--- _id: '12548' abstract: - lang: eng text: The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts. article_number: '00093' article_processing_charge: No author: - first_name: Mohammad full_name: Forghani, Mohammad last_name: Forghani - first_name: Christophe full_name: Claramunt, Christophe last_name: Claramunt - first_name: Farid full_name: Karimipour, Farid id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425 last_name: Karimipour orcid: 0000-0001-6746-4174 - first_name: Georg full_name: Heiler, Georg last_name: Heiler citation: ama: 'Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093' apa: 'Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093' chicago: Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093. ieee: M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023. ista: 'Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.' mla: Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093. short: M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023. conference: end_date: 2022-12-01 location: Orlando, FL, United States name: 'ICDMW: Conference on Data Mining Workshops' start_date: 2022-11-28 date_created: 2023-02-14T07:56:21Z date_published: 2023-02-08T00:00:00Z date_updated: 2023-08-01T13:15:48Z day: '08' ddc: - '600' department: - _id: HeEd doi: 10.1109/icdmw58026.2022.00093 external_id: isi: - '000971492200145' file: - access_level: open_access checksum: c253bee25e6dfe484f96662daa119cb6 content_type: application/pdf creator: fkarimip date_created: 2023-02-14T07:58:26Z date_updated: 2023-02-14T07:58:26Z file_id: '12549' file_name: Visual Analysis_Mobility_COVID19 - SocDM2022.pdf file_size: 1183339 relation: main_file success: 1 file_date_updated: 2023-02-14T07:58:26Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Submitted Version publication: 2022 IEEE International Conference on Data Mining Workshops publication_identifier: eisbn: - '9798350346091' eissn: - 2375-9259 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' status: public title: Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2023' ... --- _id: '12563' abstract: - lang: eng text: 'he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems.' acknowledgement: "Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\x1Eects only the authors’ views and not the views of the ERC or the European Commission. " article_processing_charge: No article_type: original author: - first_name: Andrei full_name: Krokhin, Andrei last_name: Krokhin - first_name: Jakub full_name: Opršal, Jakub id: ec596741-c539-11ec-b829-c79322a91242 last_name: Opršal orcid: 0000-0003-1245-3456 - first_name: Marcin full_name: Wrochna, Marcin last_name: Wrochna - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: ama: Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223 apa: Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223 chicago: Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223. ieee: A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023. ista: Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79. mla: Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223. short: A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79. date_created: 2023-02-16T07:03:52Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-08-01T13:11:30Z day: '01' department: - _id: UlWa doi: 10.1137/20m1378223 ec_funded: 1 external_id: arxiv: - '2003.11351' isi: - '000955000000001' intvolume: ' 52' isi: 1 issue: '1' keyword: - General Mathematics - General Computer Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2003.11351 month: '01' oa: 1 oa_version: Preprint page: 38-79 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Topology and adjunction in promise constraint satisfaction type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2023' ... --- _id: '12545' abstract: - lang: eng text: We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front. acknowledgement: 'MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.' article_number: '014608' article_processing_charge: No article_type: original author: - first_name: Mauricio Nicolas full_name: Rojas Vega, Mauricio Nicolas id: 441e7207-f91f-11ec-b67c-9e6fe3d8fd6d last_name: Rojas Vega - first_name: Pablo full_name: De Castro, Pablo last_name: De Castro - first_name: Rodrigo full_name: Soto, Rodrigo last_name: Soto citation: ama: Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608 apa: Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608 chicago: Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608. ieee: M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023. ista: Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608. mla: Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608. short: M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023). date_created: 2023-02-12T23:00:59Z date_published: 2023-01-24T00:00:00Z date_updated: 2023-08-01T13:09:45Z day: '24' department: - _id: GradSch doi: 10.1103/PhysRevE.107.014608 external_id: arxiv: - '2301.01856' isi: - '000963909800006' intvolume: ' 107' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.01856 month: '01' oa: 1 oa_version: Preprint publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Wetting dynamics by mixtures of fast and slow self-propelled particles type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '12427' abstract: - lang: eng text: 'Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent.' article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Balestrieri, Francesca id: 3ACCD756-F248-11E8-B48F-1D18A9856A87 last_name: Balestrieri citation: ama: Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239 apa: Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239 chicago: Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239. ieee: F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023. ista: Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914. mla: Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239. short: F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914. date_created: 2023-01-29T23:00:58Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-08-01T13:03:32Z day: '01' department: - _id: TiBr doi: 10.1090/proc/15239 external_id: isi: - '000898440000001' intvolume: ' 151' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.science/hal-03013498/ month: '01' oa: 1 oa_version: Preprint page: 907-914 publication: Proceedings of the American Mathematical Society publication_identifier: eissn: - 1088-6826 issn: - 0002-9939 publication_status: published publisher: American Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 151 year: '2023' ... --- _id: '12542' abstract: - lang: eng text: In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo. article_processing_charge: No article_type: letter_note 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: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006 apa: Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006 chicago: Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006. ieee: A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023. ista: Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293. mla: Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006. short: A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293. date_created: 2023-02-12T23:00:58Z date_published: 2023-02-01T00:00:00Z date_updated: 2023-08-01T13:10:27Z day: '01' department: - _id: SiHi doi: 10.1016/j.neuron.2023.01.006 external_id: isi: - '000994473300001' intvolume: ' 111' isi: 1 issue: '3' language: - iso: eng month: '02' oa_version: None page: 291-293 publication: Neuron publication_identifier: eissn: - 1097-4199 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Going back in time with TEMPO type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 111 year: '2023' ... --- _id: '12567' abstract: - lang: eng text: Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations. acknowledgement: This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program. article_number: '2128' article_processing_charge: No article_type: original author: - first_name: Achmed full_name: Mrestani, Achmed last_name: Mrestani - first_name: Katharina full_name: Lichter, Katharina id: 39302e62-fcfc-11ec-8196-8b01447dbd3d last_name: Lichter - first_name: Anna Leena full_name: Sirén, Anna Leena last_name: Sirén - first_name: Manfred full_name: Heckmann, Manfred last_name: Heckmann - first_name: Mila M. full_name: Paul, Mila M. last_name: Paul - first_name: Martin full_name: Pauli, Martin last_name: Pauli citation: ama: Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128 apa: Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128 chicago: Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128. ieee: A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023. ista: Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128. mla: Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128. short: A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023). date_created: 2023-02-19T23:00:56Z date_published: 2023-01-21T00:00:00Z date_updated: 2023-08-01T13:16:36Z day: '21' ddc: - '570' department: - _id: PeJo doi: 10.3390/ijms24032128 external_id: isi: - '000930324700001' file: - access_level: open_access checksum: 69a35dcd3e0249f902ab881b06ee2e58 content_type: application/pdf creator: dernst date_created: 2023-02-20T07:09:27Z date_updated: 2023-02-20T07:09:27Z file_id: '12569' file_name: 2023_IJMS_Mrestani.pdf file_size: 2823025 relation: main_file success: 1 file_date_updated: 2023-02-20T07:09:27Z has_accepted_license: '1' intvolume: ' 24' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version publication: International Journal of Molecular Sciences publication_identifier: eissn: - 1422-0067 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation 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: 24 year: '2023' ... --- _id: '12566' abstract: - lang: eng text: "Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs." acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria. article_number: '113733' article_processing_charge: Yes (via OA deal) 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: Faith full_name: Ellen, Faith last_name: Ellen - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 citation: ama: Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733 apa: Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733 chicago: Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733. ieee: D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023. ista: Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733. mla: Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733. short: D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023). date_created: 2023-02-19T23:00:55Z date_published: 2023-02-28T00:00:00Z date_updated: 2023-08-01T13:17:20Z day: '28' ddc: - '000' department: - _id: DaAl doi: 10.1016/j.tcs.2023.113733 ec_funded: 1 external_id: isi: - '000934262700001' file: - access_level: open_access checksum: b27c5290f2f1500c403494364ee39c9f content_type: application/pdf creator: dernst date_created: 2023-02-20T07:30:20Z date_updated: 2023-02-20T07:30:20Z file_id: '12570' file_name: 2023_TheoreticalCompScience_Alistarh.pdf file_size: 602333 relation: main_file success: 1 file_date_updated: 2023-02-20T07:30:20Z has_accepted_license: '1' intvolume: ' 948' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning - _id: 26A5D39A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '840605' name: Coordination in constrained and natural distributed systems publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Wait-free approximate agreement on graphs 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: 948 year: '2023' ... --- _id: '12681' abstract: - lang: eng text: The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT. acknowledgement: Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545). article_processing_charge: No article_type: original author: - first_name: Yves full_name: Dubief, Yves last_name: Dubief - first_name: Vincent E. full_name: Terrapon, Vincent E. last_name: Terrapon - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933 apa: Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933 chicago: Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933. ieee: Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023. ista: Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705. mla: Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933. short: Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705. date_created: 2023-02-26T23:01:01Z date_published: 2023-01-19T00:00:00Z date_updated: 2023-08-01T13:19:47Z day: '19' ddc: - '530' department: - _id: BjHo doi: 10.1146/annurev-fluid-032822-025933 external_id: isi: - '000915418100026' file: - access_level: open_access checksum: 2666aa3af2a25252d35eb8681d3edff7 content_type: application/pdf creator: dernst date_created: 2023-02-27T09:23:02Z date_updated: 2023-02-27T09:23:02Z file_id: '12690' file_name: 2023_AnnReviewFluidMech_Dubief.pdf file_size: 4036706 relation: main_file success: 1 file_date_updated: 2023-02-27T09:23:02Z has_accepted_license: '1' intvolume: ' 55' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 675-705 publication: Annual Review of Fluid Mechanics publication_identifier: eissn: - 1545-4479 issn: - 0066-4189 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Elasto-inertial turbulence 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: 55 year: '2023' ... --- _id: '12682' abstract: - lang: eng text: 'Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.' acknowledgement: 'The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).' article_processing_charge: No article_type: original author: - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Dwight full_name: Barkley, Dwight last_name: Barkley - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957 apa: Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957 chicago: Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957. ieee: M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023. ista: Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602. mla: Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957. short: M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602. date_created: 2023-02-26T23:01:01Z date_published: 2023-01-19T00:00:00Z date_updated: 2023-08-01T13:20:30Z day: '19' ddc: - '530' department: - _id: BjHo doi: 10.1146/annurev-fluid-120720-025957 external_id: isi: - '000915418100023' file: - access_level: open_access checksum: f99ef30f76cabc9e5e1946b380c16db4 content_type: application/pdf creator: dernst date_created: 2023-02-27T09:35:52Z date_updated: 2023-02-27T09:35:52Z file_id: '12691' file_name: 2023_AnnReviewFluidMech_Avila.pdf file_size: 4769537 relation: main_file success: 1 file_date_updated: 2023-02-27T09:35:52Z has_accepted_license: '1' intvolume: ' 55' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 575-602 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: Annual Review of Fluid Mechanics publication_identifier: issn: - 0066-4189 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Transition to turbulence in pipe 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 55 year: '2023' ... --- _id: '12708' abstract: - lang: eng text: Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter. acknowledgement: 'All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).' article_processing_charge: No article_type: original author: - first_name: Nuno A.M. full_name: Araújo, Nuno A.M. last_name: Araújo - first_name: Liesbeth M.C. full_name: Janssen, Liesbeth M.C. last_name: Janssen - first_name: Thomas full_name: Barois, Thomas last_name: Barois - first_name: Guido full_name: Boffetta, Guido last_name: Boffetta - first_name: Itai full_name: Cohen, Itai last_name: Cohen - first_name: Alessandro full_name: Corbetta, Alessandro last_name: Corbetta - first_name: Olivier full_name: Dauchot, Olivier last_name: Dauchot - first_name: Marjolein full_name: Dijkstra, Marjolein last_name: Dijkstra - first_name: William M. full_name: Durham, William M. last_name: Durham - first_name: Audrey full_name: Dussutour, Audrey last_name: Dussutour - first_name: Simon full_name: Garnier, Simon last_name: Garnier - first_name: Hanneke full_name: Gelderblom, Hanneke last_name: Gelderblom - first_name: Ramin full_name: Golestanian, Ramin last_name: Golestanian - first_name: Lucio full_name: Isa, Lucio last_name: Isa - first_name: Gijsje H. full_name: Koenderink, Gijsje H. last_name: Koenderink - first_name: Hartmut full_name: Löwen, Hartmut last_name: Löwen - first_name: Ralf full_name: Metzler, Ralf last_name: Metzler - first_name: Marco full_name: Polin, Marco last_name: Polin - first_name: C. Patrick full_name: Royall, C. Patrick last_name: Royall - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Anupam full_name: Sengupta, Anupam last_name: Sengupta - first_name: Cécile full_name: Sykes, Cécile last_name: Sykes - first_name: Vito full_name: Trianni, Vito last_name: Trianni - first_name: Idan full_name: Tuval, Idan last_name: Tuval - first_name: Nicolas full_name: Vogel, Nicolas last_name: Vogel - first_name: Julia M. full_name: Yeomans, Julia M. last_name: Yeomans - first_name: Iker full_name: Zuriguel, Iker last_name: Zuriguel - first_name: Alvaro full_name: Marin, Alvaro last_name: Marin - first_name: Giorgio full_name: Volpe, Giorgio last_name: Volpe citation: ama: Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e apa: Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e chicago: Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e. ieee: N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023. ista: Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704. mla: Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e. short: N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704. date_created: 2023-03-05T23:01:06Z date_published: 2023-02-06T00:00:00Z date_updated: 2023-08-01T13:28:39Z day: '06' ddc: - '540' department: - _id: AnSa doi: 10.1039/d2sm01562e ec_funded: 1 external_id: arxiv: - '2204.10059' isi: - '000940388100001' file: - access_level: open_access checksum: af95aa18b9b01e32fb8f13477c0e2687 content_type: application/pdf creator: cchlebak date_created: 2023-03-07T09:19:41Z date_updated: 2023-03-07T09:19:41Z file_id: '12711' file_name: 2023_SoftMatter_Araujo.pdf file_size: 3581939 relation: main_file success: 1 file_date_updated: 2023-03-07T09:19:41Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1695-1704 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Steering self-organisation through confinement 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: 19 year: '2023' ... --- _id: '12702' abstract: - lang: eng text: Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution. acknowledgement: BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC 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. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities. article_number: '1104' article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Sebastien full_name: Hamel, Sebastien last_name: Hamel - first_name: Mandy full_name: Bethkenhagen, Mandy id: 201939f4-803f-11ed-ab7e-d8da4bd1517f last_name: Bethkenhagen orcid: 0000-0002-1838-2129 citation: ama: Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1 apa: Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1 chicago: Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1. ieee: B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104. mla: Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1. short: B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023). date_created: 2023-03-05T23:01:04Z date_published: 2023-02-27T00:00:00Z date_updated: 2023-08-01T13:36:11Z day: '27' ddc: - '540' department: - _id: BiCh doi: 10.1038/s41467-023-36841-1 external_id: isi: - '000939678300002' pmid: - '36843123' file: - access_level: open_access checksum: 5ff61ad21511950c15abb73b18613883 content_type: application/pdf creator: cchlebak date_created: 2023-03-07T10:58:00Z date_updated: 2023-03-07T10:58:00Z file_id: '12713' file_name: 2023_NatComm_Cheng.pdf file_size: 1946443 relation: main_file success: 1 file_date_updated: 2023-03-07T10:58:00Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Thermodynamics of diamond formation from hydrocarbon mixtures in planets 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: 14 year: '2023' ... --- _id: '12719' abstract: - lang: eng text: "Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age." acknowledgement: We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses. article_number: '12' article_processing_charge: No article_type: original author: - first_name: Elena full_name: Bernabeu, Elena last_name: Bernabeu - first_name: Daniel L. full_name: Mccartney, Daniel L. last_name: Mccartney - first_name: Danni A. full_name: Gadd, Danni A. last_name: Gadd - first_name: Robert F. full_name: Hillary, Robert F. last_name: Hillary - first_name: Ake T. full_name: Lu, Ake T. last_name: Lu - first_name: Lee full_name: Murphy, Lee last_name: Murphy - first_name: Nicola full_name: Wrobel, Nicola last_name: Wrobel - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Sarah E. full_name: Harris, Sarah E. last_name: Harris - first_name: David full_name: Liewald, David last_name: Liewald - first_name: Caroline full_name: Hayward, Caroline last_name: Hayward - first_name: Cathie full_name: Sudlow, Cathie last_name: Sudlow - first_name: Simon R. full_name: Cox, Simon R. last_name: Cox - first_name: Kathryn L. full_name: Evans, Kathryn L. last_name: Evans - first_name: Steve full_name: Horvath, Steve last_name: Horvath - first_name: Andrew M. full_name: Mcintosh, Andrew M. last_name: Mcintosh - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Catalina A. full_name: Vallejos, Catalina A. last_name: Vallejos - first_name: Riccardo E. full_name: Marioni, Riccardo E. last_name: Marioni citation: ama: Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y apa: Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y chicago: Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y. ieee: E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023. ista: Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12. mla: Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y. short: E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023). date_created: 2023-03-12T23:01:02Z date_published: 2023-02-28T00:00:00Z date_updated: 2023-08-01T13:38:12Z day: '28' ddc: - '570' department: - _id: MaRo doi: 10.1186/s13073-023-01161-y external_id: isi: - '000940286600001' file: - access_level: open_access checksum: 833b837910c4db42fb5f0f34125f77a7 content_type: application/pdf creator: cchlebak date_created: 2023-03-14T10:29:47Z date_updated: 2023-03-14T10:29:47Z file_id: '12722' file_name: 2023_GenomeMed_Bernabeu.pdf file_size: 4275987 relation: main_file success: 1 file_date_updated: 2023-03-14T10:29:47Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Genome Medicine publication_identifier: eissn: - 1756-994X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Refining epigenetic prediction of chronological and biological age 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: 15 year: '2023' ... --- _id: '12704' abstract: - lang: eng text: Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice. acknowledgement: "We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein." article_processing_charge: No article_type: original author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Daniela full_name: Rus, Daniela last_name: Rus - 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: Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930 apa: Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930 chicago: Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930. ieee: M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023. ista: Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602. mla: Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930. short: M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602. date_created: 2023-03-05T23:01:04Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-01T13:36:50Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/LRA.2023.3240930 external_id: arxiv: - '2204.07373' isi: - '000936534100012' file: - access_level: open_access checksum: 5a75dcd326ea66685de2b1aaec259e85 content_type: application/pdf creator: cchlebak date_created: 2023-03-07T12:22:23Z date_updated: 2023-03-07T12:22:23Z file_id: '12714' file_name: 2023_IEEERobAutLetters_Lechner.pdf file_size: 944052 relation: main_file success: 1 file_date_updated: 2023-03-07T12:22:23Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1595-1602 publication: IEEE Robotics and Automation Letters publication_identifier: eissn: - 2377-3766 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' related_material: record: - id: '11366' relation: earlier_version status: public scopus_import: '1' status: public title: Revisiting the adversarial robustness-accuracy tradeoff in robot learning 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: 8 year: '2023' ... --- _id: '12737' abstract: - lang: eng text: The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed. acknowledgement: The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used. article_processing_charge: No article_type: original author: - first_name: Álvaro full_name: García-Romero, Álvaro last_name: García-Romero - first_name: Jessica E. full_name: Waters, Jessica E. last_name: Waters - 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: Andrew D. full_name: Bond, Andrew D. last_name: Bond - first_name: Annie L. full_name: Colebatch, Annie L. last_name: Colebatch - first_name: Raúl full_name: García-Rodríguez, Raúl last_name: García-Rodríguez - first_name: Dominic S. full_name: Wright, Dominic S. last_name: Wright citation: ama: García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057 apa: García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057 chicago: García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057. ieee: Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023. ista: García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636. mla: García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057. short: Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636. date_created: 2023-03-19T23:00:59Z date_published: 2023-03-08T00:00:00Z date_updated: 2023-08-01T13:42:59Z day: '08' department: - _id: StFr doi: 10.1021/acs.inorgchem.3c00057 external_id: isi: - '000956110300001' pmid: - '36883367' intvolume: ' 62' isi: 1 issue: '11' language: - iso: eng month: '03' oa_version: None page: 4625-4636 pmid: 1 publication: Inorganic Chemistry publication_identifier: eissn: - 1520-510X issn: - 0020-1669 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 62 year: '2023' ... --- _id: '12723' abstract: - lang: eng text: 'Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.' article_number: '106901' article_processing_charge: No article_type: original author: - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Abhishek full_name: Shiva Kumar, Abhishek id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a last_name: Shiva Kumar - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Younes full_name: Ashourishokri, Younes id: e32c111f-f6e0-11ea-865d-eb955baea334 last_name: Ashourishokri - first_name: Ayan A. full_name: Zhumekenov, Ayan A. last_name: Zhumekenov - first_name: Osman M. full_name: Bakr, Osman M. last_name: Bakr - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901 apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901 chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901. ieee: A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023. ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901. mla: Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901. short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023). date_created: 2023-03-14T13:11:59Z date_published: 2023-03-10T00:00:00Z date_updated: 2023-08-01T13:39:04Z day: '10' department: - _id: GradSch - _id: ZhAl - _id: MiLe doi: 10.1103/physrevlett.130.106901 external_id: arxiv: - '2203.09443' isi: - '000982435900002' intvolume: ' 130' isi: 1 issue: '10' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2203.09443 month: '03' oa: 1 oa_version: Preprint 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: Spin-electric coupling in lead halide perovskites type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 130 year: '2023' ... --- _id: '12724' abstract: - lang: eng text: 'We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.' article_number: '125201' article_processing_charge: No article_type: original author: - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Abhishek full_name: Shiva Kumar, Abhishek id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a last_name: Shiva Kumar - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Younes full_name: Ashourishokri, Younes id: e32c111f-f6e0-11ea-865d-eb955baea334 last_name: Ashourishokri - first_name: Ayan full_name: Zhumekenov, Ayan last_name: Zhumekenov - first_name: Osman M. full_name: Bakr, Osman M. last_name: Bakr - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201 apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201 chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201. ieee: A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023. ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201. mla: Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201. short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023). date_created: 2023-03-14T13:13:05Z date_published: 2023-03-15T00:00:00Z date_updated: 2023-08-01T13:39:47Z day: '15' department: - _id: GradSch - _id: ZhAl - _id: MiLe doi: 10.1103/physrevb.107.125201 external_id: arxiv: - '2204.04022' isi: - '000972602200006' intvolume: ' 107' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2204.04022 month: '03' 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: Effective model for studying optical properties of lead halide perovskites type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '12759' abstract: - lang: eng text: Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density. acknowledged_ssus: - _id: EM-Fac acknowledgement: "We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157)." article_number: e0277148 article_processing_charge: No article_type: original author: - first_name: Jason Seth full_name: Rothman, Jason Seth last_name: Rothman - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - first_name: Noemi full_name: Holderith, Noemi last_name: Holderith - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: R. full_name: Angus Silver, R. last_name: Angus Silver citation: ama: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148 apa: Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0277148 chicago: Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148. ieee: J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no. 3 March. Public Library of Science, 2023. ista: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148. mla: Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148. short: J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023). date_created: 2023-03-26T22:01:07Z date_published: 2023-03-17T00:00:00Z date_updated: 2023-08-01T13:46:39Z day: '17' ddc: - '570' department: - _id: PeJo doi: 10.1371/journal.pone.0277148 ec_funded: 1 external_id: isi: - '001024737400001' file: - access_level: open_access checksum: 2380331ec27cc87808826fc64419ac1c content_type: application/pdf creator: dernst date_created: 2023-03-27T06:51:09Z date_updated: 2023-03-27T06:51:09Z file_id: '12770' file_name: 2023_PLoSOne_Rothman.pdf file_size: 7290413 relation: main_file success: 1 file_date_updated: 2023-03-27T06:51:09Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: 3 March language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 2696E7FE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: V00739 name: Structural plasticity at mossy fiber-CA3 synapses publication: PLoS ONE publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy 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: 18 year: '2023' ... --- _id: '12756' abstract: - lang: eng text: ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling. acknowledgement: "We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z)." article_number: eade5224 article_processing_charge: No article_type: original author: - first_name: Fredrik full_name: Hurtig, Fredrik last_name: Hurtig - first_name: Thomas C.Q. full_name: Burgers, Thomas C.Q. last_name: Burgers - first_name: Alice full_name: Cezanne, Alice last_name: Cezanne - first_name: Xiuyun full_name: Jiang, Xiuyun last_name: Jiang - first_name: Frank N. full_name: Mol, Frank N. last_name: Mol - first_name: Jovan full_name: Traparić, Jovan last_name: Traparić - first_name: Andre Arashiro full_name: Pulschen, Andre Arashiro last_name: Pulschen - first_name: Tim full_name: Nierhaus, Tim last_name: Nierhaus - first_name: Gabriel full_name: Tarrason-Risa, Gabriel last_name: Tarrason-Risa - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Jan full_name: Löwe, Jan last_name: Löwe - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Rifka full_name: Vlijm, Rifka last_name: Vlijm - first_name: Buzz full_name: Baum, Buzz last_name: Baum citation: ama: Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224 apa: Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224 chicago: Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224. ieee: F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science Advances, vol. 9, no. 11. American Association for the Advancement of Science, 2023. ista: Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224. mla: Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.ade5224. short: F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023). date_created: 2023-03-26T22:01:06Z date_published: 2023-03-17T00:00:00Z date_updated: 2023-08-01T13:45:54Z day: '17' ddc: - '570' department: - _id: AnSa doi: 10.1126/sciadv.ade5224 ec_funded: 1 external_id: isi: - '000968083500010' file: - access_level: open_access checksum: 6d7dbe9ed86a116c8a002d62971202c5 content_type: application/pdf creator: dernst date_created: 2023-03-27T06:24:49Z date_updated: 2023-03-27T06:24:49Z file_id: '12768' file_name: 2023_ScienceAdvances_Hurtig.pdf file_size: 1826471 relation: main_file success: 1 file_date_updated: 2023-03-27T06:24:49Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '11' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' 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: The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division 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: 9 year: '2023' ... --- _id: '12758' abstract: - lang: eng text: AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding. acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021. article_number: e0282689 article_processing_charge: No article_type: original author: - first_name: Marina A. full_name: Pak, Marina A. last_name: Pak - first_name: Karina A. full_name: Markhieva, Karina A. last_name: Markhieva - first_name: Mariia S. full_name: Novikova, Mariia S. last_name: Novikova - first_name: Dmitry S. full_name: Petrov, Dmitry S. last_name: Petrov - first_name: Ilya S. full_name: Vorobyev, Ilya S. last_name: Vorobyev - first_name: Ekaterina full_name: Maksimova, Ekaterina id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87 last_name: Maksimova - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Dmitry N. full_name: Ivankov, Dmitry N. last_name: Ivankov citation: ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689 apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689 chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689. ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023. ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689. mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689. short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023). date_created: 2023-03-26T22:01:07Z date_published: 2023-03-16T00:00:00Z date_updated: 2023-08-01T13:47:14Z day: '16' ddc: - '570' department: - _id: FyKo - _id: MaRo doi: 10.1371/journal.pone.0282689 external_id: isi: - '000985134400106' file: - access_level: open_access checksum: 0281bdfccf8d76c4e08dd011c603f6b6 content_type: application/pdf creator: dernst date_created: 2023-03-27T07:09:08Z date_updated: 2023-03-27T07:09:08Z file_id: '12771' file_name: 2023_PLoSOne_Pak.pdf file_size: 856625 relation: main_file success: 1 file_date_updated: 2023-03-27T07:09:08Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: PLoS ONE publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Using AlphaFold to predict the impact of single mutations on protein stability and function 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: 18 year: '2023' ... --- _id: '12757' abstract: - lang: eng text: My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues. article_processing_charge: No article_type: review author: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285' apa: 'Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285' chicago: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.' ieee: 'L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.' ista: 'Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.' mla: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.' short: L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333. date_created: 2023-03-26T22:01:06Z date_published: 2023-03-15T00:00:00Z date_updated: 2023-08-01T13:45:12Z day: '15' ddc: - '570' department: - _id: LeSa doi: 10.1042/BCJ20210285 external_id: isi: - '000957065700001' pmid: - '36920092' has_accepted_license: '1' intvolume: ' 480' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1042/BCJ20210285 month: '03' oa: 1 oa_version: Published Version page: 319-333 pmid: 1 publication: The Biochemical Journal publication_identifier: eissn: - 1470-8728 issn: - 0264-6021 publication_status: published publisher: Portland Press quality_controlled: '1' scopus_import: '1' status: public title: 'From the ''black box'' to ''domino effect'' mechanism: What have we learned from the structures of respiratory complex I' 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: 480 year: '2023' ... --- _id: '12787' abstract: - lang: eng text: "Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results." acknowledgement: J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt) article_number: '20220685' article_processing_charge: No article_type: original author: - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Kamran full_name: Kaveh, Kamran last_name: Kaveh - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685' apa: 'Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rspa.2022.0685' chicago: 'Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.' ieee: 'J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271. The Royal Society, 2023.' ista: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.' mla: 'Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:10.1098/rspa.2022.0685.' short: 'J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).' date_created: 2023-04-02T22:01:09Z date_published: 2023-03-29T00:00:00Z date_updated: 2023-08-01T13:58:34Z day: '29' ddc: - '000' department: - _id: KrCh doi: 10.1098/rspa.2022.0685 ec_funded: 1 external_id: isi: - '000957125500002' file: - access_level: open_access checksum: 13953d349fbefcb5d21ccc6b303297eb content_type: application/pdf creator: dernst date_created: 2023-04-03T06:25:29Z date_updated: 2023-04-03T06:25:29Z file_id: '12796' file_name: 2023_ProceedingsRoyalSocietyA_Svoboda.pdf file_size: 827784 relation: main_file success: 1 file_date_updated: 2023-04-03T06:25:29Z has_accepted_license: '1' intvolume: ' 479' isi: 1 issue: '2271' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences' publication_identifier: eissn: - 1471-2946 issn: - 1364-5021 publication_status: published publisher: The Royal Society quality_controlled: '1' related_material: link: - relation: research_data url: https://doi.org/10.6084/m9.figshare.21261771.v1 scopus_import: '1' status: public title: Coexistence times in the Moran process with environmental heterogeneity 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: 479 year: '2023' ... --- _id: '12788' abstract: - lang: eng text: We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants. acknowledgement: M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). article_number: '103202' article_processing_charge: No article_type: original author: - first_name: Volker full_name: Karle, Volker id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425 last_name: Karle - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202 apa: Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of periodically kicked molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.130.103202 chicago: Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202. ieee: V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023. ista: Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202. mla: Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:10.1103/PhysRevLett.130.103202. short: V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023). date_created: 2023-04-02T22:01:10Z date_published: 2023-03-10T00:00:00Z date_updated: 2023-08-01T14:02:06Z day: '10' department: - _id: MiLe doi: 10.1103/PhysRevLett.130.103202 ec_funded: 1 external_id: arxiv: - '2206.07067' isi: - '000957635500003' intvolume: ' 130' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2206.07067 month: '03' oa: 1 oa_version: Preprint 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' related_material: link: - description: News on the ISTA website relation: press_release url: https://ista.ac.at/en/news/topology-of-rotating-molecules/ scopus_import: '1' status: public title: Topological charges of periodically kicked molecules type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 130 year: '2023' ... --- _id: '12790' abstract: - lang: eng text: Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity. acknowledgement: E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz. article_number: '104502' article_processing_charge: No article_type: original author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Tobias full_name: Holder, Tobias last_name: Holder - first_name: Erez full_name: Berg, Erez last_name: Berg - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502 apa: Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502 chicago: Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502. ieee: A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” Physical Review B, vol. 107, no. 10. American Physical Society, 2023. ista: Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502. mla: Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502. short: A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023). date_created: 2023-04-02T22:01:10Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-01T13:59:29Z day: '01' department: - _id: MaSe - _id: MiLe doi: 10.1103/PhysRevB.107.104502 external_id: arxiv: - '2211.02492' isi: - '000945526400003' intvolume: ' 107' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2211.02492 month: '03' 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' related_material: link: - description: News on the ISTA website relation: press_release url: https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/ scopus_import: '1' status: public title: Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '12791' abstract: - lang: eng text: We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra. acknowledgement: This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340)) article_number: '16' article_processing_charge: No article_type: original author: - first_name: Patricio full_name: Clark Di Leoni, Patricio last_name: Clark Di Leoni - first_name: Lokahith N full_name: Agasthya, Lokahith N id: cd100965-0804-11ed-9c55-f4878ff4e877 last_name: Agasthya - first_name: Michele full_name: Buzzicotti, Michele last_name: Buzzicotti - first_name: Luca full_name: Biferale, Luca last_name: Biferale citation: ama: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9 apa: Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00276-9 chicago: Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9. ieee: P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer Nature, 2023. ista: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16. mla: Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9. short: P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023). date_created: 2023-04-02T22:01:11Z date_published: 2023-03-20T00:00:00Z date_updated: 2023-08-01T14:03:47Z day: '20' department: - _id: CaMu doi: 10.1140/epje/s10189-023-00276-9 external_id: arxiv: - '2301.07769' isi: - '000956387200001' intvolume: ' 46' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2301.07769' month: '03' oa: 1 oa_version: Preprint publication: The European Physical Journal E publication_identifier: eissn: - 1292-895X issn: - 1292-8941 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 46 year: '2023' ... --- _id: '12830' abstract: - lang: eng text: Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization. acknowledged_ssus: - _id: PreCl - _id: Bio acknowledgement: We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Karla full_name: Huljev, Karla id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87 last_name: Huljev - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Diana C full_name: Nunes Pinheiro, Diana C id: 2E839F16-F248-11E8-B48F-1D18A9856A87 last_name: Nunes Pinheiro orcid: 0000-0003-4333-7503 - first_name: Friedrich full_name: Preusser, Friedrich last_name: Preusser - first_name: Irene full_name: Steccari, Irene id: 2705C766-9FE2-11EA-B224-C6773DDC885E last_name: Steccari - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 - 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 citation: ama: Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016 apa: Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016 chicago: Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016. ieee: K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023. ista: Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7. mla: Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016. short: K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7. date_created: 2023-04-16T22:01:07Z date_published: 2023-04-10T00:00:00Z date_updated: 2023-08-01T14:10:38Z day: '10' ddc: - '570' department: - _id: CaHe - _id: Bio doi: 10.1016/j.devcel.2023.02.016 ec_funded: 1 external_id: isi: - '000982111800001' file: - access_level: open_access checksum: c80ca2ebc241232aacdb5aa4b4c80957 content_type: application/pdf creator: dernst date_created: 2023-04-17T07:41:25Z date_updated: 2023-04-17T07:41:25Z file_id: '12842' file_name: 2023_DevelopmentalCell_Huljev.pdf file_size: 7925886 relation: main_file success: 1 file_date_updated: 2023-04-17T07:41:25Z has_accepted_license: '1' intvolume: ' 58' isi: 1 issue: '7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 582-596.e7 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 - _id: 26520D1E-B435-11E9-9278-68D0E5697425 grant_number: ALTF 850-2017 name: Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation - _id: 266BC5CE-B435-11E9-9278-68D0E5697425 grant_number: LT000429 name: Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation 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: A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish 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: 58 year: '2023' ... --- _id: '12831' abstract: - lang: eng text: The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions. acknowledgement: We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503). article_number: '134301' article_processing_charge: No article_type: original author: - first_name: Zhongda full_name: Zeng, Zhongda last_name: Zeng - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Tao full_name: Shi, Tao last_name: Shi - first_name: Richard full_name: Schmidt, Richard last_name: Schmidt citation: ama: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13). doi:10.1063/5.0135893 apa: Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893 chicago: Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893. ieee: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” The Journal of Chemical Physics, vol. 158, no. 13. American Institute of Physics, 2023. ista: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301. mla: Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:10.1063/5.0135893. short: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023). date_created: 2023-04-16T22:01:07Z date_published: 2023-04-07T00:00:00Z date_updated: 2023-08-01T14:08:47Z day: '07' ddc: - '530' department: - _id: MiLe doi: 10.1063/5.0135893 ec_funded: 1 external_id: arxiv: - '2211.08070' isi: - '000970038800001' file: - access_level: open_access checksum: 8d801babea4df48e08895c76571bb19e content_type: application/pdf creator: dernst date_created: 2023-04-17T07:28:38Z date_updated: 2023-04-17T07:28:38Z file_id: '12841' file_name: 2023_JourChemicalPhysics_Zeng.pdf file_size: 7388057 relation: main_file success: 1 file_date_updated: 2023-04-17T07:28:38Z has_accepted_license: '1' intvolume: ' 158' isi: 1 issue: '13' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 publication_status: published publisher: American Institute of Physics quality_controlled: '1' scopus_import: '1' status: public title: Variational theory of angulons and their rotational spectroscopy 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: 158 year: '2023' ... --- _id: '12839' abstract: - lang: eng text: Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport. acknowledgement: "We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54]." article_number: '011033' article_processing_charge: No article_type: original author: - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina - first_name: Jean Yves full_name: Desaules, Jean Yves last_name: Desaules - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić citation: ama: Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033 apa: Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033 chicago: Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033. ieee: M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” Physical Review X, vol. 13, no. 1. American Physical Society, 2023. ista: Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033. mla: Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:10.1103/PhysRevX.13.011033. short: M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023). date_created: 2023-04-16T22:01:09Z date_published: 2023-03-07T00:00:00Z date_updated: 2023-08-01T14:11:28Z day: '07' ddc: - '530' department: - _id: MaSe doi: 10.1103/PhysRevX.13.011033 ec_funded: 1 external_id: isi: - '000957625700001' file: - access_level: open_access checksum: ee060cea609af79bba7af74b1ce28078 content_type: application/pdf creator: dernst date_created: 2023-04-17T08:36:53Z date_updated: 2023-04-17T08:36:53Z file_id: '12845' file_name: 2023_PhysReviewX_Ljubotina.pdf file_size: 1958523 relation: main_file success: 1 file_date_updated: 2023-04-17T08:36:53Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '1' language: - iso: eng month: '03' 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 X publication_identifier: eissn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Superdiffusive energy transport in kinetically constrained models 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: 13 year: '2023' ... --- _id: '12832' abstract: - lang: eng text: The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2. acknowledged_ssus: - _id: EM-Fac acknowledgement: 'The authors thank the support from the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación. The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581 and 2021 SGR 00457. ICN2 acknowledges the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. Part of the present work has been performed in the frameworks of Universitat de Barcelona Nanoscience PhD program. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF). S. Lee. and M. Ibáñez acknowledge funding by IST Austria and the Werner Siemens Foundation. J. Llorca is a Serra Húnter Fellow and is grateful to ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2017 SGR 128. L. L.Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). Z. F. Liang acknowledges funding from MINECO SO-FPT PhD grant (SEV-2013-0295-17-1). J. W. Chen and Y. Xu thank the support from The Key Research and Development Program of Hebei Province (No. 20314305D) and the cooperative scientific research project of the “Chunhui Program” of the Ministry of Education (2018-7). This work was supported by the Natural Science Foundation of Sichuan province (NSFSC) and funded by the Science and Technology Department of Sichuan Province (2022NSFSC1229).' 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: Xiang full_name: Wang, Xiang last_name: Wang - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Ting full_name: Zhang, Ting last_name: Zhang - first_name: Lingxiao full_name: Li, Lingxiao last_name: Li - first_name: Zhifu full_name: Liang, Zhifu last_name: Liang - first_name: Jingwei full_name: Chen, Jingwei last_name: Chen - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Ahmad full_name: Ostovari Moghaddam, Ahmad last_name: Ostovari Moghaddam - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Ying full_name: Xu, Ying last_name: Xu - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: He R, Yang L, Zhang Y, et al. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 2023;58(4):287-298. doi:10.1016/j.ensm.2023.03.022 apa: He, R., Yang, L., Zhang, Y., Wang, X., Lee, S., Zhang, T., … Cabot, A. (2023). A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. Elsevier. https://doi.org/10.1016/j.ensm.2023.03.022 chicago: He, Ren, Linlin Yang, Yu Zhang, Xiang Wang, Seungho Lee, Ting Zhang, Lingxiao Li, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials. Elsevier, 2023. https://doi.org/10.1016/j.ensm.2023.03.022. ieee: R. He et al., “A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance,” Energy Storage Materials, vol. 58, no. 4. Elsevier, pp. 287–298, 2023. ista: He R, Yang L, Zhang Y, Wang X, Lee S, Zhang T, Li L, Liang Z, Chen J, Li J, Ostovari Moghaddam A, Llorca J, Ibáñez M, Arbiol J, Xu Y, Cabot A. 2023. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 58(4), 287–298. mla: He, Ren, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials, vol. 58, no. 4, Elsevier, 2023, pp. 287–98, doi:10.1016/j.ensm.2023.03.022. short: R. He, L. Yang, Y. Zhang, X. Wang, S. Lee, T. Zhang, L. Li, Z. Liang, J. Chen, J. Li, A. Ostovari Moghaddam, J. Llorca, M. Ibáñez, J. Arbiol, Y. Xu, A. Cabot, Energy Storage Materials 58 (2023) 287–298. date_created: 2023-04-16T22:01:07Z date_published: 2023-04-01T00:00:00Z date_updated: 2023-08-01T14:08:02Z day: '01' department: - _id: MaIb doi: 10.1016/j.ensm.2023.03.022 external_id: isi: - '000967601700001' intvolume: ' 58' isi: 1 issue: '4' language: - iso: eng month: '04' oa_version: None page: 287-298 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: Energy Storage Materials publication_identifier: eissn: - 2405-8297 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 58 year: '2023' ... --- _id: '12822' abstract: - lang: eng text: Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter. acknowledgement: 'Army Research Office. Grant Number: W911NF-20-1-0112' article_number: '2200129' article_processing_charge: No article_type: original author: - first_name: Quentin full_name: Martinet, Quentin id: b37485a8-d343-11eb-a0e9-df8c484ef8ab last_name: Martinet - first_name: Antoine full_name: Aubret, Antoine last_name: Aubret - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 2023;5(1). doi:10.1002/aisy.202200129 apa: Martinet, Q., Aubret, A., & Palacci, J. A. (2023). Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. Wiley. https://doi.org/10.1002/aisy.202200129 chicago: Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems. Wiley, 2023. https://doi.org/10.1002/aisy.202200129. ieee: Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking, and self‐positioning of active cogwheels,” Advanced Intelligent Systems, vol. 5, no. 1. Wiley, 2023. ista: Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129. mla: Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems, vol. 5, no. 1, 2200129, Wiley, 2023, doi:10.1002/aisy.202200129. short: Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023). date_created: 2023-04-12T08:30:03Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-08-01T14:06:50Z day: '01' ddc: - '530' department: - _id: JePa doi: 10.1002/aisy.202200129 external_id: arxiv: - '2201.03333' isi: - '000852291200001' file: - access_level: open_access checksum: d48fc41d39892e7fa0d44cb352dd46aa content_type: application/pdf creator: dernst date_created: 2023-04-17T06:44:17Z date_updated: 2023-04-17T06:44:17Z file_id: '12840' file_name: 2023_AdvancedIntelligentSystems_Martinet.pdf file_size: 2414125 relation: main_file success: 1 file_date_updated: 2023-04-17T06:44:17Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Advanced Intelligent Systems publication_identifier: issn: - 2640-4567 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Rotation control, interlocking, and self‐positioning of active cogwheels 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: 5 year: '2023' ... --- _id: '12818' abstract: - lang: eng text: The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues. acknowledgement: We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL. article_number: '1643' article_processing_charge: No article_type: original author: - first_name: Tom full_name: Brandstätter, Tom last_name: Brandstätter - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Yu Long full_name: Han, Yu Long last_name: Han - first_name: Ricard full_name: Alert, Ricard last_name: Alert - first_name: Ming full_name: Guo, Ming last_name: Guo - first_name: Chase P. full_name: Broedersz, Chase P. last_name: Broedersz citation: ama: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 2023;14. doi:10.1038/s41467-023-37054-2 apa: Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2 chicago: Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2. ieee: T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643. mla: Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature, 2023, doi:10.1038/s41467-023-37054-2. short: T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023). date_created: 2023-04-09T22:01:00Z date_published: 2023-03-24T00:00:00Z date_updated: 2023-08-01T14:05:30Z day: '24' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41467-023-37054-2 external_id: isi: - '000959887700008' pmid: - '36964141' file: - access_level: open_access checksum: 54f06f9eee11d43bab253f3492c983ba content_type: application/pdf creator: dernst date_created: 2023-04-11T06:27:00Z date_updated: 2023-04-11T06:27:00Z file_id: '12821' file_name: 2023_NatureComm_Brandstaetter.pdf file_size: 4146777 relation: main_file success: 1 file_date_updated: 2023-04-11T06:27:00Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '03' 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' scopus_import: '1' status: public title: Curvature induces active velocity waves in rotating spherical tissues 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: 14 year: '2023' ... --- _id: '12819' abstract: - lang: eng text: 'Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds.' acknowledgement: We thank N.N. Abramov for assistance with the experimental setup. The sample was fabricated using equipment of MIPT Shared Facilities Center. This research was supported by Russian Science Foundation, grant no. 21-72-30026. article_number: L031701 article_processing_charge: No article_type: letter_note author: - first_name: Alesya full_name: Sokolova, Alesya id: 2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a last_name: Sokolova orcid: 0000-0002-8308-4144 - first_name: D. A. full_name: Kalacheva, D. A. last_name: Kalacheva - first_name: G. P. full_name: Fedorov, G. P. last_name: Fedorov - first_name: O. V. full_name: Astafiev, O. V. last_name: Astafiev citation: ama: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701 apa: Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023). Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L031701 chicago: Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L031701. ieee: A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical Society, 2023. ista: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 107(3), L031701. mla: Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A, vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701. short: A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023). date_created: 2023-04-09T22:01:00Z date_published: 2023-03-22T00:00:00Z date_updated: 2023-08-01T14:06:05Z day: '22' department: - _id: JoFi doi: 10.1103/PhysRevA.107.L031701 external_id: arxiv: - '2209.05165' isi: - '000957799000006' intvolume: ' 107' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2209.05165 month: '03' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '12861' abstract: - lang: eng text: The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight," have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations. acknowledgement: 'This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.' article_number: '2086' article_processing_charge: No article_type: original author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Farbod full_name: Ekbatani, Farbod last_name: Ekbatani - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 2023;14. doi:10.1038/s41467-023-37817-x apa: Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x chicago: Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x. ieee: L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086. mla: Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer Nature, 2023, doi:10.1038/s41467-023-37817-x. short: L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023). date_created: 2023-04-23T22:01:03Z date_published: 2023-04-12T00:00:00Z date_updated: 2023-08-01T14:15:57Z day: '12' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41467-023-37817-x ec_funded: 1 external_id: isi: - '001003644100020' pmid: - '37045828' file: - access_level: open_access checksum: a4b3b7b36fbef068cabf4fb99501fef6 content_type: application/pdf creator: dernst date_created: 2023-04-25T09:13:53Z date_updated: 2023-04-25T09:13:53Z file_id: '12868' file_name: 2023_NatureComm_Schmid.pdf file_size: 1786475 relation: main_file success: 1 file_date_updated: 2023-04-25T09:13:53Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '04' 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: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quantitative assessment can stabilize indirect reciprocity under imperfect information 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: 14 year: '2023' ... --- _id: '12862' abstract: - lang: eng text: Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings. acknowledgement: "We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. " article_number: e1010983 article_processing_charge: No article_type: original author: - first_name: Shervin full_name: Safavi, Shervin last_name: Safavi - first_name: Theofanis I. full_name: Panagiotaropoulos, Theofanis I. last_name: Panagiotaropoulos - first_name: Vishal full_name: Kapoor, Vishal last_name: Kapoor - first_name: Juan F full_name: Ramirez Villegas, Juan F id: 44B06F76-F248-11E8-B48F-1D18A9856A87 last_name: Ramirez Villegas - first_name: Nikos K. full_name: Logothetis, Nikos K. last_name: Logothetis - first_name: Michel full_name: Besserve, Michel last_name: Besserve citation: ama: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983 apa: Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983 chicago: Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983. ieee: S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol. 19, no. 4. Public Library of Science, 2023. ista: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983. mla: Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983. short: S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023). date_created: 2023-04-23T22:01:03Z date_published: 2023-04-01T00:00:00Z date_updated: 2023-08-01T14:15:16Z day: '01' ddc: - '570' department: - _id: JoCs doi: 10.1371/journal.pcbi.1010983 external_id: isi: - '000962668700002' file: - access_level: open_access checksum: edeb9d09f3e41ba7c0251308b9e372e7 content_type: application/pdf creator: dernst date_created: 2023-04-25T08:59:18Z date_updated: 2023-04-25T08:59:18Z file_id: '12867' file_name: 2023_PLoSCompBio_Safavi.pdf file_size: 4737671 relation: main_file success: 1 file_date_updated: 2023-04-25T08:59:18Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://github.com/shervinsafavi/gpla.git scopus_import: '1' status: public title: Uncovering the organization of neural circuits with Generalized Phase Locking 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2023' ... --- _id: '12879' abstract: - lang: eng text: Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations. acknowledgement: KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre. article_processing_charge: No article_type: original author: - first_name: Ke full_name: Chen, Ke id: c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d last_name: Chen - first_name: Christian full_name: Kunkel, Christian last_name: Kunkel - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Karsten full_name: Reuter, Karsten last_name: Reuter - first_name: Johannes T. full_name: Margraf, Johannes T. last_name: Margraf citation: ama: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j apa: Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d3sc00841j chicago: Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j. ieee: K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” Chemical Science. Royal Society of Chemistry, 2023. ista: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science. mla: Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j. short: K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023). date_created: 2023-04-30T22:01:06Z date_published: 2023-04-10T00:00:00Z date_updated: 2023-08-01T14:18:10Z day: '10' ddc: - '000' - '540' department: - _id: BiCh doi: 10.1039/d3sc00841j external_id: isi: - '000971508100001' file: - access_level: open_access checksum: 5eeec69a51e192dcd94b955d84423836 content_type: application/pdf creator: dernst date_created: 2023-05-02T07:17:05Z date_updated: 2023-05-02T07:17:05Z file_id: '12883' file_name: 2023_ChemialScience_Chen.pdf file_size: 1515446 relation: main_file success: 1 file_date_updated: 2023-05-02T07:17:05Z has_accepted_license: '1' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '04' oa: 1 oa_version: Published Version publication: Chemical Science publication_identifier: eissn: - 2041-6539 issn: - 2041-6520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Physics-inspired machine learning of localized intensive properties tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2023' ... --- _id: '12878' abstract: - lang: eng text: Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components. acknowledgement: The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076). article_processing_charge: No article_type: original author: - first_name: Lihui full_name: Jiang, Lihui last_name: Jiang - first_name: Baolin full_name: Yao, Baolin last_name: Yao - first_name: Xiaoyan full_name: Zhang, Xiaoyan last_name: Zhang - first_name: Lixia full_name: Wu, Lixia last_name: Wu - first_name: Qijing full_name: Fu, Qijing last_name: Fu - first_name: Yiting full_name: Zhao, Yiting last_name: Zhao - first_name: Yuxin full_name: Cao, Yuxin last_name: Cao - first_name: Ruomeng full_name: Zhu, Ruomeng last_name: Zhu - first_name: Xinqi full_name: Lu, Xinqi last_name: Lu - first_name: Wuying full_name: Huang, Wuying last_name: Huang - first_name: Jianping full_name: Zhao, Jianping last_name: Zhao - first_name: Kuixiu full_name: Li, Kuixiu last_name: Li - first_name: Shuanglu full_name: Zhao, Shuanglu last_name: Zhao - first_name: Li full_name: Han, Li last_name: Han - first_name: Xuan full_name: Zhou, Xuan last_name: Zhou - first_name: Chongyu full_name: Luo, Chongyu last_name: Luo - first_name: Haiyan full_name: Zhu, Haiyan last_name: Zhu - first_name: Jing full_name: Yang, Jing last_name: Yang - first_name: Huichuan full_name: Huang, Huichuan last_name: Huang - first_name: Zhengge full_name: Zhu, Zhengge last_name: Zhu - first_name: Xiahong full_name: He, Xiahong last_name: He - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Zhongkai full_name: Zhang, Zhongkai last_name: Zhang - first_name: Changning full_name: Liu, Changning last_name: Liu - first_name: Yunlong full_name: Du, Yunlong last_name: Du citation: ama: Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 2023;115(1):155-174. doi:10.1111/tpj.16218 apa: Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218 chicago: Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal. Wiley, 2023. https://doi.org/10.1111/tpj.16218. ieee: L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal, vol. 115, no. 1. Wiley, pp. 155–174, 2023. ista: Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174. mla: Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218. short: L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174. date_created: 2023-04-30T22:01:06Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-08-01T14:16:33Z day: '01' department: - _id: JiFr doi: 10.1111/tpj.16218 external_id: isi: - '000971861400001' pmid: - '37025008 ' intvolume: ' 115' isi: 1 issue: '1' language: - iso: eng month: '07' oa_version: None page: 155-174 pmid: 1 publication: Plant Journal publication_identifier: eissn: - 1365-313X issn: - 0960-7412 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 115 year: '2023' ... --- _id: '12876' abstract: - lang: eng text: "Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data." acknowledgement: This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.]. article_number: btad158 article_processing_charge: No article_type: original author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Luboš full_name: Brim, Luboš last_name: Brim - first_name: Ondřej full_name: Huvar, Ondřej last_name: Huvar - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva - first_name: David full_name: Šafránek, David last_name: Šafránek citation: ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 2023;39(4). doi:10.1093/bioinformatics/btad158' apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158' chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.' ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” Bioinformatics, vol. 39, no. 4. Oxford Academic, 2023.' ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.' mla: 'Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:10.1093/bioinformatics/btad158.' short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023). date_created: 2023-04-30T22:01:05Z date_published: 2023-04-03T00:00:00Z date_updated: 2023-08-01T14:27:28Z day: '03' ddc: - '000' department: - _id: ToHe doi: 10.1093/bioinformatics/btad158 ec_funded: 1 external_id: isi: - '000976610800001' pmid: - '37004199' file: - access_level: open_access checksum: 2cb90ddf781baefddf47eac4b54e2a03 content_type: application/pdf creator: dernst date_created: 2023-05-02T07:39:04Z date_updated: 2023-05-02T07:39:04Z file_id: '12886' file_name: 2023_Bioinformatics_Benes.pdf file_size: 478740 relation: main_file success: 1 file_date_updated: 2023-05-02T07:39:04Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '4' language: - iso: eng month: '04' 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: Bioinformatics publication_identifier: eissn: - 1367-4811 publication_status: published publisher: Oxford Academic quality_controlled: '1' related_material: link: - relation: software url: https://doi.org/10.5281/zenodo.7688740 scopus_import: '1' status: public title: 'Boolean network sketches: A unifying framework for logical model inference' 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: 39 year: '2023' ... --- _id: '12880' abstract: - lang: eng text: Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1. acknowledgement: 'We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.' article_number: '2202548' article_processing_charge: No article_type: original author: - first_name: Jeanae M. full_name: Kaneshiro, Jeanae M. last_name: Kaneshiro - first_name: Juliana S. full_name: Capitanio, Juliana S. last_name: Capitanio - first_name: Martin W full_name: Hetzer, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: Hetzer orcid: 0000-0002-2111-992X citation: ama: Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548 apa: Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. Taylor & Francis. https://doi.org/10.1080/19491034.2023.2202548 chicago: Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus. Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548. ieee: J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” Nucleus, vol. 14, no. 1. Taylor & Francis, 2023. ista: Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548. mla: Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis, 2023, doi:10.1080/19491034.2023.2202548. short: J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023). date_created: 2023-04-30T22:01:06Z date_published: 2023-04-18T00:00:00Z date_updated: 2023-08-01T14:18:46Z day: '18' ddc: - '570' department: - _id: MaHe doi: 10.1080/19491034.2023.2202548 external_id: isi: - '000971629400001' pmid: - '37071033' file: - access_level: open_access checksum: 8e707eda84f64dbad7f03545ae0a83ef content_type: application/pdf creator: dernst date_created: 2023-05-02T07:24:55Z date_updated: 2023-05-02T07:24:55Z file_id: '12884' file_name: 2023_Nucleus_Kaneshiro.pdf file_size: 3811113 relation: main_file success: 1 file_date_updated: 2023-05-02T07:24:55Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Nucleus publication_identifier: eissn: - 1949-1042 issn: - 1949-1034 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: Lamin B1 overexpression alters chromatin organization and gene expression tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2023' ... --- _id: '12914' abstract: - lang: eng text: We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier. acknowledgement: We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done. article_number: '042216' article_processing_charge: No article_type: original author: - first_name: Fumika full_name: Suzuki, Fumika id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E last_name: Suzuki orcid: 0000-0003-4982-5970 - first_name: William G. full_name: Unruh, William G. last_name: Unruh citation: ama: Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216 apa: Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.042216 chicago: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.042216. ieee: F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” Physical Review A, vol. 107, no. 4. American Physical Society, 2023. ista: Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216. mla: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216. short: F. Suzuki, W.G. Unruh, Physical Review A 107 (2023). date_created: 2023-05-07T22:01:03Z date_published: 2023-04-20T00:00:00Z date_updated: 2023-08-01T14:33:21Z day: '20' department: - _id: MiLe doi: 10.1103/PhysRevA.107.042216 ec_funded: 1 external_id: arxiv: - '2207.13130' isi: - '000975799300006' intvolume: ' 107' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2207.13130 month: '04' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Numerical quantum clock simulations for measuring tunneling times type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '12913' abstract: - lang: eng text: The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices. acknowledgement: We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01. article_number: '2396' article_processing_charge: No article_type: original author: - first_name: J. full_name: Díez-Mérida, J. last_name: Díez-Mérida - first_name: A. full_name: Díez-Carlón, A. last_name: Díez-Carlón - first_name: S. Y. full_name: Yang, S. Y. last_name: Yang - first_name: Y. M. full_name: Xie, Y. M. last_name: Xie - first_name: X. J. full_name: Gao, X. J. last_name: Gao - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: X. full_name: Lu, X. last_name: Lu - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: K. T. full_name: Law, K. T. last_name: Law - first_name: Dmitri K. full_name: Efetov, Dmitri K. last_name: Efetov citation: ama: Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 2023;14. doi:10.1038/s41467-023-38005-7 apa: Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38005-7 chicago: Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7. ieee: J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396. mla: Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications, vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7. short: J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023). date_created: 2023-05-07T22:01:03Z date_published: 2023-04-26T00:00:00Z date_updated: 2023-08-01T14:34:00Z day: '26' ddc: - '530' department: - _id: AnHi doi: 10.1038/s41467-023-38005-7 external_id: isi: - '000979744000004' pmid: - '37100775' file: - access_level: open_access checksum: a778105665c10beb2354c92d2b295115 content_type: application/pdf creator: dernst date_created: 2023-05-08T07:26:40Z date_updated: 2023-05-08T07:26:40Z file_id: '12917' file_name: 2023_NatureComm_DiezMerida.pdf file_size: 1405588 relation: main_file success: 1 file_date_updated: 2023-05-08T07:26:40Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '04' 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' scopus_import: '1' status: public title: Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene 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: 14 year: '2023' ... --- _id: '10550' abstract: - lang: eng text: The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter. acknowledgement: "We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz." article_number: '66' article_processing_charge: No article_type: original author: - first_name: Klemens full_name: Fellner, Klemens last_name: Fellner - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Michael full_name: Kniely, Michael id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87 last_name: Kniely orcid: 0000-0001-5645-4333 - first_name: Bao Quoc full_name: Tang, Bao Quoc last_name: Tang citation: ama: Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w apa: Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w chicago: Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature, 2023. https://doi.org/10.1007/s00332-023-09926-w. ieee: K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” Journal of Nonlinear Science, vol. 33. Springer Nature, 2023. ista: Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66. mla: Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w. short: K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023). date_created: 2021-12-16T12:15:35Z date_published: 2023-06-07T00:00:00Z date_updated: 2023-08-01T14:40:33Z day: '07' ddc: - '510' department: - _id: JuFi doi: 10.1007/s00332-023-09926-w external_id: arxiv: - '2109.12019' isi: - '001002343400002' file: - access_level: open_access checksum: f3f0f0886098e31c81116cff8183750b content_type: application/pdf creator: dernst date_created: 2023-06-19T07:33:53Z date_updated: 2023-06-19T07:33:53Z file_id: '13149' file_name: 2023_JourNonlinearScience_Fellner.pdf file_size: 742315 relation: main_file success: 1 file_date_updated: 2023-06-19T07:33:53Z has_accepted_license: '1' intvolume: ' 33' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Journal of Nonlinear Science publication_identifier: eissn: - 1432-1467 issn: - 0938-8974 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion 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: 33 year: '2023' ... --- _id: '13043' abstract: - lang: eng text: "We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction\r\nof a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting along triple junctions." acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813. article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 - first_name: Tim full_name: Laux, Tim last_name: Laux citation: ama: Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 2023;25(1):37-107. doi:10.4171/IFB/484 apa: Hensel, S., & Laux, T. (2023). Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. EMS Press. https://doi.org/10.4171/IFB/484 chicago: Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries. EMS Press, 2023. https://doi.org/10.4171/IFB/484. ieee: S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” Interfaces and Free Boundaries, vol. 25, no. 1. EMS Press, pp. 37–107, 2023. ista: Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107. mla: Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries, vol. 25, no. 1, EMS Press, 2023, pp. 37–107, doi:10.4171/IFB/484. short: S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107. date_created: 2023-05-21T22:01:06Z date_published: 2023-04-20T00:00:00Z date_updated: 2023-08-01T14:43:29Z day: '20' ddc: - '510' department: - _id: JuFi doi: 10.4171/IFB/484 ec_funded: 1 external_id: arxiv: - '2108.01733' isi: - '000975817300002' file: - access_level: open_access checksum: 622422484810441e48f613e968c7e7a4 content_type: application/pdf creator: dernst date_created: 2023-05-22T07:24:13Z date_updated: 2023-05-22T07:24:13Z file_id: '13045' file_name: 2023_Interfaces_Hensel.pdf file_size: 867876 relation: main_file success: 1 file_date_updated: 2023-05-22T07:24:13Z has_accepted_license: '1' intvolume: ' 25' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 37-107 project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication: Interfaces and Free Boundaries publication_identifier: eissn: - 1463-9971 issn: - 1463-9963 publication_status: published publisher: EMS Press quality_controlled: '1' related_material: record: - id: '10013' relation: earlier_version status: public scopus_import: '1' status: public title: Weak-strong uniqueness for the mean curvature flow of double bubbles 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: 25 year: '2023' ... --- _id: '12912' abstract: - lang: eng text: The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes. acknowledgement: We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. article_number: '161101 ' article_processing_charge: No article_type: original author: - first_name: Rochus full_name: Schmid, Rochus last_name: Schmid - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711 apa: Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711 chicago: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0146711. ieee: R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing, 2023. ista: Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101. mla: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:10.1063/5.0146711. short: R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023). date_created: 2023-05-07T22:01:03Z date_published: 2023-04-24T00:00:00Z date_updated: 2023-08-01T14:34:49Z day: '24' ddc: - '540' department: - _id: BiCh doi: 10.1063/5.0146711 external_id: arxiv: - '2302.01297' isi: - '001010676000010' pmid: - '37093149' file: - access_level: open_access checksum: 4ab8c965f2fa4e17920bfa846847f137 content_type: application/pdf creator: dernst date_created: 2023-05-08T07:44:49Z date_updated: 2023-05-08T07:44:49Z file_id: '12918' file_name: 2023_JourChemicalPhysics_Schmid.pdf file_size: 6499468 relation: main_file success: 1 file_date_updated: 2023-05-08T07:44:49Z has_accepted_license: '1' intvolume: ' 158' isi: 1 issue: '16' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: link: - relation: software url: https://github.com/BingqingCheng/mu-adsorption - relation: software url: https://github.com/BingqingCheng/S0 scopus_import: '1' status: public title: Computing chemical potentials of adsorbed or confined fluids 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: 158 year: '2023' ... --- _id: '12972' abstract: - lang: eng text: Embroidery is a long-standing and high-quality approach to making logos and images on textiles. Nowadays, it can also be performed via automated machines that weave threads with high spatial accuracy. A characteristic feature of the appearance of the threads is a high degree of anisotropy. The anisotropic behavior is caused by depositing thin but long strings of thread. As a result, the stitched patterns convey both color and direction. Artists leverage this anisotropic behavior to enhance pure color images with textures, illusions of motion, or depth cues. However, designing colorful embroidery patterns with prescribed directionality is a challenging task, one usually requiring an expert designer. In this work, we propose an interactive algorithm that generates machine-fabricable embroidery patterns from multi-chromatic images equipped with user-specified directionality fields.We cast the problem of finding a stitching pattern into vector theory. To find a suitable stitching pattern, we extract sources and sinks from the divergence field of the vector field extracted from the input and use them to trace streamlines. We further optimize the streamlines to guarantee a smooth and connected stitching pattern. The generated patterns approximate the color distribution constrained by the directionality field. To allow for further artistic control, the trade-off between color match and directionality match can be interactively explored via an intuitive slider. We showcase our approach by fabricating several embroidery paths. acknowledgement: This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 715767 – MATERIALIZABLE), and FWF Lise Meitner (Grant M 3319). We thank the anonymous reviewers for their insightful feedback; Solal Pirelli, Shardul Chiplunkar, and Paola Mejia for proofreading; everyone in the visual computing group at ISTA for inspiring lunch and coffee breaks; Thibault Tricard for help producing the results of Phasor Noise. article_processing_charge: No article_type: original author: - first_name: Zhenyuan full_name: Liu, Zhenyuan id: 70f0d7cf-ae65-11ec-a14f-89dfc5505b19 last_name: Liu orcid: 0000-0001-9200-5690 - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Raphael full_name: Charrondiere, Raphael id: a3a24133-2cc7-11ec-be88-8ddaf6f464b1 last_name: Charrondiere - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 2023;42(2):397-409. doi:10.1111/cgf.14770 apa: 'Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023). Directionality-aware design of embroidery patterns. Computer Graphics Forum. Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770 ' chicago: Liu, Zhenyuan, Michael Piovarci, Christian Hafner, Raphael Charrondiere, and Bernd Bickel. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum. Wiley, 2023. https://doi.org/10.1111/cgf.14770 . ieee: Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, and B. Bickel, “Directionality-aware design of embroidery patterns,” Computer Graphics Forum, vol. 42, no. 2. Wiley, pp. 397–409, 2023. ista: Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. 2023. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 42(2), 397–409. mla: Liu, Zhenyuan, et al. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum, vol. 42, no. 2, Wiley, 2023, pp. 397–409, doi:10.1111/cgf.14770 . short: Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics Forum 42 (2023) 397–409. conference: end_date: 2023-05-12 location: Saarbrucken, Germany name: 'EG: Eurographics' start_date: 2023-05-08 date_created: 2023-05-16T08:47:25Z date_published: 2023-05-08T00:00:00Z date_updated: 2023-08-01T14:47:05Z day: '08' ddc: - '004' department: - _id: BeBi doi: '10.1111/cgf.14770 ' ec_funded: 1 external_id: isi: - '001000062600033' file: - access_level: open_access checksum: 4c188c2be4745467a8790bbf5d6491aa content_type: application/pdf creator: mpiovarc date_created: 2023-05-16T08:28:37Z date_updated: 2023-05-16T08:28:37Z file_id: '12974' file_name: Zhenyuan2023.pdf file_size: 24003702 relation: main_file success: 1 file_date_updated: 2023-05-16T08:28:37Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '2' keyword: - embroidery - design - directionality - density - image language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 397-409 project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: Computer Graphics Forum publication_identifier: issn: - 1467-8659 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Directionality-aware design of embroidery patterns 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 42 year: '2023' ... --- _id: '13033' abstract: - lang: eng text: Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases. acknowledgement: The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services. article_number: '7959' article_processing_charge: No article_type: original author: - first_name: Anna full_name: Zavadakova, Anna last_name: Zavadakova - first_name: Lucie full_name: Vistejnova, Lucie last_name: Vistejnova - first_name: Tereza full_name: Belinova, Tereza id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368 last_name: Belinova - first_name: Filip full_name: Tichanek, Filip last_name: Tichanek - first_name: Dagmar full_name: Bilikova, Dagmar last_name: Bilikova - first_name: Peter R. full_name: Mouton, Peter R. last_name: Mouton citation: ama: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z apa: Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., & Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z chicago: Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35162-z. ieee: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023. ista: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959. mla: Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:10.1038/s41598-023-35162-z. short: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023). date_created: 2023-05-19T11:12:25Z date_published: 2023-05-17T00:00:00Z date_updated: 2023-08-01T14:46:06Z day: '17' ddc: - '570' department: - _id: Bio doi: 10.1038/s41598-023-35162-z external_id: isi: - '000995271600104' file: - access_level: open_access checksum: 8c1b769693ff4288df8376e59ad1176d content_type: application/pdf creator: dernst date_created: 2023-05-22T07:57:37Z date_updated: 2023-05-22T07:57:37Z file_id: '13047' file_name: 2023_ScientificReports_Zavadakova.pdf file_size: 3055077 relation: main_file success: 1 file_date_updated: 2023-05-22T07:57:37Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '1' keyword: - Multidisciplinary language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: issn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41598-023-37265-z scopus_import: '1' status: public title: Novel stereological method for estimation of cell counts in 3D collagen scaffolds 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: 13 year: '2023' ... --- _id: '13095' abstract: - lang: eng text: Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts. acknowledgement: "We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. " article_processing_charge: No article_type: original author: - first_name: Laura full_name: Troussicot, Laura id: 3d9cac31-413c-11eb-9514-d1ec2a7fb7f3 last_name: Troussicot - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Mikael full_name: Molin, Mikael last_name: Molin - first_name: Björn M. full_name: Burmann, Björn M. last_name: Burmann - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200 apa: Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c01200 chicago: Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200. ieee: L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” Journal of the American Chemical Society, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023. ista: Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711. mla: Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:10.1021/jacs.3c01200. short: L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711. date_created: 2023-05-28T22:01:04Z date_published: 2023-05-04T00:00:00Z date_updated: 2023-08-01T14:48:09Z day: '04' ddc: - '540' department: - _id: PaSc doi: 10.1021/jacs.3c01200 external_id: isi: - '000985907400001' pmid: - '37140345' file: - access_level: open_access checksum: 0758a930ef21c62fc91b14e657479f83 content_type: application/pdf creator: dernst date_created: 2023-05-30T07:05:28Z date_updated: 2023-05-30T07:05:28Z file_id: '13098' file_name: 2023_JACS_Troussicot.pdf file_size: 6719299 relation: main_file success: 1 file_date_updated: 2023-05-30T07:05:28Z has_accepted_license: '1' intvolume: ' 145' isi: 1 issue: '19' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 10700–10711 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '12820' relation: research_data status: public scopus_import: '1' status: public title: Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR 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: 145 year: '2023' ... --- _id: '13042' abstract: - lang: eng text: Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for c>20, thus extending a result of Frieze and the author to smaller values of c. Thereafter, for c>20, we determine the limit of the probability that G(n, c/n)contains cycles of every length between the length of its shortest and its longest cycles as n→∞. acknowledgement: We would like to thank the reviewers for their helpful comments and remarks. article_number: P2.21 article_processing_charge: No article_type: original author: - first_name: Michael full_name: Anastos, Michael id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb last_name: Anastos citation: ama: Anastos M. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 2023;30(2). doi:10.37236/11471 apa: Anastos, M. (2023). A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11471 chicago: Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11471. ieee: M. Anastos, “A note on long cycles in sparse random graphs,” Electronic Journal of Combinatorics, vol. 30, no. 2. Electronic Journal of Combinatorics, 2023. ista: Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21. mla: Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics, 2023, doi:10.37236/11471. short: M. Anastos, Electronic Journal of Combinatorics 30 (2023). date_created: 2023-05-21T22:01:05Z date_published: 2023-05-05T00:00:00Z date_updated: 2023-08-01T14:44:52Z day: '05' ddc: - '510' department: - _id: MaKw doi: 10.37236/11471 external_id: arxiv: - '2105.13828' isi: - '000988285500001' file: - access_level: open_access checksum: 6269ed3b3eded6536d3d9d6baad2d5b9 content_type: application/pdf creator: dernst date_created: 2023-05-22T07:43:19Z date_updated: 2023-05-22T07:43:19Z file_id: '13046' file_name: 2023_JourCombinatorics_Anastos.pdf file_size: 448736 relation: main_file success: 1 file_date_updated: 2023-05-22T07:43:19Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: A note on long cycles in sparse random graphs 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: 30 year: '2023' ... --- _id: '12820' abstract: - lang: eng text: "Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript" article_processing_charge: No author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820 apa: Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820 chicago: Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820. ieee: P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. ista: Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820. mla: Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820. short: P. Schanda, (2023). contributor: - contributor_type: researcher first_name: Laura last_name: Troussicot - contributor_type: researcher first_name: Björn M. last_name: Burmann date_created: 2023-04-10T05:55:56Z date_published: 2023-04-18T00:00:00Z date_updated: 2023-08-01T14:48:08Z day: '18' ddc: - '570' department: - _id: PaSc doi: 10.15479/AT:ISTA:12820 file: - access_level: open_access checksum: 54a619605e44c871214fb0e07b05c6bf content_type: application/zip creator: pschanda date_created: 2023-04-14T09:39:33Z date_updated: 2023-04-14T09:39:33Z file_id: '12823' file_name: data_deposition.zip file_size: 54184807 relation: main_file success: 1 - access_level: open_access checksum: 8dede9fc78399d13144eb05c62bf5750 content_type: application/octet-stream creator: pschanda date_created: 2023-04-14T09:39:58Z date_updated: 2023-04-14T09:39:58Z file_id: '12824' file_name: README file_size: 4978 relation: main_file success: 1 file_date_updated: 2023-04-14T09:39:58Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '13095' relation: used_in_publication status: public status: public title: Research data of the publication "Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR" tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13039' abstract: - lang: eng text: We calculate reflectivities of dynamically compressed water, water-ethanol mixtures, and ammonia at infrared and optical wavelengths with density functional theory and molecular dynamics simulations. The influence of the exchange-correlation functional on the results is examined in detail. Our findings indicate that the consistent use of the HSE hybrid functional reproduces experimental results much better than the commonly used PBE functional. The HSE functional offers not only a more accurate description of the electronic band gap but also shifts the onset of molecular dissociation in the molecular dynamics simulations to significantly higher pressures. We also highlight the importance of using accurate reference standards in reflectivity experiments and reanalyze infrared and optical reflectivity data from recent experiments. Thus, our combined theoretical and experimental work explains and resolves lingering discrepancies between calculations and measurements for the investigated molecular substances under shock compression. acknowledgement: 'We thank R. Redmer for helpful discussions. M.F. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG) within the FOR 2440. M.B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Skłodowska-Curie actions (xICE Grant No. 894725) and the NOMIS foundation. A.R. and J.-A.H. acknowledge support form the French National Research Agency (ANR) through the projects POMPEI (Grant No. ANR-16-CE31-0008) and SUPER-ICES (Grant No. ANR-15-CE30-008-01). The ab initio calculations were performed at the NorthGerman Supercomputing Alliance (HLRN) facilities. ' article_number: '134109' article_processing_charge: No article_type: original author: - first_name: Martin full_name: French, Martin last_name: French - first_name: Mandy full_name: Bethkenhagen, Mandy id: 201939f4-803f-11ed-ab7e-d8da4bd1517f last_name: Bethkenhagen orcid: 0000-0002-1838-2129 - first_name: Alessandra full_name: Ravasio, Alessandra last_name: Ravasio - first_name: Jean Alexis full_name: Hernandez, Jean Alexis last_name: Hernandez citation: ama: French M, Bethkenhagen M, Ravasio A, Hernandez JA. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 2023;107(13). doi:10.1103/PhysRevB.107.134109 apa: French, M., Bethkenhagen, M., Ravasio, A., & Hernandez, J. A. (2023). Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.134109 chicago: French, Martin, Mandy Bethkenhagen, Alessandra Ravasio, and Jean Alexis Hernandez. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.134109. ieee: M. French, M. Bethkenhagen, A. Ravasio, and J. A. Hernandez, “Ab initio calculation of the reflectivity of molecular fluids under shock compression,” Physical Review B, vol. 107, no. 13. American Physical Society, 2023. ista: French M, Bethkenhagen M, Ravasio A, Hernandez JA. 2023. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 107(13), 134109. mla: French, Martin, et al. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B, vol. 107, no. 13, 134109, American Physical Society, 2023, doi:10.1103/PhysRevB.107.134109. short: M. French, M. Bethkenhagen, A. Ravasio, J.A. Hernandez, Physical Review B 107 (2023). date_created: 2023-05-21T22:01:04Z date_published: 2023-04-01T00:00:00Z date_updated: 2023-08-01T14:45:25Z day: '01' department: - _id: BiCh doi: 10.1103/PhysRevB.107.134109 external_id: isi: - '000974672600001' intvolume: ' 107' isi: 1 issue: '13' language: - iso: eng month: '04' oa_version: None 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: Ab initio calculation of the reflectivity of molecular fluids under shock compression type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '13092' abstract: - lang: eng text: There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe. acknowledgement: Open Access is funded by the Austrian Science Fund (FWF). We thank Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X., and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial support from IST Austria. article_processing_charge: No article_type: original author: - first_name: Bingfei full_name: Nan, Bingfei last_name: 'Nan' - first_name: Xuan full_name: Song, Xuan last_name: Song - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Ke full_name: Xiao, Ke last_name: Xiao - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Linlin full_name: Yang, Linlin last_name: Yang - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - 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: Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 2023;15(19):23380–23389. doi:10.1021/acsami.3c00625 apa: Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023). Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c00625 chicago: Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c00625. ieee: B. Nan et al., “Bottom-up synthesis of SnTe-based thermoelectric composites,” ACS Applied Materials and Interfaces, vol. 15, no. 19. American Chemical Society, pp. 23380–23389, 2023. ista: Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 15(19), 23380–23389. mla: Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces, vol. 15, no. 19, American Chemical Society, 2023, pp. 23380–23389, doi:10.1021/acsami.3c00625. short: B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H. Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389. date_created: 2023-05-28T22:01:03Z date_published: 2023-05-04T00:00:00Z date_updated: 2023-08-01T14:50:09Z day: '04' ddc: - '540' department: - _id: MaIb doi: 10.1021/acsami.3c00625 external_id: isi: - '000985497900001' pmid: - '37141543' file: - access_level: open_access checksum: 23893be46763c4c78daacddd019de821 content_type: application/pdf creator: dernst date_created: 2023-05-30T07:38:44Z date_updated: 2023-05-30T07:38:44Z file_id: '13099' file_name: 2023_ACSAppliedMaterials_Nan.pdf file_size: 5640829 relation: main_file success: 1 file_date_updated: 2023-05-30T07:38:44Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '19' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 23380–23389 pmid: 1 project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications 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: Bottom-up synthesis of SnTe-based thermoelectric composites 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: 15 year: '2023' ... --- _id: '13094' abstract: - lang: eng text: 'Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states.' acknowledgement: We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960). article_processing_charge: No article_type: letter_note author: - first_name: Ali full_name: Azadbakht, Ali last_name: Azadbakht - first_name: Billie full_name: Meadowcroft, Billie id: a4725fd6-932b-11ed-81e2-c098c7f37ae1 last_name: Meadowcroft - first_name: Thijs full_name: Varkevisser, Thijs last_name: Varkevisser - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Daniela J. full_name: Kraft, Daniela J. last_name: Kraft citation: ama: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375 apa: Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375 chicago: Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375. ieee: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023. ista: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273. mla: Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375. short: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273. date_created: 2023-05-28T22:01:03Z date_published: 2023-05-04T00:00:00Z date_updated: 2023-08-01T14:51:25Z day: '04' ddc: - '540' department: - _id: AnSa doi: 10.1021/acs.nanolett.3c00375 ec_funded: 1 external_id: isi: - '000985481400001' pmid: - '37141427' file: - access_level: open_access checksum: 9734d4c617bab3578ef62916b764547a content_type: application/pdf creator: dernst date_created: 2023-05-30T07:55:31Z date_updated: 2023-05-30T07:55:31Z file_id: '13100' file_name: 2023_NanoLetters_Azadbakht.pdf file_size: 3654910 relation: main_file success: 1 file_date_updated: 2023-05-30T07:55:31Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '10' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 4267–4273 pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles 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: 23 year: '2023' ... --- _id: '13093' abstract: - lang: eng text: The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated. acknowledgement: 'Open Access is funded by the Austrian Science Fund (FWF). B.N., M.L., Y.Z., K.X., and X.H. thank the China Scholarship Council (CSC) for the scholarship support. C.C. received funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. M.I. acknowledges the financial support from ISTA and the Werner Siemens Foundation. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457 and project NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/. ICN2 was supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and was funded by the CERCA Programme/Generalitat de Catalunya. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and 2021 SGR 01061. K.H.L. acknowledges support from the National Natural Science Foundation of China (22208293). This study is part of the Advanced Materials programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya.' article_processing_charge: No article_type: original author: - first_name: Bingfei full_name: Nan, Bingfei last_name: 'Nan' - first_name: Mengyao full_name: Li, Mengyao last_name: Li - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Ke full_name: Xiao, Ke last_name: Xiao - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Xu full_name: Han, Xu last_name: Han - first_name: Yong full_name: Zuo, Yong last_name: Zuo - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - 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: Nan B, Li M, Zhang Y, et al. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. 2023. doi:10.1021/acsaelm.3c00055 apa: Nan, B., Li, M., Zhang, Y., Xiao, K., Lim, K. H., Chang, C., … Cabot, A. (2023). Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. American Chemical Society. https://doi.org/10.1021/acsaelm.3c00055 chicago: Nan, Bingfei, Mengyao Li, Yu Zhang, Ke Xiao, Khak Ho Lim, Cheng Chang, Xu Han, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaelm.3c00055. ieee: B. Nan et al., “Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature,” ACS Applied Electronic Materials. American Chemical Society, 2023. ista: Nan B, Li M, Zhang Y, Xiao K, Lim KH, Chang C, Han X, Zuo Y, Li J, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2023. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. mla: Nan, Bingfei, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials, American Chemical Society, 2023, doi:10.1021/acsaelm.3c00055. short: B. Nan, M. Li, Y. Zhang, K. Xiao, K.H. Lim, C. Chang, X. Han, Y. Zuo, J. Li, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Electronic Materials (2023). date_created: 2023-05-28T22:01:03Z date_published: 2023-05-05T00:00:00Z date_updated: 2023-08-01T14:50:48Z day: '05' department: - _id: MaIb doi: 10.1021/acsaelm.3c00055 external_id: isi: - '000986859000001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acsaelm.3c00055 month: '05' oa: 1 oa_version: Published Version project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: ACS Applied Electronic Materials publication_identifier: eissn: - 2637-6113 publication_status: epub_ahead publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2023' ... --- _id: '13091' abstract: - lang: eng text: We use a function field version of the Hardy–Littlewood circle method to study the locus of free rational curves on an arbitrary smooth projective hypersurface of sufficiently low degree. On the one hand this allows us to bound the dimension of the singular locus of the moduli space of rational curves on such hypersurfaces and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin conjecture in terms of slopes with respect to the tangent bundle. acknowledgement: The authors are grateful to Paul Nelson, Per Salberger and Jason Starr for useful comments. While working on this paper the first author was supported by EPRSC grant EP/P026710/1. The research was partially conducted during the period the second author served as a Clay Research Fellow, and partially conducted during the period he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zurich Foundation. article_processing_charge: No article_type: original author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Will full_name: Sawin, Will last_name: Sawin citation: ama: Browning TD, Sawin W. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 2023;17(3):719-748. doi:10.2140/ant.2023.17.719 apa: Browning, T. D., & Sawin, W. (2023). Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2023.17.719 chicago: Browning, Timothy D, and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/ant.2023.17.719. ieee: T. D. Browning and W. Sawin, “Free rational curves on low degree hypersurfaces and the circle method,” Algebra and Number Theory, vol. 17, no. 3. Mathematical Sciences Publishers, pp. 719–748, 2023. ista: Browning TD, Sawin W. 2023. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 17(3), 719–748. mla: Browning, Timothy D., and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory, vol. 17, no. 3, Mathematical Sciences Publishers, 2023, pp. 719–48, doi:10.2140/ant.2023.17.719. short: T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748. date_created: 2023-05-28T22:01:02Z date_published: 2023-04-12T00:00:00Z date_updated: 2023-08-01T14:51:57Z day: '12' ddc: - '510' department: - _id: TiBr doi: 10.2140/ant.2023.17.719 external_id: arxiv: - '1810.06882' isi: - '000996014700004' file: - access_level: open_access checksum: 5d5d67b235905650e33cf7065d7583b4 content_type: application/pdf creator: dernst date_created: 2023-05-30T08:05:22Z date_updated: 2023-05-30T08:05:22Z file_id: '13101' file_name: 2023_AlgebraNumberTheory_Browning.pdf file_size: 1430719 relation: main_file success: 1 file_date_updated: 2023-05-30T08:05:22Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 719-748 project: - _id: 26A8D266-B435-11E9-9278-68D0E5697425 grant_number: EP-P026710-2 name: Between rational and integral points publication: Algebra and Number Theory publication_identifier: eissn: - 1944-7833 issn: - 1937-0652 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Free rational curves on low degree hypersurfaces and the circle method 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: 17 year: '2023' ... --- _id: '13117' abstract: - lang: eng text: The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194. article_number: '2998' article_processing_charge: No article_type: original author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alexander V. full_name: Poshakinskiy, Alexander V. last_name: Poshakinskiy - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Alexander N. full_name: Poddubny, Alexander N. last_name: Poddubny - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6 apa: Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6 chicago: Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6. ieee: E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998. mla: Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6. short: E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023). date_created: 2023-06-04T22:01:02Z date_published: 2023-05-24T00:00:00Z date_updated: 2023-08-02T06:10:26Z day: '24' ddc: - '530' department: - _id: JoFi doi: 10.1038/s41467-023-38761-6 ec_funded: 1 external_id: arxiv: - '2205.03293' isi: - '001001099700002' file: - access_level: open_access checksum: a857df40f0882859c48a1ff1e2001ec2 content_type: application/pdf creator: dernst date_created: 2023-06-06T07:31:20Z date_updated: 2023-06-06T07:31:20Z file_id: '13123' file_name: 2023_NaturePhysics_Redchenko.pdf file_size: 1654389 relation: main_file success: 1 file_date_updated: 2023-06-06T07:31:20Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 26B354CA-B435-11E9-9278-68D0E5697425 name: Controllable Collective States of Superconducting Qubit Ensembles - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13124' relation: research_data status: public scopus_import: '1' status: public title: Tunable directional photon scattering from a pair of superconducting qubits 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: 14 year: '2023' ... --- _id: '13106' abstract: - lang: eng text: Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification. acknowledgement: This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET). article_processing_charge: No article_type: original author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 - first_name: Liu full_name: Qiu, Liu id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac last_name: Qiu orcid: 0000-0003-4345-4267 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold - first_name: Y. full_name: Minoguchi, Y. last_name: Minoguchi - first_name: P. full_name: Rabl, P. last_name: Rabl - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science. 2023;380(6646):718-721. doi:10.1126/science.adg3812 apa: Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., & Fink, J. M. (2023). Entangling microwaves with light. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812 chicago: Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812. ieee: R. Sahu et al., “Entangling microwaves with light,” Science, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023. ista: Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721. mla: Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:10.1126/science.adg3812. short: R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721. date_created: 2023-05-31T11:39:24Z date_published: 2023-05-18T00:00:00Z date_updated: 2023-08-02T06:08:57Z day: '18' department: - _id: JoFi doi: 10.1126/science.adg3812 ec_funded: 1 external_id: arxiv: - '2301.03315' isi: - '000996515200004' intvolume: ' 380' isi: 1 issue: '6646' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.03315 month: '05' oa: 1 oa_version: Preprint page: 718-721 project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: 2671EB66-B435-11E9-9278-68D0E5697425 name: Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/ record: - id: '13122' relation: research_data status: public status: public title: Entangling microwaves with light type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 380 year: '2023' ... --- _id: '13129' abstract: - lang: eng text: "We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function." acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nicolas full_name: Clozeau, Nicolas id: fea1b376-906f-11eb-847d-b2c0cf46455b last_name: Clozeau - first_name: Marc full_name: Josien, Marc last_name: Josien - first_name: Felix full_name: Otto, Felix last_name: Otto - first_name: Qiang full_name: Xu, Qiang last_name: Xu citation: ama: 'Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. 2023. doi:10.1007/s10208-023-09613-y' apa: 'Clozeau, N., Josien, M., Otto, F., & Xu, Q. (2023). Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-023-09613-y' chicago: 'Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s10208-023-09613-y.' ieee: 'N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume element method: Periodize the ensemble instead of its realizations,” Foundations of Computational Mathematics. Springer Nature, 2023.' ista: 'Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics.' mla: 'Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics, Springer Nature, 2023, doi:10.1007/s10208-023-09613-y.' short: N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023). date_created: 2023-06-11T22:00:40Z date_published: 2023-05-30T00:00:00Z date_updated: 2023-08-02T06:12:39Z day: '30' ddc: - '510' department: - _id: JuFi doi: 10.1007/s10208-023-09613-y external_id: isi: - '000999623100001' has_accepted_license: '1' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10208-023-09613-y month: '05' oa: 1 oa_version: Published Version publication: Foundations of Computational Mathematics publication_identifier: eissn: - 1615-3383 issn: - 1615-3375 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Bias in the representative volume element method: Periodize the ensemble instead of its realizations' 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 year: '2023' ... --- _id: '13124' abstract: - lang: eng text: This dataset comprises all data shown in the figures of the submitted article "Tunable directional photon scattering from a pair of superconducting qubits" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request. article_processing_charge: No author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alexander full_name: Poshakinskiy, Alexander last_name: Poshakinskiy - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Alexander full_name: Poddubny, Alexander last_name: Poddubny - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567 apa: Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567 chicago: Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567. ieee: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023. ista: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567. mla: Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567. short: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023). date_created: 2023-06-06T07:36:50Z date_published: 2023-04-28T00:00:00Z date_updated: 2023-08-02T06:10:25Z day: '28' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.7858567 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7858567 month: '04' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13117' relation: used_in_publication status: public status: public title: Tunable directional photon scattering from a pair of superconducting qubits 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13122' abstract: - lang: eng text: Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1 article_processing_charge: No author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 citation: ama: Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417 apa: Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417 chicago: Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417. ieee: R. Sahu, “Entangling microwaves with light.” Zenodo, 2023. ista: Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417. mla: Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417. short: R. Sahu, (2023). date_created: 2023-06-06T06:46:16Z date_published: 2023-03-31T00:00:00Z date_updated: 2023-08-02T06:08:56Z day: '31' department: - _id: JoFi doi: 10.5281/ZENODO.7789417 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7789418 month: '03' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13106' relation: used_in_publication status: public status: public title: Entangling microwaves with light 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13166' abstract: - lang: eng text: Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans. acknowledgement: "We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.)." article_number: '9382' article_processing_charge: No article_type: original author: - first_name: Alexandra A. full_name: Vetrova, Alexandra A. last_name: Vetrova - first_name: Daria M. full_name: Kupaeva, Daria M. last_name: Kupaeva - first_name: Alena full_name: Kizenko, Alena id: a521c60b-0815-11ed-9b02-b8bd522477c8 last_name: Kizenko - first_name: Tatiana S. full_name: Lebedeva, Tatiana S. last_name: Lebedeva - first_name: Peter full_name: Walentek, Peter last_name: Walentek - first_name: Nikoloz full_name: Tsikolia, Nikoloz last_name: Tsikolia - first_name: Stanislav V. full_name: Kremnyov, Stanislav V. last_name: Kremnyov citation: ama: Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8 apa: Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8 chicago: Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8. ieee: A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023. ista: Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382. mla: Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8. short: A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023). date_created: 2023-06-25T22:00:46Z date_published: 2023-06-09T00:00:00Z date_updated: 2023-08-02T06:17:18Z day: '09' ddc: - '570' department: - _id: GradSch doi: 10.1038/s41598-023-35979-8 external_id: isi: - '001006690200045' pmid: - '37296138' file: - access_level: open_access checksum: baddf6b2fa9adf88263d4a3b0998f0f2 content_type: application/pdf creator: dernst date_created: 2023-06-26T09:58:53Z date_updated: 2023-06-26T09:58:53Z file_id: '13170' file_name: 2023_ScientificReports_Vetrova.pdf file_size: 4844149 relation: main_file success: 1 file_date_updated: 2023-06-26T09:58:53Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: eissn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization 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: 13 year: '2023' ... --- _id: '13138' abstract: - lang: eng text: "We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain." acknowledgement: "The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. " article_number: '184312' article_processing_charge: No article_type: original author: - first_name: Pavel full_name: Orlov, Pavel last_name: Orlov - first_name: Anastasiia full_name: Tiutiakina, Anastasiia last_name: Tiutiakina - first_name: Rustem full_name: Sharipov, Rustem last_name: Sharipov - first_name: Elena full_name: Petrova, Elena id: 0ac84990-897b-11ed-a09c-f5abb56a4ede last_name: Petrova - first_name: Vladimir full_name: Gritsev, Vladimir last_name: Gritsev - first_name: Denis V. full_name: Kurlov, Denis V. last_name: Kurlov citation: ama: Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312 apa: Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312 chicago: Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312. ieee: P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023. ista: Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312. mla: Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312. short: P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023). date_created: 2023-06-18T22:00:46Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-08-02T06:16:02Z day: '01' department: - _id: GradSch doi: 10.1103/PhysRevB.107.184312 external_id: arxiv: - '2303.00729' isi: - '001003686900004' intvolume: ' 107' isi: 1 issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2303.00729 month: '05' 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: Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '13213' abstract: - lang: eng text: The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth. acknowledgement: We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science. article_processing_charge: No article_type: original author: - first_name: C full_name: Chen, C last_name: Chen - first_name: Y full_name: Zhang, Y last_name: Zhang - first_name: J full_name: Cai, J last_name: Cai - first_name: Y full_name: Qiu, Y last_name: Qiu - first_name: L full_name: Li, L last_name: Li - first_name: C full_name: Gao, C last_name: Gao - first_name: Y full_name: Gao, Y last_name: Gao - first_name: M full_name: Ke, M last_name: Ke - first_name: S full_name: Wu, S last_name: Wu - first_name: C full_name: Wei, C last_name: Wei - first_name: J full_name: Chen, J last_name: Chen - first_name: T full_name: Xu, T last_name: Xu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: J full_name: Wang, J last_name: Wang - first_name: R full_name: Li, R last_name: Li - first_name: D full_name: Chao, D last_name: Chao - first_name: B full_name: Zhang, B last_name: Zhang - first_name: X full_name: Chen, X last_name: Chen - first_name: Z full_name: Gao, Z last_name: Gao citation: ama: Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207 apa: Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiad207 chicago: Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology. American Society of Plant Biologists, 2023. https://doi.org/10.1093/plphys/kiad207. ieee: C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” Plant Physiology, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023. ista: Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260. mla: Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207. short: C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260. date_created: 2023-07-12T07:32:58Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-08-02T06:27:55Z day: '01' ddc: - '575' department: - _id: JiFr doi: 10.1093/plphys/kiad207 external_id: isi: - '000971795800001' pmid: - '37010107' file: - access_level: open_access checksum: 5492e1d18ac3eaf202633d210fa0fb75 content_type: application/pdf creator: cchlebak date_created: 2023-07-13T13:26:33Z date_updated: 2023-07-13T13:26:33Z file_id: '13220' file_name: 2023_PlantPhys_Chen.pdf file_size: 2076977 relation: main_file success: 1 file_date_updated: 2023-07-13T13:26:33Z has_accepted_license: '1' intvolume: ' 192' isi: 1 issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2243-2260 pmid: 1 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' status: public title: Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 192 year: '2023' ... --- _id: '12478' abstract: - lang: eng text: In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype. acknowledgement: This work was supported by NIH P50 award P50GM081892-02 to the University of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322. article_number: '1049255' article_processing_charge: Yes article_type: original author: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: L full_name: Bruneaux, L last_name: Bruneaux - first_name: P full_name: Oikonomou, P last_name: Oikonomou - first_name: M full_name: Aldana, M last_name: Aldana - first_name: P full_name: Cluzel, P last_name: Cluzel citation: ama: Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1049255 apa: Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., & Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1049255 chicago: Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1049255. ieee: C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression,” Frontiers in Microbiology, vol. 14. Frontiers, 2023. ista: Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 14, 1049255. mla: Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology, vol. 14, 1049255, Frontiers, 2023, doi:10.3389/fmicb.2023.1049255. short: C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023). date_created: 2023-02-02T08:13:28Z date_published: 2023-06-20T00:00:00Z date_updated: 2023-08-02T06:25:04Z day: '20' ddc: - '570' department: - _id: CaGu doi: 10.3389/fmicb.2023.1049255 external_id: isi: - '001030002600001' pmid: - '37485524' file: - access_level: open_access checksum: 7dd322347512afaa5daf72a0154f2f07 content_type: application/pdf creator: dernst date_created: 2023-07-31T07:16:34Z date_updated: 2023-07-31T07:16:34Z file_id: '13322' file_name: 2023_FrontiersMicrobiology_Guet.pdf file_size: 6452841 relation: main_file success: 1 file_date_updated: 2023-07-31T07:16:34Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '06' 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: Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression 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: '13237' abstract: - lang: eng text: The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases. acknowledgement: The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations. article_processing_charge: No article_type: original author: - first_name: Thomas C.T. full_name: Michaels, Thomas C.T. last_name: Michaels - first_name: Daoyuan full_name: Qian, Daoyuan last_name: Qian - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Sara full_name: Linse, Sara last_name: Linse - first_name: Tuomas P.J. full_name: Knowles, Tuomas P.J. last_name: Knowles citation: ama: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397. doi:10.1038/s42254-023-00598-9 apa: Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., & Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9 chicago: Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9. ieee: T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 379–397, 2023. ista: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397. mla: Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9. short: T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397. date_created: 2023-07-16T22:01:12Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-08-02T06:28:38Z day: '01' department: - _id: AnSa doi: 10.1038/s42254-023-00598-9 external_id: isi: - '001017539800001' intvolume: ' 5' isi: 1 language: - iso: eng month: '07' oa_version: None page: 379–397 publication: Nature Reviews Physics publication_identifier: eissn: - 2522-5820 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Amyloid formation as a protein phase transition type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2023' ... --- _id: '13229' abstract: - lang: eng text: Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation. acknowledgement: This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. article_processing_charge: No article_type: original author: - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Laura full_name: Hofmann, Laura id: b88d43f2-dc74-11ea-a0a7-e41b7912e031 last_name: Hofmann - first_name: Irene full_name: Steccari, Irene id: 2705C766-9FE2-11EA-B224-C6773DDC885E last_name: Steccari - first_name: Roland full_name: Kardos, Roland id: 4039350E-F248-11E8-B48F-1D18A9856A87 last_name: Kardos - 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 citation: ama: Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 2023;21(6):e3002146. doi:10.1371/journal.pbio.3002146 apa: Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., & Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002146 chicago: Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002146. ieee: S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” PLoS Biology, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023. ista: Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146. mla: Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:10.1371/journal.pbio.3002146. short: S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146. date_created: 2023-07-16T22:01:09Z date_published: 2023-06-08T00:00:00Z date_updated: 2023-08-02T06:33:14Z day: '08' ddc: - '570' department: - _id: CaHe doi: 10.1371/journal.pbio.3002146 ec_funded: 1 external_id: isi: - '001003199100005' pmid: - '37289834' file: - access_level: open_access checksum: 8e88cb0e5a6433a2f1939a9030bed384 content_type: application/pdf creator: dernst date_created: 2023-07-18T07:59:58Z date_updated: 2023-07-18T07:59:58Z file_id: '13246' file_name: 2023_PloSBiology_Shamipour.pdf file_size: 4431723 relation: main_file success: 1 file_date_updated: 2023-07-18T07:59:58Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: e3002146 pmid: 1 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: PLoS Biology publication_identifier: eissn: - 1545-7885 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes 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: 21 year: '2023' ... --- _id: '13197' abstract: - lang: eng text: "Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop\r\nan analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally." acknowledgement: "This project has received funding from the European Research Council Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. " article_number: '065601' article_processing_charge: No article_type: original author: - first_name: Galien M full_name: Grosjean, Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: 'Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 2023;7(6). doi:10.1103/physrevmaterials.7.065601' apa: 'Grosjean, G. M., & Waitukaitis, S. R. (2023). Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.7.065601' chicago: 'Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials. American Physical Society, 2023. https://doi.org/10.1103/physrevmaterials.7.065601.' ieee: 'G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts,” Physical Review Materials, vol. 7, no. 6. American Physical Society, 2023.' ista: 'Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 7(6), 065601.' mla: 'Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials, vol. 7, no. 6, 065601, American Physical Society, 2023, doi:10.1103/physrevmaterials.7.065601.' short: G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023). date_created: 2023-07-07T12:48:01Z date_published: 2023-06-13T00:00:00Z date_updated: 2023-08-02T06:34:47Z day: '13' ddc: - '537' department: - _id: ScWa doi: 10.1103/physrevmaterials.7.065601 ec_funded: 1 external_id: arxiv: - '2304.12861' isi: - '001019565900002' file: - access_level: open_access checksum: 75584730d9cdd50eeccb4c52c509776d content_type: application/pdf creator: ggrosjea date_created: 2023-07-07T12:49:51Z date_updated: 2023-07-07T12:49:51Z file_id: '13198' file_name: Mosaic_asymmetries.pdf file_size: 1127040 relation: main_file success: 1 file_date_updated: 2023-07-07T12:49:51Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '6' keyword: - Physics and Astronomy (miscellaneous) - General Materials Science language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Materials publication_identifier: issn: - 2475-9953 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: 'Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 year: '2023' ... --- _id: '13230' abstract: - lang: eng text: 'To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.' acknowledgement: The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback. article_number: e1011104 article_processing_charge: No article_type: original author: - first_name: Julie A. full_name: Charlton, Julie A. last_name: Charlton - first_name: Wiktor F full_name: Mlynarski, Wiktor F id: 358A453A-F248-11E8-B48F-1D18A9856A87 last_name: Mlynarski - first_name: Yoon H. full_name: Bai, Yoon H. last_name: Bai - first_name: Ann M. full_name: Hermundstad, Ann M. last_name: Hermundstad - first_name: Robbe L.T. full_name: Goris, Robbe L.T. last_name: Goris citation: ama: Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6). doi:10.1371/journal.pcbi.1011104 apa: Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104 chicago: Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104. ieee: J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational Biology, vol. 19, no. 6. Public Library of Science, 2023. ista: Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104. mla: Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1011104. short: J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023). date_created: 2023-07-16T22:01:09Z date_published: 2023-06-08T00:00:00Z date_updated: 2023-08-02T06:33:50Z day: '08' ddc: - '570' department: - _id: MaJö doi: 10.1371/journal.pcbi.1011104 external_id: isi: - '001003410200003' pmid: - '37289753' file: - access_level: open_access checksum: 800761fa2c647fabd6ad034589bc526e content_type: application/pdf creator: dernst date_created: 2023-07-18T08:07:59Z date_updated: 2023-07-18T08:07:59Z file_id: '13247' file_name: 2023_PloSCompBio_Charlton.pdf file_size: 2281868 relation: main_file success: 1 file_date_updated: 2023-07-18T08:07:59Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Environmental dynamics shape perceptual decision bias 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: 19 year: '2023' ... --- _id: '13232' abstract: - lang: eng text: The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study. acknowledgement: The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals. article_number: '1014' article_processing_charge: No article_type: original author: - first_name: Dmitri full_name: Dormeshkin, Dmitri last_name: Dormeshkin - first_name: Mikalai full_name: Katsin, Mikalai last_name: Katsin - first_name: Maria full_name: Stegantseva, Maria last_name: Stegantseva - first_name: Sergey full_name: Golenchenko, Sergey last_name: Golenchenko - first_name: Michail full_name: Shapira, Michail last_name: Shapira - first_name: Simon full_name: Dubovik, Simon last_name: Dubovik - first_name: Dzmitry full_name: Lutskovich, Dzmitry last_name: Lutskovich - first_name: Anton full_name: Kavaleuski, Anton id: 62304f89-eb97-11eb-a6c2-8903dd183976 last_name: Kavaleuski orcid: 0000-0003-2091-526X - first_name: Alexander full_name: Meleshko, Alexander last_name: Meleshko citation: ama: Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6). doi:10.3390/vaccines11061014 apa: Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014 chicago: Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014. ieee: D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI, 2023. ista: Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014. mla: Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI, 2023, doi:10.3390/vaccines11061014. short: D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023). date_created: 2023-07-16T22:01:10Z date_published: 2023-06-01T00:00:00Z date_updated: 2023-08-02T06:31:19Z day: '01' ddc: - '570' department: - _id: LeSa doi: 10.3390/vaccines11061014 external_id: isi: - '001017740000001' file: - access_level: open_access checksum: 8f484c0f30f8699c589b1c29a0fd7d7f content_type: application/pdf creator: dernst date_created: 2023-07-18T07:25:43Z date_updated: 2023-07-18T07:25:43Z file_id: '13244' file_name: 2023_Vaccines_Dormeshkin.pdf file_size: 2339746 relation: main_file success: 1 file_date_updated: 2023-07-18T07:25:43Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Vaccines publication_identifier: eissn: - 2076-393X publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein 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: 11 year: '2023' ... --- _id: '13235' abstract: - lang: eng text: AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications. 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 (Grant No. 22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation. article_processing_charge: No article_type: original author: - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mingquan full_name: Li, Mingquan last_name: Li - first_name: Shanhong full_name: Wan, Shanhong last_name: Wan - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Mengyao full_name: Li, Mengyao last_name: Li - 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: Min full_name: Hong, Min last_name: Hong - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 2023;17(12):11923–11934. doi:10.1021/acsnano.3c03541' apa: 'Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023). Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c03541' chicago: 'Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li, Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c03541.' ieee: 'Y. Liu et al., “Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance,” ACS Nano, vol. 17, no. 12. American Chemical Society, pp. 11923–11934, 2023.' ista: 'Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 17(12), 11923–11934.' mla: 'Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano, vol. 17, no. 12, American Chemical Society, 2023, pp. 11923–11934, doi:10.1021/acsnano.3c03541.' short: Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong, A. Cabot, ACS Nano 17 (2023) 11923–11934. date_created: 2023-07-16T22:01:11Z date_published: 2023-06-13T00:00:00Z date_updated: 2023-08-02T06:29:55Z day: '13' department: - _id: MaIb doi: 10.1021/acsnano.3c03541 external_id: isi: - '001008564800001' pmid: - '37310395' intvolume: ' 17' isi: 1 issue: '12' language: - iso: eng month: '06' oa_version: None page: 11923–11934 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: ACS Nano publication_identifier: eissn: - 1936-086X issn: - 1936-0851 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2023' ... --- _id: '13231' abstract: - lang: eng text: We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles. acknowledgement: "We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344." article_number: '065207' article_processing_charge: No article_type: original author: - first_name: Maximilian full_name: Schörner, Maximilian last_name: Schörner - first_name: Mandy full_name: Bethkenhagen, Mandy id: 201939f4-803f-11ed-ab7e-d8da4bd1517f last_name: Bethkenhagen orcid: 0000-0002-1838-2129 - first_name: Tilo full_name: Döppner, Tilo last_name: Döppner - first_name: Dominik full_name: Kraus, Dominik last_name: Kraus - first_name: Luke B. full_name: Fletcher, Luke B. last_name: Fletcher - first_name: Siegfried H. full_name: Glenzer, Siegfried H. last_name: Glenzer - first_name: Ronald full_name: Redmer, Ronald last_name: Redmer citation: ama: Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207 apa: Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207 chicago: Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.065207. ieee: M. Schörner et al., “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” Physical Review E, vol. 107, no. 6. American Physical Society, 2023. ista: Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207. mla: Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:10.1103/PhysRevE.107.065207. short: M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023). date_created: 2023-07-16T22:01:10Z date_published: 2023-06-14T00:00:00Z date_updated: 2023-08-02T06:30:46Z day: '14' department: - _id: BiCh doi: 10.1103/PhysRevE.107.065207 external_id: arxiv: - '2301.01545' isi: - '001020265000002' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.01545 month: '06' oa: 1 oa_version: Preprint publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '13233' abstract: - lang: eng text: We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters. acknowledgement: We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). article_number: L061304 article_processing_charge: No article_type: letter_note author: - first_name: Sofya full_name: Agafonova, Sofya id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80 last_name: Agafonova - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304 apa: Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304 chicago: Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304. ieee: S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023. ista: Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304. mla: Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304. short: S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023). date_created: 2023-07-16T22:01:10Z date_published: 2023-06-20T00:00:00Z date_updated: 2023-08-02T06:31:52Z day: '20' department: - _id: MiLe - _id: OnHo doi: 10.1103/PhysRevA.107.L061304 ec_funded: 1 external_id: arxiv: - '2302.01022' isi: - '001019748000005' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2302.01022 month: '06' oa: 1 oa_version: Preprint 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 A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Finite-range bias in fitting three-body loss to the zero-range model type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '13256' abstract: - lang: eng text: The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate. acknowledgement: This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations. article_number: '82' article_processing_charge: Yes article_type: original author: - first_name: Bidyut B full_name: Goswami, Bidyut B id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b last_name: Goswami - first_name: Soon Il full_name: An, Soon Il last_name: An citation: ama: GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5 apa: GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. Npj Climate and Atmospheric Science. Springer Nature. https://doi.org/10.1038/s41612-023-00411-5 chicago: GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature, 2023. https://doi.org/10.1038/s41612-023-00411-5. ieee: B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer Nature, 2023. ista: GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82. mla: GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82, Springer Nature, 2023, doi:10.1038/s41612-023-00411-5. short: B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023). date_created: 2023-07-23T22:01:10Z date_published: 2023-07-08T00:00:00Z date_updated: 2023-08-02T06:38:07Z day: '08' ddc: - '550' department: - _id: CaMu doi: 10.1038/s41612-023-00411-5 external_id: isi: - '001024920300002' file: - access_level: open_access checksum: e9967d436a83b8ffcc6f58782e1f7500 content_type: application/pdf creator: dernst date_created: 2023-07-31T08:00:01Z date_updated: 2023-07-31T08:00:01Z file_id: '13326' file_name: 2023_npjclimate_Goswami.pdf file_size: 1750712 relation: main_file success: 1 file_date_updated: 2023-07-31T08:00:01Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: npj Climate and Atmospheric Science publication_identifier: eissn: - 2397-3722 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: An assessment of the ENSO-monsoon teleconnection in a warming climate 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: 6 year: '2023' ... --- _id: '13260' abstract: - lang: eng text: Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines. acknowledgement: This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping. article_number: evad113 article_processing_charge: Yes article_type: original author: - first_name: Carolina full_name: De Castro Barbosa Rodrigues Barata, Carolina id: 20565186-803f-11ed-ab7e-96a4ff7694ef last_name: De Castro Barbosa Rodrigues Barata - first_name: Rhonda R. full_name: Snook, Rhonda R. last_name: Snook - first_name: Michael G. full_name: Ritchie, Michael G. last_name: Ritchie - first_name: Carolin full_name: Kosiol, Carolin last_name: Kosiol citation: ama: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113' apa: 'de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., & Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome Biology and Evolution. Oxford Academic. https://doi.org/10.1093/gbe/evad113' chicago: 'Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.' ieee: 'C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” Genome biology and evolution, vol. 15, no. 7. Oxford Academic, 2023.' ista: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.' mla: 'de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:10.1093/gbe/evad113.' short: C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023). date_created: 2023-07-23T22:01:11Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-08-02T06:42:35Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evad113 external_id: isi: - '001023444700003' pmid: - '37341535' file: - access_level: open_access checksum: 70de3c4878de6efe00dc56de2df8812f content_type: application/pdf creator: dernst date_created: 2023-08-01T06:58:34Z date_updated: 2023-08-01T06:58:34Z file_id: '13339' file_name: 2023_GBE_Barata.pdf file_size: 2382587 relation: main_file success: 1 file_date_updated: 2023-08-01T06:58:34Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Genome biology and evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford Academic quality_controlled: '1' related_material: link: - relation: software url: https://github.com/carolbarata/dpseudo-n-beyond scopus_import: '1' status: public title: 'Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura' 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: 15 year: '2023' ... --- _id: '13447' abstract: - lang: eng text: Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing. article_number: '2307.03237' article_processing_charge: No author: - first_name: Daniel full_name: Huber, Daniel last_name: Huber - first_name: Marc full_name: Pinsonneault, Marc last_name: Pinsonneault - first_name: Paul full_name: Beck, Paul last_name: Beck - first_name: Timothy R. full_name: Bedding, Timothy R. last_name: Bedding - first_name: Joss Bland-Hawthorn full_name: Joss Bland-Hawthorn, Joss Bland-Hawthorn last_name: Joss Bland-Hawthorn - first_name: Sylvain N. full_name: Breton, Sylvain N. last_name: Breton - 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: William J. full_name: Chaplin, William J. last_name: Chaplin - first_name: Rafael A. full_name: Garcia, Rafael A. last_name: Garcia - first_name: Samuel K. full_name: Grunblatt, Samuel K. last_name: Grunblatt - first_name: Joyce A. full_name: Guzik, Joyce A. last_name: Guzik - first_name: Saskia full_name: Hekker, Saskia last_name: Hekker - first_name: Steven D. full_name: Kawaler, Steven D. last_name: Kawaler - first_name: Stephane full_name: Mathis, Stephane last_name: Mathis - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Travis full_name: Metcalfe, Travis last_name: Metcalfe - first_name: Benoit full_name: Mosser, Benoit last_name: Mosser - first_name: Melissa K. full_name: Ness, Melissa K. last_name: Ness - first_name: Anthony L. full_name: Piro, Anthony L. last_name: Piro - first_name: Aldo full_name: Serenelli, Aldo last_name: Serenelli - first_name: Sanjib full_name: Sharma, Sanjib last_name: Sharma - first_name: David R. full_name: Soderblom, David R. last_name: Soderblom - first_name: Keivan G. full_name: Stassun, Keivan G. last_name: Stassun - first_name: Dennis full_name: Stello, Dennis last_name: Stello - first_name: Jamie full_name: Tayar, Jamie last_name: Tayar - first_name: Gerard T. van full_name: Belle, Gerard T. van last_name: Belle - first_name: Joel C. full_name: Zinn, Joel C. last_name: Zinn citation: ama: Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237 apa: Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn, J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237 chicago: Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237. ieee: D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain survey,” arXiv. . ista: Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv, 2307.03237. mla: Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237. short: D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn, S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik, S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness, A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J. Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.). date_created: 2023-08-02T07:30:43Z date_published: 2023-07-06T00:00:00Z date_updated: 2023-08-02T07:36:00Z day: '06' department: - _id: LiBu doi: 10.48550/arXiv.2307.03237 external_id: arxiv: - '2307.03237' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2307.03237 month: '07' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Asteroseismology with the Roman galactic bulge time-domain survey type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12781' abstract: - lang: eng text: "Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n" acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vladyslav full_name: Kravchuk, Vladyslav id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87 last_name: Kravchuk citation: ama: Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781 apa: Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781 chicago: Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781. ieee: V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023. ista: Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. mla: Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781. short: V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023. date_created: 2023-03-31T12:24:42Z date_published: 2023-03-23T00:00:00Z date_updated: 2023-08-04T08:54:51Z day: '23' ddc: - '570' - '572' degree_awarded: PhD department: - _id: GradSch - _id: LeSa doi: 10.15479/at:ista:12781 ec_funded: 1 file: - access_level: closed checksum: 5ebb6345cb4119f93460c81310265a6d content_type: application/pdf creator: vkravchu date_created: 2023-04-19T14:33:41Z date_updated: 2023-04-19T14:33:41Z embargo: 2024-04-20 embargo_to: local file_id: '12852' file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf file_size: 6071553 relation: main_file - access_level: closed checksum: c12055c48411d030d2afa51de2166221 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vkravchu date_created: 2023-04-19T14:33:52Z date_updated: 2023-04-20T07:02:59Z embargo: 2024-04-20 embargo_to: local file_id: '12853' file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx file_size: 19468766 relation: source_file file_date_updated: 2023-04-20T07:02:59Z has_accepted_license: '1' language: - iso: eng month: '03' oa_version: Published Version page: '127' project: - _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E grant_number: '25541' name: 'Structural characterization of E. coli complex I: an important mechanistic model' - _id: 627abdeb-2b32-11ec-9570-ec31a97243d3 call_identifier: H2020 grant_number: '101020697' name: Structure and mechanism of respiratory chain molecular machines publication_identifier: isbn: - 978-3-99078-029-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12138' relation: part_of_dissertation status: public status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13074' abstract: - lang: eng text: "Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Elena-Alexandra full_name: Peste, Elena-Alexandra id: 32D78294-F248-11E8-B48F-1D18A9856A87 last_name: Peste citation: ama: Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074 apa: Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074 chicago: Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074. ieee: E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023. ista: Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. mla: Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074. short: E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023. date_created: 2023-05-23T17:07:53Z date_published: 2023-05-23T00:00:00Z date_updated: 2023-08-04T10:33:27Z day: '23' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl - _id: ChLa doi: 10.15479/at:ista:13074 ec_funded: 1 file: - access_level: open_access checksum: 6b3354968403cb9d48cc5a83611fb571 content_type: application/pdf creator: epeste date_created: 2023-05-24T16:11:16Z date_updated: 2023-05-24T16:11:16Z file_id: '13087' file_name: PhD_Thesis_Alexandra_Peste_final.pdf file_size: 2152072 relation: main_file success: 1 - access_level: closed checksum: 8d0df94bbcf4db72c991f22503b3fd60 content_type: application/zip creator: epeste date_created: 2023-05-24T16:12:59Z date_updated: 2023-05-24T16:12:59Z file_id: '13088' file_name: PhD_Thesis_APeste.zip file_size: 1658293 relation: source_file file_date_updated: 2023-05-24T16:12:59Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '147' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11458' relation: part_of_dissertation status: public - id: '13053' relation: part_of_dissertation status: public - id: '12299' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: Efficiency and generalization of sparse neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12964' abstract: - lang: eng text: "Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Daniel R full_name: Boocock, Daniel R id: 453AF628-F248-11E8-B48F-1D18A9856A87 last_name: Boocock orcid: 0000-0002-1585-2631 citation: ama: Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964 apa: Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964 chicago: Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964. ieee: D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023. ista: Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. mla: Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964. short: D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023. date_created: 2023-05-15T14:52:36Z date_published: 2023-05-17T00:00:00Z date_updated: 2023-08-04T11:02:40Z day: '17' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: EdHa doi: 10.15479/at:ista:12964 ec_funded: 1 file: - access_level: closed checksum: d51240675fc6dc0e3f5dc0c902695d3a content_type: application/pdf creator: dboocock date_created: 2023-05-17T13:39:54Z date_updated: 2023-05-19T07:04:25Z embargo: 2024-05-17 embargo_to: open_access file_id: '12988' file_name: thesis_boocock.pdf file_size: 40414730 relation: main_file - access_level: closed checksum: 581a2313ffeb40fe77e8a122a25a7795 content_type: application/zip creator: dboocock date_created: 2023-05-17T13:39:53Z date_updated: 2023-05-17T14:35:13Z file_id: '12989' file_name: thesis_boocock.zip file_size: 34338567 relation: source_file file_date_updated: 2023-05-19T07:04:25Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '05' oa_version: Published Version page: '146' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-032-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8602' relation: part_of_dissertation status: public status: public supervisor: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Mechanochemical pattern formation across biological scales 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: '13963' abstract: - lang: eng text: The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons. acknowledgement: "We thank A. A. Michailidis and A. Mirlin for insightful discussions. P.B., M.L., 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). D.A. was\r\nsupported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD simulations were performed using the ITensor library [60]." article_number: '054201' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Pietro full_name: Brighi, Pietro id: 4115AF5C-F248-11E8-B48F-1D18A9856A87 last_name: Brighi orcid: 0000-0002-7969-2729 - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5). doi:10.1103/physrevb.108.054201 apa: Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201 chicago: Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201. ieee: P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization proximity effect in a two-species bosonic Hubbard model,” Physical Review B, vol. 108, no. 5. American Physical Society, 2023. ista: Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201. mla: Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American Physical Society, 2023, doi:10.1103/physrevb.108.054201. short: P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023). date_created: 2023-08-05T18:25:22Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-08-07T09:51:39Z day: '01' ddc: - '530' department: - _id: MaSe doi: 10.1103/physrevb.108.054201 ec_funded: 1 external_id: arxiv: - '2303.16876' file: - access_level: open_access checksum: f763000339b5fd543c14377109920690 content_type: application/pdf creator: dernst date_created: 2023-08-07T09:48:08Z date_updated: 2023-08-07T09:48:08Z file_id: '13981' file_name: 2023_PhysRevB_Brighi.pdf file_size: 3051398 relation: main_file success: 1 file_date_updated: 2023-08-07T09:48:08Z has_accepted_license: '1' intvolume: ' 108' issue: '5' language: - iso: eng month: '08' 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 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: Many-body localization proximity effect in a two-species bosonic Hubbard model 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: 108 year: '2023' ... --- _id: '13966' abstract: - lang: eng text: We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams, we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation energies up to n=5, with quadratic scaling in the number of basis functions. Our technique reduces the computational complexity of the molecular many-fermion correlation problem, opening up the possibility of low-scaling, accurate stochastic computations for a wide class of many-body systems described by Hugenholtz diagrams. acknowledgement: We acknowledge stimulating discussions with Sergey Varganov, Artur Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov, Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L. acknowledges support by the FWF under Project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). The authors acknowledge support by the state of Baden-Württemberg through bwHPC. article_number: '045115' article_processing_charge: No article_type: original author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Quoc P full_name: Ho, Quoc P id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87 last_name: Ho - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: T. V. full_name: Tscherbul, T. V. last_name: Tscherbul citation: ama: 'Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115' apa: 'Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.045115' chicago: 'Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.045115.' ieee: 'G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling,” Physical Review B, vol. 108, no. 4. American Physical Society, 2023.' ista: 'Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 108(4), 045115.' mla: 'Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.' short: G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023). date_created: 2023-08-06T22:01:10Z date_published: 2023-07-15T00:00:00Z date_updated: 2023-08-07T08:41:29Z day: '15' department: - _id: MiLe - _id: TaHa doi: 10.1103/PhysRevB.108.045115 ec_funded: 1 external_id: arxiv: - '2203.12666' intvolume: ' 108' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2203.12666 month: '07' oa: 1 oa_version: Preprint project: - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities - _id: 26B96266-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02751 name: Algebro-Geometric Applications of Factorization Homology - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' 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: 'Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '13970' article_processing_charge: No article_type: original author: - first_name: Amiera full_name: Madani, Amiera last_name: Madani - first_name: Eric T. full_name: Sletten, Eric T. last_name: Sletten - first_name: Cristian full_name: Cavedon, Cristian last_name: Cavedon - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X citation: ama: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271 apa: Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B. (2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271 chicago: Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger, and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271. ieee: A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,” Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023. ista: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 100, 271–286. mla: Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271. short: A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 271–286. date_created: 2023-08-06T22:01:11Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-08-07T08:21:45Z day: '01' department: - _id: BaPi doi: 10.15227/orgsyn.100.0271 intvolume: ' 100' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.15227/orgsyn.100.0271 month: '07' oa: 1 oa_version: Published Version page: 271-286 publication: Organic Syntheses publication_identifier: eissn: - 2333-3553 issn: - 0078-6209 publication_status: published publisher: Organic Syntheses quality_controlled: '1' scopus_import: '1' status: public title: Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2023' ... --- _id: '13127' abstract: - lang: eng text: Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense. acknowledged_ssus: - _id: LifeSc acknowledgement: We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT. article_number: '3232' article_processing_charge: Yes article_type: original author: - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Katarína full_name: Bod'Ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'Ová orcid: 0000-0002-7214-0171 - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y apa: Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y chicago: Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y. ieee: B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232. mla: Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y. short: B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023). date_created: 2023-06-11T22:00:40Z date_published: 2023-06-03T00:00:00Z date_updated: 2023-08-07T13:09:09Z day: '03' ddc: - '570' department: - _id: SyCr - _id: GaTk doi: 10.1038/s41467-023-38947-y ec_funded: 1 external_id: isi: - '001002562700005' pmid: - '37270641' file: - access_level: open_access checksum: 4af0393e3ed47b3fc46e68b81c3c1007 content_type: application/pdf creator: dernst date_created: 2023-06-13T08:05:46Z date_updated: 2023-06-13T08:05:46Z file_id: '13132' file_name: 2023_NatureComm_CasillasPerez.pdf file_size: 2358167 relation: main_file success: 1 file_date_updated: 2023-06-13T08:05:46Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '12945' relation: research_data status: public scopus_import: '1' status: public title: Dynamic pathogen detection and social feedback shape collective hygiene in ants 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: '12945' abstract: - lang: eng text: "basic data for use in code for experimental data analysis for manuscript under revision: \r\nDynamic pathogen detection and social feedback shape collective hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S" acknowledged_ssus: - _id: LifeSc acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Cremer S. Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945' apa: 'Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12945' chicago: 'Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12945.' ieee: 'S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.' ista: 'Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12945.' mla: 'Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12945.' short: S. Cremer, (2023). contributor: - contributor_type: data_collector first_name: Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - contributor_type: data_collector first_name: Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - contributor_type: researcher first_name: Katarina last_name: Bodova - contributor_type: supervisor first_name: Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 date_created: 2023-05-11T21:35:17Z date_published: 2023-05-12T00:00:00Z date_updated: 2023-08-07T13:09:09Z day: '12' ddc: - '570' department: - _id: SyCr doi: 10.15479/AT:ISTA:12945 file: - access_level: open_access checksum: 3eadf17fd59ad8c98bf10bf63061863c content_type: application/zip creator: scremer date_created: 2023-05-12T08:04:04Z date_updated: 2023-05-12T08:04:04Z file_id: '12947' file_name: Experimental_data.zip file_size: 3414674 relation: main_file success: 1 - access_level: open_access checksum: 1b5e8e01a0989154a76b44e6d8d68f89 content_type: application/octet-stream creator: scremer date_created: 2023-05-12T08:04:08Z date_updated: 2023-05-12T08:04:08Z file_id: '12948' file_name: README_Experimental_Data.md file_size: 2113 relation: main_file success: 1 file_date_updated: 2023-05-12T08:04:08Z has_accepted_license: '1' keyword: - collective behavior - host-pathogen interactions - social immunity - epidemiology - social insects - probabilistic modeling month: '05' oa: 1 oa_version: None publisher: Institute of Science and Technology Austria related_material: record: - id: '13127' relation: used_in_publication status: public status: public title: 'Data from: "Dynamic pathogen detection and social feedback shape collective hygiene in ants" ' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12885' abstract: - lang: eng text: 'High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ' acknowledged_ssus: - _id: EM-Fac - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 citation: ama: 'Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885' apa: 'Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885' chicago: 'Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.' ieee: 'M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.' ista: 'Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.' mla: 'Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.' short: 'M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-02T07:58:57Z date_published: 2023-04-28T00:00:00Z date_updated: 2023-08-14T07:25:26Z day: '28' ddc: - '546' - '541' degree_awarded: PhD department: - _id: GradSch - _id: MaIb doi: 10.15479/at:ista:12885 ec_funded: 1 file: - access_level: closed checksum: 9347b0e09425f56fdcede5d3528404dc content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mcalcabr date_created: 2023-05-02T07:43:18Z date_updated: 2023-05-02T07:43:18Z file_id: '12887' file_name: Thesis_Calcabrini.docx file_size: 99627036 relation: source_file - access_level: open_access checksum: 2d188b76621086cd384f0b9264b0a576 content_type: application/pdf creator: mcalcabr date_created: 2023-05-02T07:42:45Z date_updated: 2023-05-02T07:42:45Z file_id: '12888' file_name: Thesis_Calcabrini_pdfa.pdf file_size: 8742220 relation: main_file success: 1 file_date_updated: 2023-05-02T07:43:18Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '82' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-028-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10806' relation: part_of_dissertation status: public - id: '10042' relation: part_of_dissertation status: public - id: '12237' relation: part_of_dissertation status: public - id: '9118' relation: part_of_dissertation status: public - id: '10123' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 title: 'Nanoparticle-based semiconductor solids: From synthesis to consolidation' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12087' abstract: - lang: eng text: Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups. acknowledgement: H.Z. is 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. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Melchior full_name: Wirth, Melchior id: 88644358-0A0E-11EA-8FA5-49A33DDC885E last_name: Wirth orcid: 0000-0002-0519-4241 - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x apa: Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x chicago: Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x. ieee: M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 717–750, 2023. ista: Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750. mla: Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 717–50, doi:10.1007/s00023-022-01220-x. short: M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750. date_created: 2022-09-11T22:01:57Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-14T11:39:28Z day: '01' ddc: - '510' department: - _id: JaMa doi: 10.1007/s00023-022-01220-x ec_funded: 1 external_id: arxiv: - '2105.08303' isi: - '000837499800002' file: - access_level: open_access checksum: 8c7b185eba5ccd92ef55c120f654222c content_type: application/pdf creator: dernst date_created: 2023-08-14T11:38:28Z date_updated: 2023-08-14T11:38:28Z file_id: '14051' file_name: 2023_AnnalesHenriPoincare_Wirth.pdf file_size: 554871 relation: main_file success: 1 file_date_updated: 2023-08-14T11:38:28Z has_accepted_license: '1' intvolume: ' 24' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 717-750 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 - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Curvature-dimension conditions for symmetric quantum Markov semigroups 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: 24 year: '2023' ... --- _id: '9652' abstract: - lang: eng text: In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities. acknowledgement: 'This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.' article_processing_charge: No article_type: original author: - first_name: Michael full_name: Dymond, Michael last_name: Dymond - first_name: Vojtech full_name: Kaluza, Vojtech id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E last_name: Kaluza orcid: 0000-0002-2512-8698 citation: ama: Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. doi:10.1007/s11856-022-2448-6 apa: Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6 chicago: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6. ieee: M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023. ista: Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554. mla: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6. short: M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554. date_created: 2021-07-14T07:01:28Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-14T11:26:34Z day: '01' ddc: - '515' - '516' department: - _id: UlWa doi: 10.1007/s11856-022-2448-6 external_id: arxiv: - '1903.05923' isi: - '000904950300003' file: - access_level: open_access checksum: 6fa0a3207dd1d6467c309fd1bcc867d1 content_type: application/pdf creator: vkaluza date_created: 2021-07-14T07:41:50Z date_updated: 2021-07-14T07:41:50Z file_id: '9653' file_name: separated_nets.pdf file_size: 900422 relation: main_file file_date_updated: 2021-07-14T07:41:50Z has_accepted_license: '1' intvolume: ' 253' isi: 1 keyword: - Lipschitz - bilipschitz - bounded displacement - modulus of continuity - separated net - non-realisable density - Burago--Kleiner construction language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 501-554 publication: Israel Journal of Mathematics publication_identifier: eissn: - 1565-8511 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Highly irregular separated nets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 253 year: '2023' ... --- _id: '12113' abstract: - lang: eng text: The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices. acknowledgement: Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15). article_number: '156101' article_processing_charge: No article_type: original author: - first_name: Li full_name: Zhang, Li last_name: Zhang - first_name: Xingyu full_name: Liu, Xingyu last_name: Liu - first_name: Ting full_name: Wu, Ting last_name: Wu - first_name: Shengduo full_name: Xu, Shengduo id: 12ab8624-4c8a-11ec-9e11-e1ac2438f22f last_name: Xu - first_name: Guoquan full_name: Suo, Guoquan last_name: Suo - first_name: Xiaohui full_name: Ye, Xiaohui last_name: Ye - first_name: Xiaojiang full_name: Hou, Xiaojiang last_name: Hou - first_name: Yanling full_name: Yang, Yanling last_name: Yang - first_name: Qingfeng full_name: Liu, Qingfeng last_name: Liu - first_name: Hongqiang full_name: Wang, Hongqiang last_name: Wang citation: ama: Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 2023;613. doi:10.1016/j.apsusc.2022.156101 apa: Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101 chicago: Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101. ieee: L. Zhang et al., “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” Applied Surface Science, vol. 613. Elsevier, 2023. ista: Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101. mla: Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science, vol. 613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101. short: L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023). date_created: 2023-01-12T11:55:02Z date_published: 2023-03-15T00:00:00Z date_updated: 2023-08-14T11:47:06Z day: '15' department: - _id: MaIb doi: 10.1016/j.apsusc.2022.156101 external_id: isi: - '000911497000001' intvolume: ' 613' isi: 1 keyword: - Surfaces - Coatings and Films - Condensed Matter Physics - Surfaces and Interfaces - General Physics and Astronomy - General Chemistry language: - iso: eng month: '03' oa_version: None publication: Applied Surface Science publication_identifier: issn: - 0169-4332 publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 613 year: '2023' ... --- _id: '10173' abstract: - lang: eng text: We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods. acknowledgement: "I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\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: Nicolas full_name: Clozeau, Nicolas id: fea1b376-906f-11eb-847d-b2c0cf46455b last_name: Clozeau citation: ama: 'Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w' apa: 'Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w' chicago: 'Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization  for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-022-00254-w.' ieee: 'N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.' ista: 'Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378.' mla: 'Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization  for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w.' short: 'N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.' date_created: 2021-10-23T10:50:22Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-08-14T11:51:47Z day: '01' ddc: - '510' department: - _id: JuFi doi: 10.1007/s40072-022-00254-w external_id: arxiv: - '2102.07452' isi: - '000799715600001' file: - access_level: open_access checksum: f83dcaecdbd3ace862c4ed97a20e8501 content_type: application/pdf creator: dernst date_created: 2023-08-14T11:51:04Z date_updated: 2023-08-14T11:51:04Z file_id: '14052' file_name: 2023_StochPartialDiffEquations_Clozeau.pdf file_size: 1635193 relation: main_file success: 1 file_date_updated: 2023-08-14T11:51:04Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1254–1378 publication: 'Stochastics and Partial Differential Equations: Analysis and Computations' publication_identifier: issn: - 2194-0401 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields 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: '11741' abstract: - lang: eng text: Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble. acknowledgement: "The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\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: 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: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-022-01156-7 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer Nature, pp. 1183–1218, 2023. ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218. mla: Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:10.1007/s00440-022-01156-7. short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218. date_created: 2022-08-07T22:02:00Z date_published: 2023-04-01T00:00:00Z date_updated: 2023-08-14T12:48:09Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00440-022-01156-7 external_id: arxiv: - '2106.10200' isi: - '000830344500001' file: - access_level: open_access checksum: b9247827dae5544d1d19c37abe547abc content_type: application/pdf creator: dernst date_created: 2023-08-14T12:47:32Z date_updated: 2023-08-14T12:47:32Z file_id: '14054' file_name: 2023_ProbabilityTheory_Cipolloni.pdf file_size: 782278 relation: main_file success: 1 file_date_updated: 2023-08-14T12:47:32Z has_accepted_license: '1' intvolume: ' 185' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1183–1218 publication: Probability Theory and Related Fields publication_identifier: eissn: - 1432-2064 issn: - 0178-8051 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quenched universality for deformed 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: 185 year: '2023' ... --- _id: '12331' abstract: - lang: eng text: High carrier mobility is critical to improving thermoelectric performance over a broad temperature range. However, traditional doping inevitably deteriorates carrier mobility. Herein, we develop a strategy for fine tuning of defects to improve carrier mobility. To begin, n-type PbTe is created by compensating for the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering, resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is introduced to compensate for the remaining intrinsic Pb vacancies. We find that excess Ag exhibits a dynamic doping process with increasing temperatures, increasing both the carrier concentration and carrier mobility throughout a wide temperature range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier concentration suppresses the bipolar thermal conductivity at high temperatures. The final step is using iodine to optimize the carrier concentration to ∼1019 cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of ∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance carrier mobility and improve thermoelectric performance. acknowledgement: The National Key Research and Development Program of China (2018YFA0702100), the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Natural Science Foundation of China (51571007 and 51772012), the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian Science Fund (FWF). article_processing_charge: No article_type: original author: - first_name: Siqi full_name: Wang, Siqi last_name: Wang - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Shulin full_name: Bai, Shulin last_name: Bai - first_name: Bingchao full_name: Qin, Bingchao last_name: Qin - first_name: Yingcai full_name: Zhu, Yingcai last_name: Zhu - first_name: Shaoping full_name: Zhan, Shaoping last_name: Zhan - first_name: Junqing full_name: Zheng, Junqing last_name: Zheng - first_name: Shuwei full_name: Tang, Shuwei last_name: Tang - first_name: Li Dong full_name: Zhao, Li Dong last_name: Zhao citation: ama: Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542 apa: Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c03542 chicago: Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542. ieee: S. Wang et al., “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023. ista: Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763. mla: Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542. short: S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763. date_created: 2023-01-22T23:00:55Z date_published: 2023-01-24T00:00:00Z date_updated: 2023-08-14T12:57:44Z day: '24' ddc: - '540' department: - _id: MaIb doi: 10.1021/acs.chemmater.2c03542 external_id: isi: - '000914749700001' file: - access_level: open_access checksum: b21dca2aa7a80c068bc256bdd1fea9df content_type: application/pdf creator: dernst date_created: 2023-08-14T12:57:25Z date_updated: 2023-08-14T12:57:25Z file_id: '14055' file_name: 2023_ChemistryMaterials_Wang.pdf file_size: 2961043 relation: main_file success: 1 file_date_updated: 2023-08-14T12:57:25Z has_accepted_license: '1' intvolume: ' 35' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 755-763 project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications publication: Chemistry of Materials publication_identifier: eissn: - 1520-5002 issn: - 0897-4756 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe 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: 35 year: '2023' ... --- _id: '11999' abstract: - lang: eng text: 'A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.' acknowledgement: 'This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Alan M full_name: Arroyo Guevara, Alan M id: 3207FDC6-F248-11E8-B48F-1D18A9856A87 last_name: Arroyo Guevara orcid: 0000-0003-2401-8670 - first_name: Fabian full_name: Klute, Fabian last_name: Klute - first_name: Irene full_name: Parada, Irene last_name: Parada - first_name: Birgit full_name: Vogtenhuber, Birgit last_name: Vogtenhuber - first_name: Raimund full_name: Seidel, Raimund last_name: Seidel - first_name: Tilo full_name: Wiedera, Tilo last_name: Wiedera citation: ama: Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9 apa: Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9 chicago: Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9. ieee: A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023. ista: Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770. mla: Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9. short: A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770. date_created: 2022-08-28T22:02:01Z date_published: 2023-04-01T00:00:00Z date_updated: 2023-08-14T12:51:25Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1007/s00454-022-00394-9 ec_funded: 1 external_id: arxiv: - '1909.07347' isi: - '000840292800001' file: - access_level: open_access checksum: def7ae3b28d9fd6aec16450e40090302 content_type: application/pdf creator: alisjak date_created: 2022-08-29T11:23:15Z date_updated: 2022-08-29T11:23:15Z file_id: '12006' file_name: 2022_DiscreteandComputionalGeometry_Arroyo.pdf file_size: 1002218 relation: main_file success: 1 file_date_updated: 2022-08-29T11:23:15Z has_accepted_license: '1' intvolume: ' 69' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 745–770 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Inserting one edge into a simple drawing is hard 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: 69 year: '2023' ... --- _id: '12330' abstract: - lang: eng text: 'The design and implementation of efficient concurrent data structures has seen significant attention. However, most of this work has focused on concurrent data structures providing good worst-case guarantees, although, in real workloads, objects are often accessed at different rates. Efficient distribution-adaptive data structures, such as splay-trees, are known in the sequential case; however, they often are hard to translate efficiently to the concurrent case. We investigate distribution-adaptive concurrent data structures, and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements “move up,” whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations, while being amenable to efficient concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity for performance, and can outperform the only previously-known distribution-adaptive concurrent design in certain workloads.' article_processing_charge: No article_type: original author: - first_name: Vitalii full_name: Aksenov, Vitalii id: 2980135A-F248-11E8-B48F-1D18A9856A87 last_name: Aksenov - 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: Alexandra full_name: Drozdova, Alexandra last_name: Drozdova - first_name: Amirkeivan full_name: Mohtashami, Amirkeivan last_name: Mohtashami citation: ama: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x' apa: 'Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00441-x' chicago: 'Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.' ieee: 'V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” Distributed Computing, vol. 36. Springer Nature, pp. 395–418, 2023.' ista: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.' mla: 'Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 395–418, doi:10.1007/s00446-022-00441-x.' short: V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418. date_created: 2023-01-22T23:00:55Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-08-14T12:54:32Z day: '01' department: - _id: DaAl doi: 10.1007/s00446-022-00441-x external_id: arxiv: - '2008.01009' isi: - '000913424000001' intvolume: ' 36' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2008.01009 month: '09' oa: 1 oa_version: Preprint page: 395-418 publication: Distributed Computing publication_identifier: eissn: - 1432-0452 issn: - 0178-2770 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'The splay-list: A distribution-adaptive concurrent skip-list' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2023' ... --- _id: '12159' abstract: - lang: eng text: The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies. acknowledgement: 'We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793 apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793 chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793. ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023. ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457. mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793. short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457. date_created: 2023-01-12T12:09:17Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-16T08:18:47Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.16793 external_id: isi: - '000900762000001' pmid: - '36433653' file: - access_level: open_access checksum: b10e0f8fa3dc4d72aaf77a557200978a content_type: application/pdf creator: dernst date_created: 2023-08-16T08:15:41Z date_updated: 2023-08-16T08:15:41Z file_id: '14062' file_name: 2023_MolecularEcology_Shipilina.pdf file_size: 7144607 relation: main_file success: 1 file_date_updated: 2023-08-16T08:15:41Z has_accepted_license: '1' intvolume: ' 32' isi: 1 issue: '6' keyword: - Genetics - Ecology - Evolution - Behavior and Systematics language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1441-1457 pmid: 1 project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: The maintenance of alternative adaptive peaks in snapdragons - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: On the origin and structure of haplotype blocks 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: 32 year: '2023' ... --- _id: '12114' abstract: - lang: eng text: 'Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.' acknowledgement: The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”. article_number: '100079' article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Olga O. full_name: Lebedenko, Olga O. last_name: Lebedenko - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Nikolai R. full_name: Skrynnikov, Nikolai R. last_name: Skrynnikov - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079' apa: 'Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079' chicago: 'Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.' ieee: 'D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.' ista: 'Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.' mla: 'Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.' short: 'D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).' date_created: 2023-01-12T11:55:38Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-08-16T09:37:25Z day: '01' ddc: - '570' department: - _id: PaSc doi: 10.1016/j.yjsbx.2022.100079 external_id: pmid: - '36578472' file: - access_level: open_access checksum: b4b1c10a31018aafe053b7d55a470e54 content_type: application/pdf creator: dernst date_created: 2023-08-16T09:36:28Z date_updated: 2023-08-16T09:36:28Z file_id: '14064' file_name: 2023_JourStrucBiologyX_Gauto.pdf file_size: 5132322 relation: main_file success: 1 file_date_updated: 2023-08-16T09:36:28Z has_accepted_license: '1' intvolume: ' 7' keyword: - Structural Biology language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: 'Journal of Structural Biology: X' publication_identifier: issn: - 2590-1524 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD 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: 7 year: '2023' ... --- _id: '12163' abstract: - lang: eng text: Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time. acknowledgement: The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints. article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Albert full_name: Auer, Albert id: 3018E8C2-F248-11E8-B48F-1D18A9856A87 last_name: Auer orcid: 0000-0002-3580-2906 - first_name: Gabriel full_name: Brognara, Gabriel id: D96FFDA0-A884-11E9-9968-DC26E6697425 last_name: Brognara - first_name: Hanifatul R full_name: Budiman, Hanifatul R id: 55380f95-15b2-11ec-abd3-aff8e230696b last_name: Budiman - first_name: Lukasz M full_name: Kowalski, Lukasz M id: e3a512e2-4bbe-11eb-a68a-e3857a7844c2 last_name: Kowalski - first_name: Ivana full_name: Matijevic, Ivana id: 83c17ce3-15b2-11ec-abd3-f486545870bd last_name: Matijevic citation: ama: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540 apa: Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540 chicago: Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540. ieee: M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023. ista: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777. mla: Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540. short: M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777. date_created: 2023-01-12T12:09:58Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-16T08:32:29Z day: '01' ddc: - '570' department: - _id: MaLo doi: 10.1002/1873-3468.14540 external_id: isi: - '000891573000001' pmid: - '36448231' file: - access_level: open_access checksum: 7492244d3f9c5faa1347ef03f6e5bc84 content_type: application/pdf creator: dernst date_created: 2023-08-16T08:31:04Z date_updated: 2023-08-16T08:31:04Z file_id: '14063' file_name: 2023_FEBSLetters_Loose.pdf file_size: 3148143 relation: main_file success: 1 file_date_updated: 2023-08-16T08:31:04Z has_accepted_license: '1' intvolume: ' 597' isi: 1 issue: '6' keyword: - Cell Biology - Genetics - Molecular Biology - Biochemistry - Structural Biology - Biophysics language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 762-777 pmid: 1 publication: FEBS Letters publication_identifier: eissn: - 1873-3468 issn: - 0014-5793 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: In vitro reconstitution of small GTPase regulation 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: 597 year: '2023' ... --- _id: '12164' abstract: - lang: eng text: 'A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity.' acknowledgement: A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22). article_processing_charge: No article_type: original author: - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig - first_name: Danny full_name: Hendler, Danny last_name: Hendler - first_name: Alessia full_name: Milani, Alessia last_name: Milani - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5 apa: Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5 chicago: Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5. ieee: M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023. ista: Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43. mla: Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5. short: M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43. date_created: 2023-01-12T12:10:08Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-16T08:39:36Z day: '01' department: - _id: KrPi doi: 10.1007/s00446-022-00439-5 external_id: isi: - '000890138700001' intvolume: ' 36' isi: 1 keyword: - Computational Theory and Mathematics - Computer Networks and Communications - Hardware and Architecture - Theoretical Computer Science language: - iso: eng main_file_link: - open_access: '1' url: https://drops.dagstuhl.de/opus/volltexte/2019/11310/ month: '03' oa: 1 oa_version: Preprint page: 29-43 publication: Distributed Computing publication_identifier: eissn: - 1432-0452 issn: - 0178-2770 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Long-lived counters with polylogarithmic amortized step complexity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2023' ... --- _id: '12172' abstract: - lang: eng text: In industrial reactors and equipment, non-ideality is quite a common phenomenon rather than an exception. These deviations from ideality impact the process's overall efficiency and the effectiveness of the equipment. To recognize the associated non-ideality, one needs to have enough understanding of the formulation of the equations and in-depth knowledge of the residence time distribution (RTD) data of real reactors. In the current work, step input and pulse input were used to create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the aforementioned configuration, experiments were run at various flow rates to validate the developed characteristic equations. To produce RTD data, distilled water was utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior of tracer concentration exits age distribution, and cumulative fraction for each setup and each input was plotted and experimental results were compared with perfect behavior. Deviation of concentration exit age distribution and cumulative fractional distribution from ideal behavior is more in pulse input as compared to a step input. For ideal cases, the exit age distribution curve and cumulative fraction curves are independent of the type of input. But a significant difference was observed for the two cases, which may be due to non-measurable fluctuations in volumetric flow rate, non-achievement of instant injection of tracer in case of pulse input, and slight variations in the sampling period. Further, with increasing flow rate, concentration, exit age, and cumulative fractional curves shifted upward, and this behavior matches with the actual case. article_processing_charge: No article_type: original author: - first_name: Bushra full_name: Khatoon, Bushra last_name: Khatoon - first_name: Shoaib full_name: Kamil, Shoaib id: 185a19af-dc7d-11ea-9b2f-8eb2201959e9 last_name: Kamil - first_name: Hitesh full_name: Babu, Hitesh last_name: Babu - first_name: M. full_name: Siraj Alam, M. last_name: Siraj Alam citation: ama: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part 1):40-47. doi:10.1016/j.matpr.2022.11.037' apa: 'Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037' chicago: 'Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings. Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.' ieee: 'B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings, vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.' ista: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part 1), 40–47.' mla: 'Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier, 2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.' short: 'B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings 78 (2023) 40–47.' date_created: 2023-01-12T12:11:26Z date_published: 2023-03-20T00:00:00Z date_updated: 2023-08-16T09:08:11Z day: '20' department: - _id: BjHo doi: 10.1016/j.matpr.2022.11.037 intvolume: ' 78' issue: Part 1 keyword: - General Medicine language: - iso: eng month: '03' oa_version: None page: 40-47 publication: 'Materials Today: Proceedings' publication_identifier: issn: - 2214-7853 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Experimental analysis of Cascade CSTRs with step and pulse inputs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 78 year: '2023' ... --- _id: '12515' abstract: - lang: eng text: "Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues." acknowledgement: This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study. article_number: '1097467' article_processing_charge: No article_type: original author: - first_name: Irene full_name: Ortiz-Leal, Irene last_name: Ortiz-Leal - first_name: Mateo V. full_name: Torres, Mateo V. last_name: Torres - first_name: Victor M full_name: Vargas Barroso, Victor M id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87 last_name: Vargas Barroso - first_name: Luis Eusebio full_name: Fidalgo, Luis Eusebio last_name: Fidalgo - first_name: Ana María full_name: López-Beceiro, Ana María last_name: López-Beceiro - first_name: Jorge A. full_name: Larriva-Sahd, Jorge A. last_name: Larriva-Sahd - first_name: Pablo full_name: Sánchez-Quinteiro, Pablo last_name: Sánchez-Quinteiro citation: ama: Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467 apa: Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467 chicago: Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers, 2023. https://doi.org/10.3389/fnana.2022.1097467. ieee: I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2023. ista: Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467. mla: Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467. short: I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023). date_created: 2023-02-05T23:01:00Z date_published: 2023-01-10T00:00:00Z date_updated: 2023-08-16T11:37:52Z day: '10' ddc: - '570' department: - _id: PeJo doi: 10.3389/fnana.2022.1097467 external_id: isi: - '000919786900001' pmid: - '36704406' file: - access_level: open_access checksum: 49cd40f3bda6f267079427042e7d15e3 content_type: application/pdf creator: dernst date_created: 2023-02-06T07:56:14Z date_updated: 2023-02-06T07:56:14Z file_id: '12518' file_name: 2022_FrontiersNeuroanatomy_OrtizLeal.pdf file_size: 21943473 relation: main_file success: 1 file_date_updated: 2023-02-06T07:56:14Z has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Neuroanatomy publication_identifier: eissn: - 1662-5129 publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway 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: 16 year: '2023' ... --- _id: '12106' abstract: - lang: eng text: Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells. acknowledgement: We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society. article_processing_charge: No article_type: original author: - first_name: Jake full_name: Yeung, Jake id: 123012b2-db30-11eb-b4d8-a35840c0551b last_name: Yeung orcid: 0000-0003-1732-1559 - first_name: Maria full_name: Florescu, Maria last_name: Florescu - first_name: Peter full_name: Zeller, Peter last_name: Zeller - first_name: Buys Anton full_name: De Barbanson, Buys Anton last_name: De Barbanson - first_name: Max D. full_name: Wellenstein, Max D. last_name: Wellenstein - first_name: Alexander full_name: Van Oudenaarden, Alexander last_name: Van Oudenaarden citation: ama: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3 apa: Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3 chicago: Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3. ieee: J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023. ista: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823. mla: Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3. short: J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823. date_created: 2023-01-08T23:00:53Z date_published: 2023-06-01T00:00:00Z date_updated: 2023-08-16T11:32:33Z day: '01' ddc: - '570' department: - _id: ScienComp doi: 10.1038/s41587-022-01560-3 external_id: isi: - '000909067600003' file: - access_level: open_access checksum: 668447a1c8d360b68f8aaf9e08ed644f content_type: application/pdf creator: dernst date_created: 2023-08-16T11:30:45Z date_updated: 2023-08-16T11:30:45Z file_id: '14066' file_name: 2023_NatureBioTech_Yeung.pdf file_size: 12040976 relation: main_file success: 1 file_date_updated: 2023-08-16T11:30:45Z has_accepted_license: '1' intvolume: ' 41' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 813–823 publication: Nature Biotechnology publication_identifier: eissn: - 1546-1696 issn: - 1087-0156 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: scChIX-seq infers dynamic relationships between histone modifications in single 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: 41 year: '2023' ... --- _id: '12183' abstract: - lang: eng text: We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit. acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. article_processing_charge: No article_type: original author: - first_name: Chiara full_name: Boccato, Chiara id: 342E7E22-F248-11E8-B48F-1D18A9856A87 last_name: Boccato - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3 apa: Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3 chicago: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3. ieee: C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560, 2023. ista: Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560. mla: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3. short: C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560. date_created: 2023-01-15T23:00:52Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-08-16T11:34:03Z day: '01' department: - _id: RoSe doi: 10.1007/s00023-022-01252-3 ec_funded: 1 external_id: arxiv: - '2205.15284' isi: - '000910751800002' intvolume: ' 24' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2205.15284 month: '05' oa: 1 oa_version: Preprint page: 1505-1560 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The Bose Gas in a box with Neumann boundary conditions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2023' ... --- _id: '12544' abstract: - lang: eng text: Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software. acknowledgement: "P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access is funded by the Austrian Science Fund (FWF)." article_processing_charge: No article_type: original author: - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346 apa: Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. American Chemical Society. https://doi.org/10.1021/acs.jcim.2c01346 chicago: Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling. American Chemical Society, 2023. https://doi.org/10.1021/acs.jcim.2c01346. ieee: P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023. ista: Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985. mla: Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:10.1021/acs.jcim.2c01346. short: P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985. date_created: 2023-02-12T23:00:59Z date_published: 2023-02-13T00:00:00Z date_updated: 2023-08-16T12:22:07Z day: '13' ddc: - '510' - '540' department: - _id: HeEd doi: 10.1021/acs.jcim.2c01346 ec_funded: 1 external_id: isi: - '000920370700001' pmid: - '36638318' file: - access_level: open_access checksum: 7d20562269edff1e31b9d6019d4983b0 content_type: application/pdf creator: dernst date_created: 2023-08-16T12:21:13Z date_updated: 2023-08-16T12:21:13Z file_id: '14070' file_name: 2023_JCIM_Koehl.pdf file_size: 8069223 relation: main_file success: 1 file_date_updated: 2023-08-16T12:21:13Z has_accepted_license: '1' intvolume: ' 63' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 973-985 pmid: 1 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: Journal of Chemical Information and Modeling publication_identifier: eissn: - 1549-960X issn: - 1549-9596 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives 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: 63 year: '2023' ... --- _id: '12543' abstract: - lang: eng text: Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts. acknowledged_ssus: - _id: LifeSc acknowledgement: We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C. article_processing_charge: No article_type: original author: - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Michaela full_name: Hönigsberger, Michaela id: 953894f3-25bd-11ec-8556-f70a9d38ef60 last_name: Hönigsberger - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Florian full_name: Wiesenhofer, Florian id: 39523C54-F248-11E8-B48F-1D18A9856A87 last_name: Wiesenhofer - first_name: Niklas full_name: Kampleitner, Niklas id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87 last_name: Kampleitner - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Thomas full_name: Schmitt, Thomas last_name: Schmitt - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6 apa: Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6 chicago: Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6. ieee: M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023. ista: Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460. mla: Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6. short: M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460. date_created: 2023-02-12T23:00:59Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-16T11:55:48Z day: '01' ddc: - '570' department: - _id: SyCr - _id: LifeSc - _id: JiFr doi: 10.1038/s41559-023-01981-6 ec_funded: 1 external_id: isi: - '000924572800001' pmid: - '36732670' file: - access_level: open_access checksum: 8244f4650a0e7aeea488d1bcd4a31702 content_type: application/pdf creator: dernst date_created: 2023-08-16T11:54:59Z date_updated: 2023-08-16T11:54:59Z file_id: '14069' file_name: 2023_NatureEcoEvo_Stock.pdf file_size: 1600499 relation: main_file success: 1 file_date_updated: 2023-08-16T11:54:59Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 450-460 pmid: 1 project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution publication: Nature Ecology and Evolution publication_identifier: eissn: - 2397-334X publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/ scopus_import: '1' status: public title: Pathogen evasion of social immunity 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: 7 year: '2023' ... --- _id: '12521' abstract: - lang: eng text: Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated. acknowledgement: We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117). article_number: qrac004 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004' apa: 'Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004' chicago: 'Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.' ieee: 'A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.' ista: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.' mla: 'Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.' short: A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023). date_created: 2023-02-06T13:59:12Z date_published: 2023-02-01T00:00:00Z date_updated: 2023-08-16T11:44:32Z day: '01' ddc: - '570' department: - _id: GradSch - _id: BeVi doi: 10.1093/evlett/qrac004 ec_funded: 1 external_id: isi: - '001021692200001' pmid: - '37065438' file: - access_level: open_access checksum: a240a041cb9b9b7c8ba93a4706674a3f content_type: application/pdf creator: dernst date_created: 2023-08-16T11:43:33Z date_updated: 2023-08-16T11:43:33Z file_id: '14068' file_name: 2023_EvLetters_Mrnjavac.pdf file_size: 2592189 relation: main_file success: 1 file_date_updated: 2023-08-16T11:43:33Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '1' keyword: - Genetics - Ecology - Evolution - Behavior and Systematics language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Evolution Letters publication_identifier: issn: - 2056-3744 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution' 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: 7 year: '2023' ...