior near the edges. Moreover, we establish the local laws near the edges on the optimal scale. In particular, we prove that the entries of the resolvent are close to some functionals depending only on the eigenvalues of A, B and the subordination functions with optimal convergence rates. Our proofs and calculations are based on the techniques developed for the additive model A+UBU∗ in (J. Funct. Anal. 271 (2016) 672–719; Comm. Math.\r\nPhys. 349 (2017) 947–990; Adv. Math. 319 (2017) 251–291; J. Funct. Anal. 279 (2020) 108639), and our results can be regarded as the counterparts of (J. Funct. Anal. 279 (2020) 108639) for the multiplicative model. " acknowledgement: "The first author is partially supported by NSF Grant DMS-2113489 and grateful for the AMS-SIMONS travel grant (2020–2023). The second author is supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nThe authors would like to thank the Editor, Associate Editor and an anonymous referee for their many critical suggestions which have significantly improved the paper. We also want to thank Zhigang Bao and Ji Oon Lee for many helpful discussions and comments." article_processing_charge: No article_type: original author: - first_name: Xiucai full_name: Ding, Xiucai last_name: Ding - first_name: Hong Chang full_name: Ji, Hong Chang id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d last_name: Ji citation: ama: Ding X, Ji HC. Local laws for multiplication of random matrices. The Annals of Applied Probability. 2023;33(4):2981-3009. doi:10.1214/22-aap1882 apa: Ding, X., & Ji, H. C. (2023). Local laws for multiplication of random matrices. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1882 chicago: Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1882. ieee: X. Ding and H. C. Ji, “Local laws for multiplication of random matrices,” The Annals of Applied Probability, vol. 33, no. 4. Institute of Mathematical Statistics, pp. 2981–3009, 2023. ista: Ding X, Ji HC. 2023. Local laws for multiplication of random matrices. The Annals of Applied Probability. 33(4), 2981–3009. mla: Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability, vol. 33, no. 4, Institute of Mathematical Statistics, 2023, pp. 2981–3009, doi:10.1214/22-aap1882. short: X. Ding, H.C. Ji, The Annals of Applied Probability 33 (2023) 2981–3009. date_created: 2024-01-08T13:03:18Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-01-09T08:16:41Z day: '01' department: - _id: LaEr doi: 10.1214/22-aap1882 ec_funded: 1 external_id: arxiv: - '2010.16083' intvolume: ' 33' issue: '4' keyword: - Statistics - Probability and Uncertainty - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2010.16083 month: '08' oa: 1 oa_version: Preprint page: 2981-3009 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: The Annals of Applied Probability publication_identifier: issn: - 1050-5164 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Local laws for multiplication of random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2023' ... --- _id: '14756' abstract: - lang: eng text: "We prove the r-spin cobordism hypothesis in the setting of (weak) 2-categories for every positive integer r: the 2-groupoid of 2-dimensional fully extended r-spin TQFTs with given target is equivalent to the homotopy fixed points of an induced Spin 2r -action. In particular, such TQFTs are classified by fully dualisable objects together with a trivialisation of the rth power of their Serre automorphisms. For r=1, we recover the oriented case (on which our proof builds), while ordinary spin structures correspond to r=2.\r\nTo construct examples, we explicitly describe Spin 2r​-homotopy fixed points in the equivariant completion of any symmetric monoidal 2-category. We also show that every object in a 2-category of Landau–Ginzburg models gives rise to fully extended spin TQFTs and that half of these do not factor through the oriented bordism 2-category." acknowledgement: "N.C. is supported by the DFG Heisenberg Programme.\r\nWe are grateful to Tobias Dyckerhoff, Lukas Müller, Ingo Runkel, and Christopher Schommer-Pries for helpful discussions." article_processing_charge: Yes article_type: original author: - first_name: Nils full_name: Carqueville, Nils last_name: Carqueville - first_name: Lorant full_name: Szegedy, Lorant id: 7943226E-220E-11EA-94C7-D59F3DDC885E last_name: Szegedy orcid: 0000-0003-2834-5054 citation: ama: Carqueville N, Szegedy L. Fully extended r-spin TQFTs. Quantum Topology. 2023;14(3):467-532. doi:10.4171/qt/193 apa: Carqueville, N., & Szegedy, L. (2023). Fully extended r-spin TQFTs. Quantum Topology. European Mathematical Society. https://doi.org/10.4171/qt/193 chicago: Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology. European Mathematical Society, 2023. https://doi.org/10.4171/qt/193. ieee: N. Carqueville and L. Szegedy, “Fully extended r-spin TQFTs,” Quantum Topology, vol. 14, no. 3. European Mathematical Society, pp. 467–532, 2023. ista: Carqueville N, Szegedy L. 2023. Fully extended r-spin TQFTs. Quantum Topology. 14(3), 467–532. mla: Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology, vol. 14, no. 3, European Mathematical Society, 2023, pp. 467–532, doi:10.4171/qt/193. short: N. Carqueville, L. Szegedy, Quantum Topology 14 (2023) 467–532. date_created: 2024-01-08T13:14:48Z date_published: 2023-10-16T00:00:00Z date_updated: 2024-01-09T09:27:46Z day: '16' ddc: - '530' department: - _id: MiLe doi: 10.4171/qt/193 file: - access_level: open_access checksum: b0590aff6e7ec89cc149ba94d459d3a3 content_type: application/pdf creator: dernst date_created: 2024-01-09T09:25:34Z date_updated: 2024-01-09T09:25:34Z file_id: '14764' file_name: 2023_QuantumTopol_Carqueville.pdf file_size: 707344 relation: main_file success: 1 file_date_updated: 2024-01-09T09:25:34Z has_accepted_license: '1' intvolume: ' 14' issue: '3' keyword: - Geometry and Topology - Mathematical Physics language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 467-532 publication: Quantum Topology publication_identifier: issn: - 1663-487X publication_status: published publisher: European Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Fully extended r-spin TQFTs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14751' abstract: - lang: eng text: 'We consider zero-error communication over a two-transmitter deterministic adversarial multiple access channel (MAC) governed by an adversary who has access to the transmissions of both senders (hence called omniscient ) and aims to maliciously corrupt the communication. None of the encoders, jammer and decoder is allowed to randomize using private or public randomness. This enforces a combinatorial nature of the problem. Our model covers a large family of channels studied in the literature, including all deterministic discrete memoryless noisy or noiseless MACs. In this work, given an arbitrary two-transmitter deterministic omniscient adversarial MAC, we characterize when the capacity region: 1) has nonempty interior (in particular, is two-dimensional); 2) consists of two line segments (in particular, has empty interior); 3) consists of one line segment (in particular, is one-dimensional); 4) or only contains (0,0) (in particular, is zero-dimensional). This extends a recent result by Wang et al. (201 9) from the point-to-point setting to the multiple access setting. Indeed, our converse arguments build upon their generalized Plotkin bound and involve delicate case analysis. One of the technical challenges is to take care of both “joint confusability” and “marginal confusability”. In particular, the treatment of marginal confusability does not follow from the point-to-point results by Wang et al. Our achievability results follow from random coding with expurgation.' acknowledgement: "The author would like to thank Amitalok J. Budkuley and Sidharth Jaggi for many helpful discussions at the early stage of this work. He would also like to thank Nir Ailon, Qi Cao, and Chandra Nair for discussions on a related problem regarding zero-error binary adder MACs.\r\nThe work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]" article_processing_charge: No article_type: original author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 citation: ama: Zhang Y. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 2023;69(7):4093-4127. doi:10.1109/tit.2023.3257239 apa: Zhang, Y. (2023). Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tit.2023.3257239 chicago: Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/tit.2023.3257239. ieee: Y. Zhang, “Zero-error communication over adversarial MACs,” IEEE Transactions on Information Theory, vol. 69, no. 7. Institute of Electrical and Electronics Engineers, pp. 4093–4127, 2023. ista: Zhang Y. 2023. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 69(7), 4093–4127. mla: Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory, vol. 69, no. 7, Institute of Electrical and Electronics Engineers, 2023, pp. 4093–127, doi:10.1109/tit.2023.3257239. short: Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 4093–4127. date_created: 2024-01-08T13:04:54Z date_published: 2023-07-01T00:00:00Z date_updated: 2024-01-09T08:45:24Z day: '01' department: - _id: MaMo doi: 10.1109/tit.2023.3257239 external_id: arxiv: - '2101.12426' intvolume: ' 69' issue: '7' keyword: - Computer Science Applications - Information Systems language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2101.12426 month: '07' oa: 1 oa_version: Preprint page: 4093-4127 publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Zero-error communication over adversarial MACs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2023' ... --- _id: '14755' abstract: - lang: eng text: We consider the sharp interface limit for the scalar-valued and vector-valued Allen–Cahn equation with homogeneous Neumann boundary condition in a bounded smooth domain Ω of arbitrary dimension N ⩾ 2 in the situation when a two-phase diffuse interface has developed and intersects the boundary ∂ Ω. The limit problem is mean curvature flow with 90°-contact angle and we show convergence in strong norms for well-prepared initial data as long as a smooth solution to the limit problem exists. To this end we assume that the limit problem has a smooth solution on [ 0 , T ] for some time T > 0. Based on the latter we construct suitable curvilinear coordinates and set up an asymptotic expansion for the scalar-valued and the vector-valued Allen–Cahn equation. In order to estimate the difference of the exact and approximate solutions with a Gronwall-type argument, a spectral estimate for the linearized Allen–Cahn operator in both cases is required. The latter will be shown in a separate paper, cf. (Moser (2021)). acknowledgement: "The author gratefully acknowledges support through DFG, GRK 1692 “Curvature,\r\nCycles and Cohomology” during parts of the work." article_processing_charge: No article_type: original author: - first_name: Maximilian full_name: Moser, Maximilian id: a60047a9-da77-11eb-85b4-c4dc385ebb8c last_name: Moser citation: ama: 'Moser M. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 2023;131(3-4):297-383. doi:10.3233/asy-221775' apa: 'Moser, M. (2023). Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. IOS Press. https://doi.org/10.3233/asy-221775' chicago: 'Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis. IOS Press, 2023. https://doi.org/10.3233/asy-221775.' ieee: 'M. Moser, “Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result,” Asymptotic Analysis, vol. 131, no. 3–4. IOS Press, pp. 297–383, 2023.' ista: 'Moser M. 2023. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 131(3–4), 297–383.' mla: 'Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis, vol. 131, no. 3–4, IOS Press, 2023, pp. 297–383, doi:10.3233/asy-221775.' short: M. Moser, Asymptotic Analysis 131 (2023) 297–383. date_created: 2024-01-08T13:13:28Z date_published: 2023-02-02T00:00:00Z date_updated: 2024-01-09T09:22:16Z day: '02' department: - _id: JuFi doi: 10.3233/asy-221775 external_id: arxiv: - '2105.07100' intvolume: ' 131' issue: 3-4 keyword: - General Mathematics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2105.07100 month: '02' oa: 1 oa_version: Preprint page: 297-383 publication: Asymptotic Analysis publication_identifier: eissn: - 1875-8576 issn: - 0921-7134 publication_status: published publisher: IOS Press quality_controlled: '1' scopus_import: '1' status: public title: 'Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2023' ... --- _id: '14757' abstract: - lang: eng text: The cerebral cortex is comprised of a vast cell-type diversity sequentially generated by cortical progenitor cells. Faithful progenitor lineage progression requires the tight orchestration of distinct molecular and cellular mechanisms regulating proper progenitor proliferation behavior and differentiation. Correct execution of developmental programs involves a complex interplay of cell intrinsic and tissue-wide mechanisms. Many studies over the past decades have been able to determine a plethora of genes critically involved in cortical development. However, only a few made use of genetic paradigms with sparse and global gene deletion to probe cell-autonomous vs. tissue-wide contribution. In this chapter, we will elaborate on the importance of dissecting the cell-autonomous and tissue-wide mechanisms to gain a precise understanding of gene function during radial glial progenitor lineage progression. article_processing_charge: No author: - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: 'Villalba Requena A, Amberg N, Hippenmeyer S. Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Huttner W, ed. Neocortical Neurogenesis in Development and Evolution. Wiley; 2023:169-191. doi:10.1002/9781119860914.ch10' apa: Villalba Requena, A., Amberg, N., & Hippenmeyer, S. (2023). Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution (pp. 169–191). Wiley. https://doi.org/10.1002/9781119860914.ch10 chicago: Villalba Requena, Ana, Nicole Amberg, and Simon Hippenmeyer. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” In Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, 169–91. Wiley, 2023. https://doi.org/10.1002/9781119860914.ch10. ieee: A. Villalba Requena, N. Amberg, and S. Hippenmeyer, “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression,” in Neocortical Neurogenesis in Development and Evolution, W. Huttner, Ed. Wiley, 2023, pp. 169–191. ista: 'Villalba Requena A, Amberg N, Hippenmeyer S. 2023.Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Neocortical Neurogenesis in Development and Evolution. , 169–191.' mla: Villalba Requena, Ana, et al. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, Wiley, 2023, pp. 169–91, doi:10.1002/9781119860914.ch10. short: A. Villalba Requena, N. Amberg, S. Hippenmeyer, in:, W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution, Wiley, 2023, pp. 169–191. date_created: 2024-01-08T13:16:36Z date_published: 2023-08-08T00:00:00Z date_updated: 2024-01-09T09:46:57Z day: '08' department: - _id: SiHi doi: 10.1002/9781119860914.ch10 editor: - first_name: Wieland full_name: Huttner, Wieland last_name: Huttner language: - iso: eng month: '08' oa_version: None page: 169-191 publication: Neocortical Neurogenesis in Development and Evolution publication_identifier: eisbn: - '9781119860914' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14759' abstract: - lang: eng text: "Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz \U0001D445\U0001D439 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method." acknowledgement: We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript. article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald orcid: 0000-0002-5869-1604 - first_name: Fritz R full_name: Diorico, Fritz R id: 2E054C4C-F248-11E8-B48F-1D18A9856A87 last_name: Diorico orcid: 0000-0002-4947-8924 - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X citation: ama: Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 2023;62(1):1-7. doi:10.1364/ao.474118 apa: Wald, S., Diorico, F. R., & Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. Optica Publishing Group. https://doi.org/10.1364/ao.474118 chicago: Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics. Optica Publishing Group, 2023. https://doi.org/10.1364/ao.474118. ieee: S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” Applied Optics, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023. ista: Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7. mla: Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:10.1364/ao.474118. short: S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7. date_created: 2024-01-08T13:19:14Z date_published: 2023-01-01T00:00:00Z date_updated: 2024-01-09T10:10:34Z day: '01' department: - _id: OnHo doi: 10.1364/ao.474118 external_id: arxiv: - '2208.11591' intvolume: ' 62' issue: '1' keyword: - Atomic and Molecular Physics - and Optics - Engineering (miscellaneous) - Electrical and Electronic Engineering language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2208.11591 month: '01' oa: 1 oa_version: Preprint page: 1-7 publication: Applied Optics publication_identifier: eissn: - 2155-3165 issn: - 1559-128X publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ...