--- _id: '7231' abstract: - lang: eng text: Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature. alternative_title: - LNCS article_processing_charge: No author: - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Yu full_name: Jiang, Yu last_name: Jiang - 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: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8' apa: 'Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8' chicago: Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8. ieee: H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141. ista: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.' mla: Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8. short: H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141. conference: end_date: 2019-08-29 location: Amsterdam, The Netherlands name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2019-08-27 date_created: 2020-01-05T23:00:47Z date_published: 2019-08-13T00:00:00Z date_updated: 2023-09-06T14:55:15Z day: '13' department: - _id: ToHe doi: 10.1007/978-3-030-29662-9_8 external_id: arxiv: - '1907.11514' isi: - '000611677700008' intvolume: ' 11750' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.11514 month: '08' oa: 1 oa_version: Preprint page: 123-141 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 17th International Conference on Formal Modeling and Analysis of Timed Systems publication_identifier: eissn: - 1611-3349 isbn: - 978-3-0302-9661-2 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11750 year: '2019' ... --- _id: '7340' abstract: - lang: eng text: Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling. acknowledgement: We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments. article_number: e50793 article_processing_charge: No article_type: original author: - first_name: Niko Paresh full_name: Amin-Wetzel, Niko Paresh id: E95D3014-9D8C-11E9-9C80-D2F8E5697425 last_name: Amin-Wetzel - first_name: Lisa full_name: Neidhardt, Lisa last_name: Neidhardt - first_name: Yahui full_name: Yan, Yahui last_name: Yan - first_name: Matthias P. full_name: Mayer, Matthias P. last_name: Mayer - first_name: David full_name: Ron, David last_name: Ron citation: ama: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793 apa: Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793 chicago: Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793. ieee: N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793. mla: Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793. short: N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019). date_created: 2020-01-19T23:00:39Z date_published: 2019-12-24T00:00:00Z date_updated: 2023-09-06T14:58:02Z day: '24' ddc: - '570' department: - _id: MaDe doi: 10.7554/eLife.50793 external_id: isi: - '000512303700001' pmid: - '31873072' file: - access_level: open_access checksum: 29fcbcd8c1fc7f11a596ed7f14ea1c82 content_type: application/pdf creator: dernst date_created: 2020-11-19T11:37:41Z date_updated: 2020-11-19T11:37:41Z file_id: '8777' file_name: 2019_eLife_AminWetzel.pdf file_size: 4817384 relation: main_file success: 1 file_date_updated: 2020-11-19T11:37:41Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2019' ... --- _id: '7422' abstract: - lang: eng text: Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions. article_number: '054108' article_processing_charge: No article_type: original author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Joris full_name: Paijmans, Joris last_name: Paijmans - first_name: Laurens full_name: Bossen, Laurens last_name: Bossen - first_name: Thomas full_name: Miedema, Thomas last_name: Miedema - first_name: Martijn full_name: Wehrens, Martijn last_name: Wehrens - first_name: Nils B. full_name: Becker, Nils B. last_name: Becker - first_name: Kazunari full_name: Kaizu, Kazunari last_name: Kaizu - first_name: Koichi full_name: Takahashi, Koichi last_name: Takahashi - first_name: Marileen full_name: Dogterom, Marileen last_name: Dogterom - first_name: Pieter Rein full_name: ten Wolde, Pieter Rein last_name: ten Wolde citation: ama: Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867 apa: Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867 chicago: Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867. ieee: T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019. ista: Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108. mla: Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867. short: T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019). date_created: 2020-01-30T10:34:36Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-09-06T14:59:28Z day: '07' department: - _id: GaTk doi: 10.1063/1.5064867 external_id: arxiv: - '1708.09364' isi: - '000458109300009' intvolume: ' 150' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.09364 month: '02' oa: 1 oa_version: Preprint publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' status: public title: eGFRD in all dimensions type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 150 year: '2019' ... --- _id: '7230' abstract: - lang: eng text: Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G. alternative_title: - LNCS article_processing_charge: No 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: Martin full_name: Derka, Martin last_name: Derka - first_name: Irene full_name: Parada, Irene last_name: Parada citation: ama: 'Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18' apa: 'Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18' chicago: Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18. ieee: A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243. ista: 'Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.' mla: Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18. short: A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243. conference: end_date: 2019-09-20 location: Prague, Czech Republic name: 'GD: Graph Drawing and Network Visualization' start_date: 2019-09-17 date_created: 2020-01-05T23:00:47Z date_published: 2019-11-28T00:00:00Z date_updated: 2023-09-06T14:56:00Z day: '28' department: - _id: UlWa doi: 10.1007/978-3-030-35802-0_18 ec_funded: 1 external_id: arxiv: - '1908.08129' isi: - '000612918800018' intvolume: ' 11904' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.08129 month: '11' oa: 1 oa_version: Preprint page: 230-243 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 27th International Symposium on Graph Drawing and Network Visualization publication_identifier: eissn: - 1611-3349 isbn: - 978-3-0303-5801-3 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Extending simple drawings type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11904 year: '2019' ... --- _id: '7420' abstract: - lang: eng text: β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic. article_number: jcs233387 article_processing_charge: No article_type: original author: - first_name: Pranshu full_name: Sahgal, Pranshu last_name: Sahgal - first_name: Jonna H full_name: Alanko, Jonna H id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87 last_name: Alanko orcid: 0000-0002-7698-3061 - first_name: Jaroslav full_name: Icha, Jaroslav last_name: Icha - first_name: Ilkka full_name: Paatero, Ilkka last_name: Paatero - first_name: Hellyeh full_name: Hamidi, Hellyeh last_name: Hamidi - first_name: Antti full_name: Arjonen, Antti last_name: Arjonen - first_name: Mika full_name: Pietilä, Mika last_name: Pietilä - first_name: Anne full_name: Rokka, Anne last_name: Rokka - first_name: Johanna full_name: Ivaska, Johanna last_name: Ivaska citation: ama: Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387 apa: Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387 chicago: Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387. ieee: P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019. ista: Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387. mla: Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387. short: P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019). date_created: 2020-01-30T10:31:42Z date_published: 2019-06-07T00:00:00Z date_updated: 2023-09-06T15:01:00Z day: '07' department: - _id: MiSi doi: 10.1242/jcs.233387 external_id: isi: - '000473327900017' pmid: - '31076515' intvolume: ' 132' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1242/jcs.233387 month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' status: public title: GGA2 and RAB13 promote activity-dependent β1-integrin recycling type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 132 year: '2019' ... --- _id: '7423' abstract: - lang: eng text: 'We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors.' article_processing_charge: No article_type: original author: - first_name: Gernot full_name: Akemann, Gernot last_name: Akemann - first_name: Tomasz full_name: Checinski, Tomasz last_name: Checinski - first_name: Dangzheng full_name: Liu, Dangzheng id: 2F947E34-F248-11E8-B48F-1D18A9856A87 last_name: Liu - first_name: Eugene full_name: Strahov, Eugene last_name: Strahov citation: ama: 'Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479. doi:10.1214/18-aihp888' apa: 'Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888' chicago: 'Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.' ieee: 'G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.' ista: 'Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.' mla: 'Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.' short: G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479. date_created: 2020-01-30T10:36:50Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-09-06T14:58:39Z day: '01' department: - _id: LaEr doi: 10.1214/18-aihp888 external_id: arxiv: - '1704.05224' isi: - '000456070200013' intvolume: ' 55' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.05224 month: '02' oa: 1 oa_version: Preprint page: 441-479 publication: Annales de l'Institut Henri Poincaré, Probabilités et Statistiques publication_identifier: issn: - 0246-0203 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' status: public title: 'Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 55 year: '2019' ... --- _id: '7411' abstract: - lang: eng text: "Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.\r\nThe fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at)." alternative_title: - LNCS article_processing_charge: No author: - first_name: Hamza M full_name: Abusalah, Hamza M id: 40297222-F248-11E8-B48F-1D18A9856A87 last_name: Abusalah - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michael full_name: Walter, Michael id: 488F98B0-F248-11E8-B48F-1D18A9856A87 last_name: Walter orcid: 0000-0003-3186-2482 citation: ama: 'Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible proofs of sequential work. In: Advances in Cryptology – EUROCRYPT 2019. Vol 11477. Springer International Publishing; 2019:277-291. doi:10.1007/978-3-030-17656-3_10' apa: 'Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2019). Reversible proofs of sequential work. In Advances in Cryptology – EUROCRYPT 2019 (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International Publishing. https://doi.org/10.1007/978-3-030-17656-3_10' chicago: Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “Reversible Proofs of Sequential Work.” In Advances in Cryptology – EUROCRYPT 2019, 11477:277–91. Springer International Publishing, 2019. https://doi.org/10.1007/978-3-030-17656-3_10. ieee: H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “Reversible proofs of sequential work,” in Advances in Cryptology – EUROCRYPT 2019, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291. ista: Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291. mla: Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” Advances in Cryptology – EUROCRYPT 2019, vol. 11477, Springer International Publishing, 2019, pp. 277–91, doi:10.1007/978-3-030-17656-3_10. short: H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019, pp. 277–291. conference: end_date: 2019-05-23 location: Darmstadt, Germany name: International Conference on the Theory and Applications of Cryptographic Techniques start_date: 2019-05-19 date_created: 2020-01-30T09:26:14Z date_published: 2019-04-24T00:00:00Z date_updated: 2023-09-06T15:26:06Z day: '24' department: - _id: KrPi doi: 10.1007/978-3-030-17656-3_10 ec_funded: 1 external_id: isi: - '000483516200010' intvolume: ' 11477' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/252 month: '04' oa: 1 oa_version: Submitted Version page: 277-291 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Advances in Cryptology – EUROCRYPT 2019 publication_identifier: eissn: - 1611-3349 isbn: - '9783030176556' - '9783030176563' issn: - 0302-9743 publication_status: published publisher: Springer International Publishing quality_controlled: '1' scopus_import: '1' status: public title: Reversible proofs of sequential work type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11477 year: '2019' ... --- _id: '7437' abstract: - lang: eng text: 'Most of today''s distributed machine learning systems assume reliable networks: whenever two machines exchange information (e.g., gradients or models), the network should guarantee the delivery of the message. At the same time, recent work exhibits the impressive tolerance of machine learning algorithms to errors or noise arising from relaxed communication or synchronization. In this paper, we connect these two trends, and consider the following question: Can we design machine learning systems that are tolerant to network unreliability during training? With this motivation, we focus on a theoretical problem of independent interest-given a standard distributed parameter server architecture, if every communication between the worker and the server has a non-zero probability p of being dropped, does there exist an algorithm that still converges, and at what speed? The technical contribution of this paper is a novel theoretical analysis proving that distributed learning over unreliable network can achieve comparable convergence rate to centralized or distributed learning over reliable networks. Further, we prove that the influence of the packet drop rate diminishes with the growth of the number of parameter servers. We map this theoretical result onto a real-world scenario, training deep neural networks over an unreliable network layer, and conduct network simulation to validate the system improvement by allowing the networks to be unreliable.' article_processing_charge: No author: - first_name: Chen full_name: Yu, Chen last_name: Yu - first_name: Hanlin full_name: Tang, Hanlin last_name: Tang - first_name: Cedric full_name: Renggli, Cedric last_name: Renggli - first_name: Simon full_name: Kassing, Simon last_name: Kassing - first_name: Ankit full_name: Singla, Ankit last_name: Singla - 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: Ce full_name: Zhang, Ce last_name: Zhang - first_name: Ji full_name: Liu, Ji last_name: Liu citation: ama: 'Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks. In: 36th International Conference on Machine Learning, ICML 2019. Vol 2019-June. IMLS; 2019:12481-12512.' apa: 'Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., … Liu, J. (2019). Distributed learning over unreliable networks. In 36th International Conference on Machine Learning, ICML 2019 (Vol. 2019–June, pp. 12481–12512). Long Beach, CA, United States: IMLS.' chicago: Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.” In 36th International Conference on Machine Learning, ICML 2019, 2019–June:12481–512. IMLS, 2019. ieee: C. Yu et al., “Distributed learning over unreliable networks,” in 36th International Conference on Machine Learning, ICML 2019, Long Beach, CA, United States, 2019, vol. 2019–June, pp. 12481–12512. ista: 'Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu J. 2019. Distributed learning over unreliable networks. 36th International Conference on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning vol. 2019–June, 12481–12512.' mla: Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” 36th International Conference on Machine Learning, ICML 2019, vol. 2019–June, IMLS, 2019, pp. 12481–512. short: C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang, J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS, 2019, pp. 12481–12512. conference: end_date: 2019-06-15 location: Long Beach, CA, United States name: 'ICML: International Conference on Machine Learning' start_date: 2019-06-10 date_created: 2020-02-02T23:01:06Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-06T15:21:48Z day: '01' department: - _id: DaAl external_id: arxiv: - '1810.07766' isi: - '000684034307036' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.07766 month: '06' oa: 1 oa_version: Preprint page: 12481-12512 publication: 36th International Conference on Machine Learning, ICML 2019 publication_identifier: isbn: - '9781510886988' publication_status: published publisher: IMLS quality_controlled: '1' scopus_import: '1' status: public title: Distributed learning over unreliable networks type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2019-June year: '2019' ... --- _id: '7412' abstract: - lang: eng text: We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These algorithms search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby state that addresses the violation, while (we hope) not introducing many new violations. An important class of focused local search algorithms with provable performance guarantees has recently arisen from algorithmizations of the Lovász local lemma (LLL), a nonconstructive tool for proving the existence of satisfying states by introducing a background measure on the state space. While powerful, the state transitions of algorithms in this class must be, in a precise sense, perfectly compatible with the background measure. In many applications this is a very restrictive requirement, and one needs to step outside the class. Here we introduce the notion of measure distortion and develop a framework for analyzing arbitrary focused stochastic local search algorithms, recovering LLL algorithmizations as the special case of no distortion. Our framework takes as input an arbitrary algorithm of such type and an arbitrary probability measure and shows how to use the measure as a yardstick of algorithmic progress, even for algorithms designed independently of the measure. article_processing_charge: No article_type: original author: - first_name: Dimitris full_name: Achlioptas, Dimitris last_name: Achlioptas - first_name: Fotis full_name: Iliopoulos, Fotis last_name: Iliopoulos - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Achlioptas D, Iliopoulos F, Kolmogorov V. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 2019;48(5):1583-1602. doi:10.1137/16m109332x apa: Achlioptas, D., Iliopoulos, F., & Kolmogorov, V. (2019). A local lemma for focused stochastical algorithms. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16m109332x chicago: Achlioptas, Dimitris, Fotis Iliopoulos, and Vladimir Kolmogorov. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing. SIAM, 2019. https://doi.org/10.1137/16m109332x. ieee: D. Achlioptas, F. Iliopoulos, and V. Kolmogorov, “A local lemma for focused stochastical algorithms,” SIAM Journal on Computing, vol. 48, no. 5. SIAM, pp. 1583–1602, 2019. ista: Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602. mla: Achlioptas, Dimitris, et al. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing, vol. 48, no. 5, SIAM, 2019, pp. 1583–602, doi:10.1137/16m109332x. short: D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 1583–1602. date_created: 2020-01-30T09:27:32Z date_published: 2019-10-31T00:00:00Z date_updated: 2023-09-06T15:25:29Z day: '31' department: - _id: VlKo doi: 10.1137/16m109332x ec_funded: 1 external_id: arxiv: - '1809.01537' isi: - '000493900200005' intvolume: ' 48' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.01537 month: '10' oa: 1 oa_version: Preprint page: 1583-1602 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: SIAM quality_controlled: '1' scopus_import: '1' status: public title: A local lemma for focused stochastical algorithms type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 48 year: '2019' ... --- _id: '7413' abstract: - lang: eng text: We consider Bose gases consisting of N particles trapped in a box with volume one and interacting through a repulsive potential with scattering length of order N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s predictions. 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: Christian full_name: Brennecke, Christian last_name: Brennecke - first_name: Serena full_name: Cenatiempo, Serena last_name: Cenatiempo - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein citation: ama: Boccato C, Brennecke C, Cenatiempo S, Schlein B. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 2019;222(2):219-335. doi:10.4310/acta.2019.v222.n2.a1 apa: Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2019). Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. International Press of Boston. https://doi.org/10.4310/acta.2019.v222.n2.a1 chicago: Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica. International Press of Boston, 2019. https://doi.org/10.4310/acta.2019.v222.n2.a1. ieee: C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Bogoliubov theory in the Gross–Pitaevskii limit,” Acta Mathematica, vol. 222, no. 2. International Press of Boston, pp. 219–335, 2019. ista: Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335. mla: Boccato, Chiara, et al. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica, vol. 222, no. 2, International Press of Boston, 2019, pp. 219–335, doi:10.4310/acta.2019.v222.n2.a1. short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Acta Mathematica 222 (2019) 219–335. date_created: 2020-01-30T09:30:41Z date_published: 2019-06-07T00:00:00Z date_updated: 2023-09-06T15:24:31Z day: '07' department: - _id: RoSe doi: 10.4310/acta.2019.v222.n2.a1 external_id: arxiv: - '1801.01389' isi: - '000495865300001' intvolume: ' 222' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.01389 month: '06' oa: 1 oa_version: Preprint page: 219-335 publication: Acta Mathematica publication_identifier: eissn: - 1871-2509 issn: - 0001-5962 publication_status: published publisher: International Press of Boston quality_controlled: '1' scopus_import: '1' status: public title: Bogoliubov theory in the Gross–Pitaevskii limit type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 222 year: '2019' ... --- _id: '7393' abstract: - lang: eng text: The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow. article_number: eaav9963 article_processing_charge: No article_type: original author: - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Tomas full_name: Larsson, Tomas last_name: Larsson - first_name: Marina full_name: Panova, Marina last_name: Panova - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963' apa: 'Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963' chicago: 'Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.' ieee: 'H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.' ista: 'Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.' mla: 'Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.' short: H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019). date_created: 2020-01-29T15:58:27Z date_published: 2019-12-04T00:00:00Z date_updated: 2023-09-06T15:35:56Z day: '04' ddc: - '570' department: - _id: NiBa doi: 10.1126/sciadv.aav9963 ec_funded: 1 external_id: isi: - '000505069600008' pmid: - '31840052' file: - access_level: open_access checksum: af99a5dcdc66c6d6102051faf3be48d8 content_type: application/pdf creator: dernst date_created: 2020-02-03T13:33:25Z date_updated: 2020-07-14T12:47:57Z file_id: '7442' file_name: 2019_ScienceAdvances_Morales.pdf file_size: 1869449 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: AAAS quality_controlled: '1' scopus_import: '1' status: public title: 'Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 5 year: '2019' ... --- _id: '7397' abstract: - lang: eng text: Polymer additives can substantially reduce the drag of turbulent flows and the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal, i.e. inde-pendent of the type of polymer and solvent used. Until recently, the consensus was that,in this limit, flows are in a marginal state where only a minimal level of turbulence activ-ity persists. Observations in direct numerical simulations using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg number (Wi), turbulence expresses long periods of hibernation if the domainsize is small. However, with increasing pipe length, the temporal hibernation continuouslyalters to spatio-temporal intermittency and here the flow consists of turbulent puffs sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully relaminarises,in agreement with recent experiments. At even larger Wi, a different instability is en-countered causing a drag increase towards MDR. Our findings hence link earlier minimalflow unit simulations with recent experiments and confirm that the addition of polymersinitially suppresses Newtonian turbulence and leads to a reverse transition. The MDRstate on the other hand results from a separate instability and the underlying dynamicscorresponds to the recently proposed state of elasto-inertial-turbulence (EIT). article_processing_charge: No article_type: original author: - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: George H full_name: Choueiri, George H id: 448BD5BC-F248-11E8-B48F-1D18A9856A87 last_name: Choueiri - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486 apa: Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486 chicago: Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486. ieee: J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019. ista: Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 874, 699–719. mla: Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics, vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486. short: J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719. date_created: 2020-01-29T16:05:19Z date_published: 2019-09-10T00:00:00Z date_updated: 2023-09-06T15:36:36Z day: '10' department: - _id: BjHo doi: 10.1017/jfm.2019.486 external_id: arxiv: - '1808.04080' isi: - '000475349900001' intvolume: ' 874' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.04080 month: '09' oa: 1 oa_version: Preprint page: 699-719 publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: CUP quality_controlled: '1' scopus_import: '1' status: public title: Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 874 year: '2019' ... --- _id: '5678' abstract: - lang: eng text: "The order-k Voronoi tessellation of a locally finite set \U0001D44B⊆ℝ\U0001D45B decomposes ℝ\U0001D45B into convex domains whose points have the same k nearest neighbors in X. Assuming X is a stationary Poisson point process, we give explicit formulas for the expected number and total area of faces of a given dimension per unit volume of space. We also develop a relaxed version of discrete Morse theory and generalize by counting only faces, for which the k nearest points in X are within a given distance threshold." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Edelsbrunner H, Nikitenko A. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 2019;62(4):865–878. doi:10.1007/s00454-018-0049-2 apa: Edelsbrunner, H., & Nikitenko, A. (2019). Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. Springer. https://doi.org/10.1007/s00454-018-0049-2 chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry. Springer, 2019. https://doi.org/10.1007/s00454-018-0049-2. ieee: H. Edelsbrunner and A. Nikitenko, “Poisson–Delaunay Mosaics of Order k,” Discrete and Computational Geometry, vol. 62, no. 4. Springer, pp. 865–878, 2019. ista: Edelsbrunner H, Nikitenko A. 2019. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 62(4), 865–878. mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry, vol. 62, no. 4, Springer, 2019, pp. 865–878, doi:10.1007/s00454-018-0049-2. short: H. Edelsbrunner, A. Nikitenko, Discrete and Computational Geometry 62 (2019) 865–878. date_created: 2018-12-16T22:59:20Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-07T12:07:12Z day: '01' ddc: - '516' department: - _id: HeEd doi: 10.1007/s00454-018-0049-2 ec_funded: 1 external_id: arxiv: - '1709.09380' isi: - '000494042900008' file: - access_level: open_access checksum: f9d00e166efaccb5a76bbcbb4dcea3b4 content_type: application/pdf creator: dernst date_created: 2019-02-06T10:10:46Z date_updated: 2020-07-14T12:47:10Z file_id: '5932' file_name: 2018_DiscreteCompGeometry_Edelsbrunner.pdf file_size: 599339 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 62' isi: 1 issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 865–878 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Discrete and Computational Geometry publication_identifier: eissn: - '14320444' issn: - '01795376' publication_status: published publisher: Springer quality_controlled: '1' related_material: record: - id: '6287' relation: dissertation_contains status: public scopus_import: '1' status: public title: Poisson–Delaunay Mosaics of Order k 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: 62 year: '2019' ... --- _id: '5828' abstract: - lang: eng text: Hippocampus is needed for both spatial working and reference memories. Here, using a radial eight-arm maze, we examined how the combined demand on these memories influenced CA1 place cell assemblies while reference memories were partially updated. This was contrasted with control tasks requiring only working memory or the update of reference memory. Reference memory update led to the reward-directed place field shifts at newly rewarded arms and to the gradual strengthening of firing in passes between newly rewarded arms but not between those passes that included a familiar-rewarded arm. At the maze center, transient network synchronization periods preferentially replayed trajectories of the next chosen arm in reference memory tasks but the previously visited arm in the working memory task. Hence, reference memory demand was uniquely associated with a gradual, goal novelty-related reorganization of place cell assemblies and with trajectory replay that reflected the animal's decision of which arm to visit next. article_processing_charge: No article_type: original author: - first_name: Haibing full_name: Xu, Haibing id: 310349D0-F248-11E8-B48F-1D18A9856A87 last_name: Xu - first_name: Peter full_name: Baracskay, Peter id: 361CC00E-F248-11E8-B48F-1D18A9856A87 last_name: Baracskay - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Xu H, Baracskay P, O’Neill J, Csicsvari JL. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 2019;101(1):119-132.e4. doi:10.1016/j.neuron.2018.11.015 apa: Xu, H., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.11.015 chicago: Xu, Haibing, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2018.11.015. ieee: H. Xu, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze,” Neuron, vol. 101, no. 1. Elsevier, p. 119–132.e4, 2019. ista: Xu H, Baracskay P, O’Neill J, Csicsvari JL. 2019. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 101(1), 119–132.e4. mla: Xu, Haibing, et al. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron, vol. 101, no. 1, Elsevier, 2019, p. 119–132.e4, doi:10.1016/j.neuron.2018.11.015. short: H. Xu, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 101 (2019) 119–132.e4. date_created: 2019-01-13T22:59:10Z date_published: 2019-01-02T00:00:00Z date_updated: 2023-09-07T12:06:37Z day: '02' department: - _id: JoCs doi: 10.1016/j.neuron.2018.11.015 ec_funded: 1 external_id: isi: - '000454791500014' intvolume: ' 101' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.1016/j.neuron.2018.11.015 month: '01' oa: 1 oa_version: Published Version page: 119-132.e4 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex publication: Neuron publication_identifier: issn: - '10974199' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/reading-rats-minds/ record: - id: '837' relation: dissertation_contains status: public scopus_import: '1' status: public title: Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 101 year: '2019' ... --- _id: '5856' abstract: - lang: eng text: We give a bound on the ground-state energy of a system of N non-interacting fermions in a three-dimensional cubic box interacting with an impurity particle via point interactions. We show that the change in energy compared to the system in the absence of the impurity is bounded in terms of the gas density and the scattering length of the interaction, independently of N. Our bound holds as long as the ratio of the mass of the impurity to the one of the gas particles is larger than a critical value m∗ ∗≈ 0.36 , which is the same regime for which we recently showed stability of the system. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Moser T, Seiringer R. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 2019;20(4):1325–1365. doi:10.1007/s00023-018-00757-0 apa: Moser, T., & Seiringer, R. (2019). Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-00757-0 chicago: Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare. Springer, 2019. https://doi.org/10.1007/s00023-018-00757-0. ieee: T. Moser and R. Seiringer, “Energy contribution of a point-interacting impurity in a Fermi gas,” Annales Henri Poincare, vol. 20, no. 4. Springer, pp. 1325–1365, 2019. ista: Moser T, Seiringer R. 2019. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 20(4), 1325–1365. mla: Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare, vol. 20, no. 4, Springer, 2019, pp. 1325–1365, doi:10.1007/s00023-018-00757-0. short: T. Moser, R. Seiringer, Annales Henri Poincare 20 (2019) 1325–1365. date_created: 2019-01-20T22:59:17Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-09-07T12:37:42Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00023-018-00757-0 ec_funded: 1 external_id: arxiv: - '1807.00739' isi: - '000462444300008' file: - access_level: open_access checksum: 255e42f957a8e2b10aad2499c750a8d6 content_type: application/pdf creator: dernst date_created: 2019-01-28T15:27:17Z date_updated: 2020-07-14T12:47:12Z file_id: '5894' file_name: 2019_Annales_Moser.pdf file_size: 859846 relation: main_file file_date_updated: 2020-07-14T12:47:12Z has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1325–1365 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Annales Henri Poincare publication_identifier: issn: - '14240637' publication_status: published publisher: Springer quality_controlled: '1' related_material: record: - id: '52' relation: dissertation_contains status: public scopus_import: '1' status: public title: Energy contribution of a point-interacting impurity in a Fermi gas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '6957' abstract: - lang: eng text: "In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable. The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent. In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.\r\n\r\nThe aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest. \r\n\r\nWhile the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different. \r\n\r\nIn shear flows, turbulence at onset is transient in nature. \ Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Chaitanya S full_name: Paranjape, Chaitanya S id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87 last_name: Paranjape citation: ama: Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:10.15479/AT:ISTA:6957 apa: Paranjape, C. S. (2019). Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6957 chicago: Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6957. ieee: C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute of Science and Technology Austria, 2019. ista: Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria. mla: Paranjape, Chaitanya S. Onset of Turbulence in Plane Poiseuille Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6957. short: C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of Science and Technology Austria, 2019. date_created: 2019-10-22T12:08:43Z date_published: 2019-10-24T00:00:00Z date_updated: 2023-09-07T12:53:25Z day: '24' ddc: - '532' degree_awarded: PhD department: - _id: BjHo doi: 10.15479/AT:ISTA:6957 file: - access_level: closed checksum: 7ba298ba0ce7e1d11691af6b8eaf0a0a content_type: application/zip creator: cparanjape date_created: 2019-10-23T09:54:43Z date_updated: 2020-07-14T12:47:46Z file_id: '6962' file_name: Chaitanya_Paranjape_source_files_tex_figures.zip file_size: 45828099 relation: source_file - access_level: open_access checksum: 642697618314e31ac31392da7909c2d9 content_type: application/pdf creator: cparanjape date_created: 2019-10-23T10:37:09Z date_updated: 2020-07-14T12:47:46Z file_id: '6963' file_name: Chaitanya_Paranjape_Thesis.pdf file_size: 19504197 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' keyword: - Instabilities - Turbulence - Nonlinear dynamics language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '138' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Onset of turbulence in plane Poiseuille flow type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '6182' abstract: - lang: eng text: "We consider large random matrices with a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent away from the spectral edges, generalizing the recent result of Ajanki et al. [‘Stability of the matrix Dyson equation and random matrices with correlations’, Probab. Theory Related Fields 173(1–2) (2019), 293–373] to allow slow correlation decay and arbitrary expectation. The main novel tool is\r\na systematic diagrammatic control of a multivariate cumulant expansion." article_number: e8 article_processing_charge: No article_type: original author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - 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: Erdös L, Krüger TH, Schröder DJ. Random matrices with slow correlation decay. Forum of Mathematics, Sigma. 2019;7. doi:10.1017/fms.2019.2 apa: Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Random matrices with slow correlation decay. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2019.2 chicago: Erdös, László, Torben H Krüger, and Dominik J Schröder. “Random Matrices with Slow Correlation Decay.” Forum of Mathematics, Sigma. Cambridge University Press, 2019. https://doi.org/10.1017/fms.2019.2. ieee: L. Erdös, T. H. Krüger, and D. J. Schröder, “Random matrices with slow correlation decay,” Forum of Mathematics, Sigma, vol. 7. Cambridge University Press, 2019. ista: Erdös L, Krüger TH, Schröder DJ. 2019. Random matrices with slow correlation decay. Forum of Mathematics, Sigma. 7, e8. mla: Erdös, László, et al. “Random Matrices with Slow Correlation Decay.” Forum of Mathematics, Sigma, vol. 7, e8, Cambridge University Press, 2019, doi:10.1017/fms.2019.2. short: L. Erdös, T.H. Krüger, D.J. Schröder, Forum of Mathematics, Sigma 7 (2019). date_created: 2019-03-28T09:05:23Z date_published: 2019-03-26T00:00:00Z date_updated: 2023-09-07T12:54:12Z day: '26' ddc: - '510' department: - _id: LaEr doi: 10.1017/fms.2019.2 ec_funded: 1 external_id: arxiv: - '1705.10661' isi: - '000488847100001' file: - access_level: open_access checksum: 933a472568221c73b2c3ce8c87bf6d15 content_type: application/pdf creator: dernst date_created: 2019-09-17T14:24:13Z date_updated: 2020-07-14T12:47:22Z file_id: '6883' file_name: 2019_Forum_Erdoes.pdf file_size: 1520344 relation: main_file file_date_updated: 2020-07-14T12:47:22Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Forum of Mathematics, Sigma publication_identifier: eissn: - '20505094' publication_status: published publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '6179' relation: dissertation_contains status: public scopus_import: '1' status: public title: Random matrices with slow correlation decay 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: 7 year: '2019' ... --- _id: '6186' abstract: - lang: eng text: "We prove that the local eigenvalue statistics of real symmetric Wigner-type\r\nmatrices near the cusp points of the eigenvalue density are universal. Together\r\nwith the companion paper [arXiv:1809.03971], which proves the same result for\r\nthe complex Hermitian symmetry class, this completes the last remaining case of\r\nthe Wigner-Dyson-Mehta universality conjecture after bulk and edge\r\nuniversalities have been established in the last years. We extend the recent\r\nDyson Brownian motion analysis at the edge [arXiv:1712.03881] to the cusp\r\nregime using the optimal local law from [arXiv:1809.03971] and the accurate\r\nlocal shape analysis of the density from [arXiv:1506.05095, arXiv:1804.07752].\r\nWe also present a PDE-based method to improve the estimate on eigenvalue\r\nrigidity via the maximum principle of the heat flow related to the Dyson\r\nBrownian motion." article_processing_charge: No 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: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - 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, Krüger TH, Schröder DJ. Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . 2019;1(4):615–707. doi:10.2140/paa.2019.1.615' apa: 'Cipolloni, G., Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . MSP. https://doi.org/10.2140/paa.2019.1.615' chicago: 'Cipolloni, Giorgio, László Erdös, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” Pure and Applied Analysis . MSP, 2019. https://doi.org/10.2140/paa.2019.1.615.' ieee: 'G. Cipolloni, L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices, II: The real symmetric case,” Pure and Applied Analysis , vol. 1, no. 4. MSP, pp. 615–707, 2019.' ista: 'Cipolloni G, Erdös L, Krüger TH, Schröder DJ. 2019. Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . 1(4), 615–707.' mla: 'Cipolloni, Giorgio, et al. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” Pure and Applied Analysis , vol. 1, no. 4, MSP, 2019, pp. 615–707, doi:10.2140/paa.2019.1.615.' short: G. Cipolloni, L. Erdös, T.H. Krüger, D.J. Schröder, Pure and Applied Analysis 1 (2019) 615–707. date_created: 2019-03-28T10:21:17Z date_published: 2019-10-12T00:00:00Z date_updated: 2023-09-07T12:54:12Z day: '12' department: - _id: LaEr doi: 10.2140/paa.2019.1.615 ec_funded: 1 external_id: arxiv: - '1811.04055' intvolume: ' 1' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.04055 month: '10' oa: 1 oa_version: Preprint page: 615–707 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: 'Pure and Applied Analysis ' publication_identifier: eissn: - 2578-5885 issn: - 2578-5893 publication_status: published publisher: MSP quality_controlled: '1' related_material: record: - id: '6179' relation: dissertation_contains status: public status: public title: 'Cusp universality for random matrices, II: The real symmetric case' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2019' ... --- _id: '6900' abstract: - lang: eng text: Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks. article_processing_charge: No author: - first_name: Sarah A full_name: Cepeda Humerez, Sarah A id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87 last_name: Cepeda Humerez - first_name: Jakob full_name: Ruess, Jakob last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290 apa: Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information in time-varying signals. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007290 chicago: Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007290. ieee: S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” PLoS computational biology, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019. ista: Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290. mla: Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290. short: S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290. date_created: 2019-09-22T22:00:37Z date_published: 2019-09-03T00:00:00Z date_updated: 2023-09-07T12:55:21Z day: '03' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007290 external_id: isi: - '000489741800021' pmid: - '31479447' file: - access_level: open_access checksum: 81bdce1361c9aa8395d6fa635fb6ab47 content_type: application/pdf creator: kschuh date_created: 2019-10-01T10:53:45Z date_updated: 2020-07-14T12:47:44Z file_id: '6925' file_name: 2019_PLoS_Cepeda-Humerez.pdf file_size: 3081855 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: e1007290 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: PLoS computational biology publication_identifier: eissn: - '15537358' publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '6473' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Estimating information in time-varying signals 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: '2019' ... --- _id: '7186' abstract: - lang: eng text: "Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: EM-Fac - _id: SSU alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 citation: ama: Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:10.15479/AT:ISTA:7186 apa: Schwayer, C. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7186 chicago: Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7186. ieee: C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019. ista: Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria. mla: Schwayer, Cornelia. Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7186. short: C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019. date_created: 2019-12-16T14:26:14Z date_published: 2019-12-16T00:00:00Z date_updated: 2023-09-07T12:56:42Z day: '16' ddc: - '570' degree_awarded: PhD department: - _id: CaHe doi: 10.15479/AT:ISTA:7186 file: - access_level: closed checksum: 585583c1c875c5d9525703a539668a7c content_type: application/zip creator: cschwayer date_created: 2019-12-19T15:18:11Z date_updated: 2020-07-14T12:47:52Z file_id: '7194' file_name: DocumentSourceFiles.zip file_size: 19431292 relation: source_file - access_level: open_access checksum: 9b9b24351514948d27cec659e632e2cd content_type: application/pdf creator: cschwayer date_created: 2019-12-19T15:19:21Z date_updated: 2020-07-14T12:47:52Z file_id: '7195' file_name: Thesis_CS_final.pdf file_size: 19226428 relation: main_file file_date_updated: 2020-07-14T12:47:52Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '107' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1096' relation: dissertation_contains status: public - id: '7001' relation: part_of_dissertation status: public status: public supervisor: - 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 title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '6681' abstract: - lang: eng text: "The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stephan Y full_name: Zhechev, Stephan Y id: 3AA52972-F248-11E8-B48F-1D18A9856A87 last_name: Zhechev citation: ama: Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:10.15479/AT:ISTA:6681 apa: Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681 chicago: Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681. ieee: S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019. ista: Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria. mla: Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681. short: S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019. date_created: 2019-07-26T11:14:34Z date_published: 2019-08-08T00:00:00Z date_updated: 2023-09-07T13:10:36Z day: '08' ddc: - '514' degree_awarded: PhD department: - _id: UlWa doi: 10.15479/AT:ISTA:6681 file: - access_level: open_access checksum: 3231e7cbfca3b5687366f84f0a57a0c0 content_type: application/pdf creator: szhechev date_created: 2019-08-07T13:02:50Z date_updated: 2020-07-14T12:47:37Z file_id: '6771' file_name: Stephan_Zhechev_thesis.pdf file_size: 1464227 relation: main_file - access_level: closed checksum: 85d65eb27b4377a9e332ee37a70f08b6 content_type: application/octet-stream creator: szhechev date_created: 2019-08-07T13:03:22Z date_updated: 2020-07-14T12:47:37Z file_id: '6772' file_name: Stephan_Zhechev_thesis.tex file_size: 303988 relation: source_file - access_level: closed checksum: 86b374d264ca2dd53e712728e253ee75 content_type: application/zip creator: szhechev date_created: 2019-08-07T13:03:34Z date_updated: 2020-07-14T12:47:37Z file_id: '6773' file_name: supplementary_material.zip file_size: 1087004 relation: supplementary_material file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '104' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6774' relation: part_of_dissertation status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: Algorithmic aspects of homotopy theory and embeddability tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '8182' abstract: - lang: eng text: "Suppose that $n\\neq p^k$ and $n\\neq 2p^k$ for all $k$ and all primes $p$. We prove that for any Hausdorff compactum $X$ with a free action of the symmetric group $\\mathfrak S_n$ there exists an $\\mathfrak S_n$-equivariant map $X \\to\r\n{\\mathbb R}^n$ whose image avoids the diagonal $\\{(x,x\\dots,x)\\in {\\mathbb R}^n|x\\in {\\mathbb R}\\}$.\r\n Previously, the special cases of this statement for certain $X$ were usually proved using the equivartiant obstruction theory. Such calculations are difficult and may become infeasible past the first (primary) obstruction. We\r\ntake a different approach which allows us to prove the vanishing of all obstructions simultaneously. The essential step in the proof is classifying the possible degrees of $\\mathfrak S_n$-equivariant maps from the boundary\r\n$\\partial\\Delta^{n-1}$ of $(n-1)$-simplex to itself. Existence of equivariant maps between spaces is important for many questions arising from discrete mathematics and geometry, such as Kneser's conjecture, the Square Peg conjecture, the Splitting Necklace problem, and the Topological Tverberg conjecture, etc. We demonstrate the utility of our result applying it to one such question, a specific instance of envy-free division problem." article_number: '1910.12628' article_processing_charge: No author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Sergey full_name: Kudrya, Sergey id: ecf01965-d252-11ea-95a5-8ada5f6c6a67 last_name: Kudrya citation: ama: Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv. apa: Avvakumov, S., & Kudrya, S. (n.d.). Vanishing of all equivariant obstructions and the mapping degree. arXiv. arXiv. chicago: Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv. arXiv, n.d. ieee: S. Avvakumov and S. Kudrya, “Vanishing of all equivariant obstructions and the mapping degree,” arXiv. arXiv. ista: Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv, 1910.12628. mla: Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv, 1910.12628, arXiv. short: S. Avvakumov, S. Kudrya, ArXiv (n.d.). date_created: 2020-07-30T10:45:08Z date_published: 2019-10-28T00:00:00Z date_updated: 2023-09-07T13:12:17Z day: '28' department: - _id: UlWa external_id: arxiv: - '1910.12628' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.12628 month: '10' oa: 1 oa_version: Preprint project: - _id: 26611F5C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31312 name: Algorithms for Embeddings and Homotopy Theory publication: arXiv publication_status: submitted publisher: arXiv related_material: record: - id: '11446' relation: later_version status: public - id: '8156' relation: dissertation_contains status: public status: public title: Vanishing of all equivariant obstructions and the mapping degree type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8185' abstract: - lang: eng text: "In this paper we study envy-free division problems. The classical approach to some of such problems, used by David Gale, reduces to considering continuous maps of a simplex to itself and finding sufficient conditions when this map hits the center of the simplex. The mere continuity is not sufficient for such a conclusion, the usual assumption (for example, in the Knaster--Kuratowski--Mazurkiewicz and the Gale theorem) is a certain boundary condition.\r\n We follow Erel Segal-Halevi, Fr\\'ed\\'eric Meunier, and Shira Zerbib, and replace the boundary condition by another assumption, which has the economic meaning of possibility for a player to prefer an empty part in the segment\r\npartition problem. We solve the problem positively when $n$, the number of players that divide the segment, is a prime power, and we provide counterexamples for every $n$ which is not a prime power. We also provide counterexamples relevant to a wider class of fair or envy-free partition problems when $n$ is odd and not a prime power." article_number: '1907.11183' article_processing_charge: No author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Roman full_name: Karasev, Roman last_name: Karasev citation: ama: Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv. doi:10.48550/arXiv.1907.11183 apa: Avvakumov, S., & Karasev, R. (n.d.). Envy-free division using mapping degree. arXiv. https://doi.org/10.48550/arXiv.1907.11183 chicago: Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1907.11183. ieee: S. Avvakumov and R. Karasev, “Envy-free division using mapping degree,” arXiv. . ista: Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv, 1907.11183. mla: Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” ArXiv, 1907.11183, doi:10.48550/arXiv.1907.11183. short: S. Avvakumov, R. Karasev, ArXiv (n.d.). date_created: 2020-07-30T10:45:51Z date_published: 2019-07-25T00:00:00Z date_updated: 2023-09-07T13:12:17Z day: '25' department: - _id: UlWa doi: 10.48550/arXiv.1907.11183 external_id: arxiv: - '1907.11183' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.11183 month: '07' oa: 1 oa_version: Preprint project: - _id: 26611F5C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31312 name: Algorithms for Embeddings and Homotopy Theory publication: arXiv publication_status: submitted related_material: link: - relation: later_version url: https://doi.org/10.1112/mtk.12059 record: - id: '8156' relation: dissertation_contains status: public status: public title: Envy-free division using mapping degree type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7524' abstract: - lang: eng text: "We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$ and inverse temperature $\\beta$ differs from the one of the non-interacting system by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$. Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ = \\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho \\ll 1$ and if $\\beta \\rho \\gtrsim 1$." article_processing_charge: No author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Simon full_name: Mayer, Simon id: 30C4630A-F248-11E8-B48F-1D18A9856A87 last_name: Mayer - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:191003372. apa: Deuchert, A., Mayer, S., & Seiringer, R. (n.d.). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372. ArXiv. chicago: Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” ArXiv:1910.03372. ArXiv, n.d. ieee: A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” arXiv:1910.03372. ArXiv. ista: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372, . mla: Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” ArXiv:1910.03372, ArXiv. short: A. Deuchert, S. Mayer, R. Seiringer, ArXiv:1910.03372 (n.d.). date_created: 2020-02-26T08:46:40Z date_published: 2019-10-08T00:00:00Z date_updated: 2023-09-07T13:12:41Z day: '08' department: - _id: RoSe ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.03372 month: '10' oa: 1 oa_version: Preprint page: '61' project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: arXiv:1910.03372 publication_status: draft publisher: ArXiv related_material: record: - id: '7790' relation: later_version status: public - id: '7514' relation: dissertation_contains status: public scopus_import: 1 status: public title: The free energy of the two-dimensional dilute Bose gas. I. Lower bound type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6608' abstract: - lang: eng text: We use the canonical bases produced by the tri-partition algorithm in (Edelsbrunner and Ölsböck, 2018) to open and close holes in a polyhedral complex, K. In a concrete application, we consider the Delaunay mosaic of a finite set, we let K be an Alpha complex, and we use the persistence diagram of the distance function to guide the hole opening and closing operations. The dependences between the holes define a partial order on the cells in K that characterizes what can and what cannot be constructed using the operations. The relations in this partial order reveal structural information about the underlying filtration of complexes beyond what is expressed by the persistence diagram. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Katharina full_name: Ölsböck, Katharina id: 4D4AA390-F248-11E8-B48F-1D18A9856A87 last_name: Ölsböck orcid: 0000-0002-4672-8297 citation: ama: Edelsbrunner H, Ölsböck K. Holes and dependences in an ordered complex. Computer Aided Geometric Design. 2019;73:1-15. doi:10.1016/j.cagd.2019.06.003 apa: Edelsbrunner, H., & Ölsböck, K. (2019). Holes and dependences in an ordered complex. Computer Aided Geometric Design. Elsevier. https://doi.org/10.1016/j.cagd.2019.06.003 chicago: Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in an Ordered Complex.” Computer Aided Geometric Design. Elsevier, 2019. https://doi.org/10.1016/j.cagd.2019.06.003. ieee: H. Edelsbrunner and K. Ölsböck, “Holes and dependences in an ordered complex,” Computer Aided Geometric Design, vol. 73. Elsevier, pp. 1–15, 2019. ista: Edelsbrunner H, Ölsböck K. 2019. Holes and dependences in an ordered complex. Computer Aided Geometric Design. 73, 1–15. mla: Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in an Ordered Complex.” Computer Aided Geometric Design, vol. 73, Elsevier, 2019, pp. 1–15, doi:10.1016/j.cagd.2019.06.003. short: H. Edelsbrunner, K. Ölsböck, Computer Aided Geometric Design 73 (2019) 1–15. date_created: 2019-07-07T21:59:20Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-09-07T13:15:29Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.cagd.2019.06.003 ec_funded: 1 external_id: isi: - '000485207800001' file: - access_level: open_access checksum: 7c99be505dc7533257d42eb1830cef04 content_type: application/pdf creator: kschuh date_created: 2019-07-08T15:24:26Z date_updated: 2020-07-14T12:47:34Z file_id: '6624' file_name: Elsevier_2019_Edelsbrunner.pdf file_size: 2665013 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 73' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 1-15 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Computer Aided Geometric Design publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '7460' relation: dissertation_contains status: public scopus_import: '1' status: public title: Holes and dependences in an ordered complex 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: 73 year: '2019' ... --- _id: '6677' abstract: - lang: eng text: "The Fiat-Shamir heuristic transforms a public-coin interactive proof into a non-interactive argument, by replacing the verifier with a cryptographic hash function that is applied to the protocol’s transcript. Constructing hash functions for which this transformation is sound is a central and long-standing open question in cryptography.\r\n\r\nWe show that solving the END−OF−METERED−LINE problem is no easier than breaking the soundness of the Fiat-Shamir transformation when applied to the sumcheck protocol. In particular, if the transformed protocol is sound, then any hard problem in #P gives rise to a hard distribution in the class CLS, which is contained in PPAD. Our result opens up the possibility of sampling moderately-sized games for which it is hard to find a Nash equilibrium, by reducing the inversion of appropriately chosen one-way functions to #SAT.\r\n\r\nOur main technical contribution is a stateful incrementally verifiable procedure that, given a SAT instance over n variables, counts the number of satisfying assignments. This is accomplished via an exponential sequence of small steps, each computable in time poly(n). Incremental verifiability means that each intermediate state includes a sumcheck-based proof of its correctness, and the proof can be updated and verified in time poly(n)." article_processing_charge: No author: - first_name: Arka Rai full_name: Choudhuri, Arka Rai last_name: Choudhuri - first_name: Pavel full_name: Hubáček, Pavel last_name: Hubáček - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Alon full_name: Rosen, Alon last_name: Rosen - first_name: Guy N. full_name: Rothblum, Guy N. last_name: Rothblum citation: ama: 'Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum GN. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019. ACM Press; 2019:1103-1114. doi:10.1145/3313276.3316400' apa: 'Choudhuri, A. R., Hubáček, P., Kamath Hosdurg, C., Pietrzak, K. Z., Rosen, A., & Rothblum, G. N. (2019). Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019 (pp. 1103–1114). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316400' chicago: Choudhuri, Arka Rai, Pavel Hubáček, Chethan Kamath Hosdurg, Krzysztof Z Pietrzak, Alon Rosen, and Guy N. Rothblum. “Finding a Nash Equilibrium Is No Easier than Breaking Fiat-Shamir.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019, 1103–14. ACM Press, 2019. https://doi.org/10.1145/3313276.3316400. ieee: A. R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K. Z. Pietrzak, A. Rosen, and G. N. Rothblum, “Finding a Nash equilibrium is no easier than breaking Fiat-Shamir,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019, Phoenix, AZ, United States, 2019, pp. 1103–1114. ista: 'Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum GN. 2019. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019. STOC: Symposium on Theory of Computing, 1103–1114.' mla: Choudhuri, Arka Rai, et al. “Finding a Nash Equilibrium Is No Easier than Breaking Fiat-Shamir.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019, ACM Press, 2019, pp. 1103–14, doi:10.1145/3313276.3316400. short: A.R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K.Z. Pietrzak, A. Rosen, G.N. Rothblum, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019, ACM Press, 2019, pp. 1103–1114. conference: end_date: 2019-06-26 location: Phoenix, AZ, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2019-06-23 date_created: 2019-07-24T09:20:53Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T13:15:55Z day: '01' department: - _id: KrPi doi: 10.1145/3313276.3316400 ec_funded: 1 external_id: isi: - '000523199100100' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/549 month: '06' oa: 1 oa_version: Preprint page: 1103-1114 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019 publication_identifier: isbn: - '9781450367059' publication_status: published publisher: ACM Press quality_controlled: '1' related_material: record: - id: '7896' relation: dissertation_contains status: public scopus_import: '1' status: public title: Finding a Nash equilibrium is no easier than breaking Fiat-Shamir type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '5986' abstract: - lang: eng text: "Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm (with \U0001D442(\U0001D45B8) being a crude bound on the run-time) to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of \U0001D442(\U0001D45B7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Anna full_name: Lubiw, Anna last_name: Lubiw - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. 2019;61(4):880-898. doi:10.1007/s00454-018-0035-8 apa: Lubiw, A., Masárová, Z., & Wagner, U. (2019). A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-018-0035-8 chicago: Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” Discrete & Computational Geometry. Springer Nature, 2019. https://doi.org/10.1007/s00454-018-0035-8. ieee: A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge-labelled triangulations,” Discrete & Computational Geometry, vol. 61, no. 4. Springer Nature, pp. 880–898, 2019. ista: Lubiw A, Masárová Z, Wagner U. 2019. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. 61(4), 880–898. mla: Lubiw, Anna, et al. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” Discrete & Computational Geometry, vol. 61, no. 4, Springer Nature, 2019, pp. 880–98, doi:10.1007/s00454-018-0035-8. short: A. Lubiw, Z. Masárová, U. Wagner, Discrete & Computational Geometry 61 (2019) 880–898. date_created: 2019-02-14T11:54:08Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T13:17:36Z day: '01' ddc: - '000' department: - _id: UlWa doi: 10.1007/s00454-018-0035-8 external_id: arxiv: - '1710.02741' isi: - '000466130000009' file: - access_level: open_access checksum: e1bff88f1d77001b53b78c485ce048d7 content_type: application/pdf creator: dernst date_created: 2019-02-14T11:57:22Z date_updated: 2020-07-14T12:47:14Z file_id: '5988' file_name: 2018_DiscreteGeometry_Lubiw.pdf file_size: 556276 relation: main_file file_date_updated: 2020-07-14T12:47:14Z has_accepted_license: '1' intvolume: ' 61' isi: 1 issue: '4' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 880-898 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '683' relation: earlier_version status: public - id: '7944' relation: dissertation_contains status: public scopus_import: '1' status: public title: A proof of the orbit conjecture for flipping edge-labelled triangulations 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 61 year: '2019' ... --- _id: '5886' abstract: - lang: eng text: Problems involving quantum impurities, in which one or a few particles are interacting with a macroscopic environment, represent a pervasive paradigm, spanning across atomic, molecular, and condensed-matter physics. In this paper we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron–a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon–a quasiparticle formed out of a rotating molecule in a bosonic bath. We benchmark these approaches against established theories, evaluating their accuracy as a function of the impurity-bath coupling. article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - 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 citation: ama: 'Li X, Bighin G, Yakaboylu E, Lemeshko M. Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics. 2019. doi:10.1080/00268976.2019.1567852' apa: 'Li, X., Bighin, G., Yakaboylu, E., & Lemeshko, M. (2019). Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics. Taylor and Francis. https://doi.org/10.1080/00268976.2019.1567852' chicago: 'Li, Xiang, Giacomo Bighin, Enderalp Yakaboylu, and Mikhail Lemeshko. “Variational Approaches to Quantum Impurities: From the Fröhlich Polaron to the Angulon.” Molecular Physics. Taylor and Francis, 2019. https://doi.org/10.1080/00268976.2019.1567852.' ieee: 'X. Li, G. Bighin, E. Yakaboylu, and M. Lemeshko, “Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon,” Molecular Physics. Taylor and Francis, 2019.' ista: 'Li X, Bighin G, Yakaboylu E, Lemeshko M. 2019. Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics.' mla: 'Li, Xiang, et al. “Variational Approaches to Quantum Impurities: From the Fröhlich Polaron to the Angulon.” Molecular Physics, Taylor and Francis, 2019, doi:10.1080/00268976.2019.1567852.' short: X. Li, G. Bighin, E. Yakaboylu, M. Lemeshko, Molecular Physics (2019). date_created: 2019-01-27T22:59:10Z date_published: 2019-01-18T00:00:00Z date_updated: 2023-09-07T13:16:42Z day: '18' ddc: - '530' department: - _id: MiLe doi: 10.1080/00268976.2019.1567852 ec_funded: 1 external_id: isi: - '000474641400008' file: - access_level: open_access checksum: 178964744b636a6f036372f4f090a657 content_type: application/pdf creator: dernst date_created: 2019-01-29T08:32:57Z date_updated: 2020-07-14T12:47:13Z file_id: '5896' file_name: 2019_MolecularPhysics_Li.pdf file_size: 1309966 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Molecular Physics publication_identifier: issn: - '00268976' publication_status: published publisher: Taylor and Francis quality_controlled: '1' related_material: record: - id: '8958' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon' 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: '2019' ... --- _id: '6556' abstract: - lang: eng text: 'Motivated by fixed-parameter tractable (FPT) problems in computational topology, we consider the treewidth tw(M) of a compact, connected 3-manifold M, defined to be the minimum treewidth of the face pairing graph of any triangulation T of M. In this setting the relationship between the topology of a 3-manifold and its treewidth is of particular interest. First, as a corollary of work of Jaco and Rubinstein, we prove that for any closed, orientable 3-manifold M the treewidth tw(M) is at most 4g(M)-2, where g(M) denotes Heegaard genus of M. In combination with our earlier work with Wagner, this yields that for non-Haken manifolds the Heegaard genus and the treewidth are within a constant factor. Second, we characterize all 3-manifolds of treewidth one: These are precisely the lens spaces and a single other Seifert fibered space. Furthermore, we show that all remaining orientable Seifert fibered spaces over the 2-sphere or a non-orientable surface have treewidth two. In particular, for every spherical 3-manifold we exhibit a triangulation of treewidth at most two. Our results further validate the parameter of treewidth (and other related parameters such as cutwidth or congestion) to be useful for topological computing, and also shed more light on the scope of existing FPT-algorithms in the field.' alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Kristóf full_name: Huszár, Kristóf id: 33C26278-F248-11E8-B48F-1D18A9856A87 last_name: Huszár orcid: 0000-0002-5445-5057 - first_name: Jonathan full_name: Spreer, Jonathan last_name: Spreer citation: ama: 'Huszár K, Spreer J. 3-manifold triangulations with small treewidth. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:44:1-44:20. doi:10.4230/LIPIcs.SoCG.2019.44' apa: 'Huszár, K., & Spreer, J. (2019). 3-manifold triangulations with small treewidth. In 35th International Symposium on Computational Geometry (Vol. 129, p. 44:1-44:20). Portland, Oregon, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2019.44' chicago: Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” In 35th International Symposium on Computational Geometry, 129:44:1-44:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPIcs.SoCG.2019.44. ieee: K. Huszár and J. Spreer, “3-manifold triangulations with small treewidth,” in 35th International Symposium on Computational Geometry, Portland, Oregon, United States, 2019, vol. 129, p. 44:1-44:20. ista: 'Huszár K, Spreer J. 2019. 3-manifold triangulations with small treewidth. 35th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 44:1-44:20.' mla: Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20, doi:10.4230/LIPIcs.SoCG.2019.44. short: K. Huszár, J. Spreer, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20. conference: end_date: 2019-06-21 location: Portland, Oregon, United States name: 'SoCG: Symposium on Computational Geometry' start_date: 2019-06-18 date_created: 2019-06-11T20:09:57Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T13:18:26Z day: '01' ddc: - '516' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2019.44 external_id: arxiv: - '1812.05528' file: - access_level: open_access checksum: 29d18c435368468aa85823dabb157e43 content_type: application/pdf creator: kschuh date_created: 2019-06-12T06:45:33Z date_updated: 2020-07-14T12:47:33Z file_id: '6557' file_name: 2019_LIPIcs-Huszar.pdf file_size: 905885 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 129' keyword: - computational 3-manifold topology - fixed-parameter tractability - layered triangulations - structural graph theory - treewidth - cutwidth - Heegaard genus language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 44:1-44:20 publication: 35th International Symposium on Computational Geometry publication_identifier: isbn: - 978-3-95977-104-7 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '8032' relation: part_of_dissertation status: public scopus_import: '1' status: public title: 3-manifold triangulations with small treewidth tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2019' ... --- _id: '7093' abstract: - lang: eng text: "In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.\r\nIn view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).\r\nWe derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1))." article_processing_charge: No article_type: original author: - first_name: Kristóf full_name: Huszár, Kristóf id: 33C26278-F248-11E8-B48F-1D18A9856A87 last_name: Huszár orcid: 0000-0002-5445-5057 - first_name: Jonathan full_name: Spreer, Jonathan last_name: Spreer - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 2019;10(2):70–98. doi:10.20382/JOGC.V10I2A5 apa: Huszár, K., Spreer, J., & Wagner, U. (2019). On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. Computational Geometry Laborartoy. https://doi.org/10.20382/JOGC.V10I2A5 chicago: Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry. Computational Geometry Laborartoy, 2019. https://doi.org/10.20382/JOGC.V10I2A5. ieee: K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” Journal of Computational Geometry, vol. 10, no. 2. Computational Geometry Laborartoy, pp. 70–98, 2019. ista: Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 10(2), 70–98. mla: Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry, vol. 10, no. 2, Computational Geometry Laborartoy, 2019, pp. 70–98, doi:10.20382/JOGC.V10I2A5. short: K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019) 70–98. date_created: 2019-11-23T12:14:09Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-09-07T13:18:26Z day: '01' ddc: - '514' department: - _id: UlWa doi: 10.20382/JOGC.V10I2A5 external_id: arxiv: - '1712.00434' file: - access_level: open_access checksum: c872d590d38d538404782bca20c4c3f5 content_type: application/pdf creator: khuszar date_created: 2019-11-23T12:35:16Z date_updated: 2020-07-14T12:47:49Z file_id: '7094' file_name: 479-1917-1-PB.pdf file_size: 857590 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 10' issue: '2' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 70–98 publication: Journal of Computational Geometry publication_identifier: issn: - 1920-180X publication_status: published publisher: Computational Geometry Laborartoy quality_controlled: '1' related_material: record: - id: '285' relation: earlier_version status: public - id: '8032' relation: part_of_dissertation status: public status: public title: On the treewidth of triangulated 3-manifolds 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2019' ... --- _id: '7197' abstract: - lang: eng text: During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner. acknowledged_ssus: - _id: LifeSc - _id: Bio article_number: '5744' article_processing_charge: No article_type: original author: - first_name: Paulo R full_name: Dos Santos Caldas, Paulo R id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87 last_name: Dos Santos Caldas orcid: 0000-0001-6730-4461 - first_name: Maria D full_name: Lopez Pelegrin, Maria D id: 319AA9CE-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Pelegrin - first_name: Daniel J. G. full_name: Pearce, Daniel J. G. last_name: Pearce - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Jan full_name: Brugués, Jan last_name: Brugués - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 2019;10. doi:10.1038/s41467-019-13702-4 apa: Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., & Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13702-4 chicago: Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13702-4. ieee: P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744. mla: Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications, vol. 10, 5744, Springer Nature, 2019, doi:10.1038/s41467-019-13702-4. short: P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019). date_created: 2019-12-20T12:22:57Z date_published: 2019-12-17T00:00:00Z date_updated: 2023-09-07T13:18:51Z day: '17' ddc: - '570' department: - _id: MaLo - _id: BjHo doi: 10.1038/s41467-019-13702-4 ec_funded: 1 external_id: isi: - '000503009300001' file: - access_level: open_access checksum: a1b44b427ba341383197790d0e8789fa content_type: application/pdf creator: dernst date_created: 2019-12-23T07:34:56Z date_updated: 2020-07-14T12:47:53Z file_id: '7208' file_name: 2019_NatureComm_Caldas.pdf file_size: 8488733 relation: main_file file_date_updated: 2020-07-14T12:47:53Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: 260D98C8-B435-11E9-9278-68D0E5697425 name: Reconstitution of Bacterial Cell Division Using Purified Components publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8358' relation: dissertation_contains status: public scopus_import: '1' status: public title: Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2019' ... --- _id: '7210' abstract: - lang: eng text: The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization. article_number: '138' article_processing_charge: No article_type: original author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2019;2. doi:10.1038/s42003-019-0373-y apa: Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2019). Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0373-y chicago: Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0373-y. ieee: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Population structure determines the tradeoff between fixation probability and fixation time,” Communications Biology, vol. 2. Springer Nature, 2019. ista: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2019. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2, 138. mla: Tkadlec, Josef, et al. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology, vol. 2, 138, Springer Nature, 2019, doi:10.1038/s42003-019-0373-y. short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology 2 (2019). date_created: 2019-12-23T13:36:50Z date_published: 2019-04-23T00:00:00Z date_updated: 2023-09-07T13:19:22Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.1038/s42003-019-0373-y ec_funded: 1 external_id: isi: - '000465425700006' pmid: - '31044163' file: - access_level: open_access checksum: d1a69bfe73767e4246f0a38e4e1554dd content_type: application/pdf creator: dernst date_created: 2019-12-23T13:39:30Z date_updated: 2020-07-14T12:47:53Z file_id: '7211' file_name: 2019_CommBio_Tkadlec.pdf file_size: 1670274 relation: main_file file_date_updated: 2020-07-14T12:47:53Z has_accepted_license: '1' intvolume: ' 2' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Communications Biology publication_identifier: issn: - 2399-3642 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '7196' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Population structure determines the tradeoff between fixation probability and fixation time 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2019' ... --- _id: '10190' abstract: - lang: eng text: 'The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning.' acknowledgement: "The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n" article_number: '124' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Viktor full_name: Toman, Viktor id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87 last_name: Toman orcid: 0000-0001-9036-063X citation: ama: 'Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. Vol 3. ACM; 2019. doi:10.1145/3360550' apa: 'Chatterjee, K., Pavlogiannis, A., & Toman, V. (2019). Value-centric dynamic partial order reduction. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360550' chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Vol. 3. ACM, 2019. https://doi.org/10.1145/3360550. ieee: K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Athens, Greece, 2019, vol. 3. ista: 'Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.' mla: Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, vol. 3, 124, ACM, 2019, doi:10.1145/3360550. short: K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019. conference: end_date: 2019-10-25 location: Athens, Greece name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications' start_date: 2019-10-23 date_created: 2021-10-27T14:57:06Z date_published: 2019-10-10T00:00:00Z date_updated: 2023-09-07T13:30:27Z day: '10' ddc: - '000' department: - _id: GradSch - _id: KrCh doi: 10.1145/3360550 external_id: arxiv: - '1909.00989' file: - access_level: open_access checksum: 2149979c46964c4d117af06ccb6c0834 content_type: application/pdf creator: cchlebak date_created: 2021-11-12T11:41:56Z date_updated: 2021-11-12T11:41:56Z file_id: '10278' file_name: 2019_ACM_Chatterjee.pdf file_size: 570829 relation: main_file success: 1 file_date_updated: 2021-11-12T11:41:56Z has_accepted_license: '1' intvolume: ' 3' keyword: - safety - risk - reliability and quality - software language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/doi/10.1145/3360550 month: '10' oa: 1 oa_version: Published Version project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications publication_identifier: eissn: - 2475-1421 publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '10199' relation: dissertation_contains status: public status: public title: Value-centric dynamic partial order reduction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 3 year: '2019' ... --- _id: '6673' abstract: - lang: eng text: Several classic problems in graph processing and computational geometry are solved via incremental algorithms, which split computation into a series of small tasks acting on shared state, which gets updated progressively. While the sequential variant of such algorithms usually specifies a fixed (but sometimes random) order in which the tasks should be performed, a standard approach to parallelizing such algorithms is to relax this constraint to allow for out-of-order parallel execution. This is the case for parallel implementations of Dijkstra's single-source shortest-paths (SSSP) algorithm, and for parallel Delaunay mesh triangulation. While many software frameworks parallelize incremental computation in this way, it is still not well understood whether this relaxed ordering approach can still provide any complexity guarantees. In this paper, we address this problem, and analyze the efficiency guarantees provided by a range of incremental algorithms when parallelized via relaxed schedulers. We show that, for algorithms such as Delaunay mesh triangulation and sorting by insertion, schedulers with a maximum relaxation factor of k in terms of the maximum priority inversion allowed will introduce a maximum amount of wasted work of O(łog n poly(k)), where n is the number of tasks to be executed. For SSSP, we show that the additional work is O(poly(k), dmax / wmin), where dmax is the maximum distance between two nodes, and wmin is the minimum such distance. In practical settings where n >> k, this suggests that the overheads of relaxation will be outweighed by the improved scalability of the relaxed scheduler. On the negative side, we provide lower bounds showing that certain algorithms will inherently incur a non-trivial amount of wasted work due to scheduler relaxation, even for relatively benign relaxed schedulers. article_processing_charge: No 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: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze orcid: 0000-0001-5634-0731 - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval citation: ama: 'Alistarh D-A, Nadiradze G, Koval N. Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. In: 31st ACM Symposium on Parallelism in Algorithms and Architectures. ACM Press; 2019:145-154. doi:10.1145/3323165.3323201' apa: 'Alistarh, D.-A., Nadiradze, G., & Koval, N. (2019). Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. In 31st ACM Symposium on Parallelism in Algorithms and Architectures (pp. 145–154). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3323165.3323201' chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Nikita Koval. “Efficiency Guarantees for Parallel Incremental Algorithms under Relaxed Schedulers.” In 31st ACM Symposium on Parallelism in Algorithms and Architectures, 145–54. ACM Press, 2019. https://doi.org/10.1145/3323165.3323201. ieee: D.-A. Alistarh, G. Nadiradze, and N. Koval, “Efficiency guarantees for parallel incremental algorithms under relaxed schedulers,” in 31st ACM Symposium on Parallelism in Algorithms and Architectures, Phoenix, AZ, United States, 2019, pp. 145–154. ista: 'Alistarh D-A, Nadiradze G, Koval N. 2019. Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. 31st ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 145–154.' mla: Alistarh, Dan-Adrian, et al. “Efficiency Guarantees for Parallel Incremental Algorithms under Relaxed Schedulers.” 31st ACM Symposium on Parallelism in Algorithms and Architectures, ACM Press, 2019, pp. 145–54, doi:10.1145/3323165.3323201. short: D.-A. Alistarh, G. Nadiradze, N. Koval, in:, 31st ACM Symposium on Parallelism in Algorithms and Architectures, ACM Press, 2019, pp. 145–154. conference: end_date: 2019-06-24 location: Phoenix, AZ, United States name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures' start_date: 2019-06-22 date_created: 2019-07-24T08:59:36Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T13:31:39Z day: '01' department: - _id: DaAl doi: 10.1145/3323165.3323201 ec_funded: 1 external_id: arxiv: - '2003.09363' isi: - '000507618500018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2003.09363 month: '06' oa: 1 oa_version: Preprint page: 145-154 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: 31st ACM Symposium on Parallelism in Algorithms and Architectures publication_identifier: isbn: - '9781450361842' publication_status: published publisher: ACM Press quality_controlled: '1' related_material: record: - id: '10429' relation: dissertation_contains status: public scopus_import: '1' status: public title: Efficiency guarantees for parallel incremental algorithms under relaxed schedulers type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '7398' abstract: - lang: eng text: 'Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation.' article_processing_charge: No article_type: original author: - first_name: Fatma Asli full_name: Erdem, Fatma Asli last_name: Erdem - first_name: Marija full_name: Ilic, Marija last_name: Ilic - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Jakub full_name: Gołacki, Jakub last_name: Gołacki - first_name: Gert full_name: Lubec, Gert last_name: Lubec - first_name: Michael full_name: Freissmuth, Michael last_name: Freissmuth - first_name: Walter full_name: Sandtner, Walter last_name: Sandtner citation: ama: Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 2019;151(8):1035-1050. doi:10.1085/jgp.201912318 apa: Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth, M., & Sandtner, W. (2019). A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. Rockefeller University Press. https://doi.org/10.1085/jgp.201912318 chicago: Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology. Rockefeller University Press, 2019. https://doi.org/10.1085/jgp.201912318. ieee: F. A. Erdem et al., “A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2,” The Journal of General Physiology, vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019. ista: Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 151(8), 1035–1050. mla: Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology, vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:10.1085/jgp.201912318. short: F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth, W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050. date_created: 2020-01-29T16:06:29Z date_published: 2019-07-03T00:00:00Z date_updated: 2023-09-07T14:52:23Z day: '03' ddc: - '570' department: - _id: RySh doi: 10.1085/jgp.201912318 external_id: isi: - '000478792500008' pmid: - '31270129' file: - access_level: open_access checksum: 5706b4ccd74ee3e50bf7ecb2a203df71 content_type: application/pdf creator: dernst date_created: 2020-02-05T07:20:32Z date_updated: 2020-07-14T12:47:57Z file_id: '7450' file_name: 2019_JGP_Erdem.pdf file_size: 2641297 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 151' isi: 1 issue: '8' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version page: 1035-1050 pmid: 1 publication: The Journal of General Physiology publication_identifier: eissn: - 1540-7748 issn: - 0022-1295 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2 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: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 151 year: '2019' ... --- _id: '7395' abstract: - lang: eng text: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs. article_processing_charge: No article_type: original author: - first_name: James A full_name: Letts, James A id: 322DA418-F248-11E8-B48F-1D18A9856A87 last_name: Letts orcid: 0000-0002-9864-3586 - first_name: Karol full_name: Fiedorczuk, Karol id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0 last_name: Fiedorczuk - first_name: Gianluca full_name: Degliesposti, Gianluca last_name: Degliesposti - first_name: Mark full_name: Skehel, Mark last_name: Skehel - 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: Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 2019;75(6):1131-1146.e6. doi:10.1016/j.molcel.2019.07.022 apa: Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov, L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2019.07.022 chicago: Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell. Cell Press, 2019. https://doi.org/10.1016/j.molcel.2019.07.022. ieee: J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov, “Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk,” Molecular Cell, vol. 75, no. 6. Cell Press, p. 1131–1146.e6, 2019. ista: Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 75(6), 1131–1146.e6. mla: Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell, vol. 75, no. 6, Cell Press, 2019, p. 1131–1146.e6, doi:10.1016/j.molcel.2019.07.022. short: J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular Cell 75 (2019) 1131–1146.e6. date_created: 2020-01-29T16:02:33Z date_published: 2019-09-19T00:00:00Z date_updated: 2023-09-07T14:53:06Z day: '19' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.molcel.2019.07.022 ec_funded: 1 external_id: isi: - '000486614200006' pmid: - '31492636' file: - access_level: open_access checksum: 5202f53a237d6650ece038fbf13bdcea content_type: application/pdf creator: dernst date_created: 2020-02-04T10:37:28Z date_updated: 2020-07-14T12:47:57Z file_id: '7447' file_name: 2019_MolecularCell_Letts.pdf file_size: 9654895 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1131-1146.e6 pmid: 1 project: - _id: 2590DB08-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '701309' name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 75 year: '2019' ... --- _id: '7405' abstract: - lang: eng text: Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena. article_number: e44494 article_processing_charge: No article_type: original author: - first_name: Salvador full_name: Dura-Bernal, Salvador last_name: Dura-Bernal - first_name: Benjamin full_name: Suter, Benjamin id: 4952F31E-F248-11E8-B48F-1D18A9856A87 last_name: Suter orcid: 0000-0002-9885-6936 - first_name: Padraig full_name: Gleeson, Padraig last_name: Gleeson - first_name: Matteo full_name: Cantarelli, Matteo last_name: Cantarelli - first_name: Adrian full_name: Quintana, Adrian last_name: Quintana - first_name: Facundo full_name: Rodriguez, Facundo last_name: Rodriguez - first_name: David J full_name: Kedziora, David J last_name: Kedziora - first_name: George L full_name: Chadderdon, George L last_name: Chadderdon - first_name: Cliff C full_name: Kerr, Cliff C last_name: Kerr - first_name: Samuel A full_name: Neymotin, Samuel A last_name: Neymotin - first_name: Robert A full_name: McDougal, Robert A last_name: McDougal - first_name: Michael full_name: Hines, Michael last_name: Hines - first_name: Gordon MG full_name: Shepherd, Gordon MG last_name: Shepherd - first_name: William W full_name: Lytton, William W last_name: Lytton citation: ama: Dura-Bernal S, Suter B, Gleeson P, et al. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 2019;8. doi:10.7554/elife.44494 apa: Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez, F., … Lytton, W. W. (2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.44494 chicago: Dura-Bernal, Salvador, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.44494. ieee: S. Dura-Bernal et al., “NetPyNE, a tool for data-driven multiscale modeling of brain circuits,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. 2019. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8, e44494. mla: Dura-Bernal, Salvador, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” ELife, vol. 8, e44494, eLife Sciences Publications, 2019, doi:10.7554/elife.44494. short: S. Dura-Bernal, B. Suter, P. Gleeson, M. Cantarelli, A. Quintana, F. Rodriguez, D.J. Kedziora, G.L. Chadderdon, C.C. Kerr, S.A. Neymotin, R.A. McDougal, M. Hines, G.M. Shepherd, W.W. Lytton, ELife 8 (2019). date_created: 2020-01-30T09:08:01Z date_published: 2019-05-31T00:00:00Z date_updated: 2023-09-07T14:27:52Z day: '31' ddc: - '570' department: - _id: PeJo doi: 10.7554/elife.44494 external_id: isi: - '000468968400001' pmid: - '31025934' file: - access_level: open_access checksum: 7014189c11c10a12feeeae37f054871d content_type: application/pdf creator: dernst date_created: 2020-02-04T08:41:47Z date_updated: 2020-07-14T12:47:57Z file_id: '7444' file_name: 2019_eLife_DuraBernal.pdf file_size: 6182359 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: NetPyNE, a tool for data-driven multiscale modeling of brain circuits 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2019' ... --- _id: '7400' abstract: - lang: eng text: 'Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.' article_processing_charge: No article_type: original author: - first_name: Paris full_name: Veltsos, Paris last_name: Veltsos - first_name: Kate E. full_name: Ridout, Kate E. last_name: Ridout - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Santiago C. full_name: González-Martínez, Santiago C. last_name: González-Martínez - first_name: Aline full_name: Muyle, Aline last_name: Muyle - first_name: Olivier full_name: Emery, Olivier last_name: Emery - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Vojtech full_name: Hudzieczek, Vojtech last_name: Hudzieczek - first_name: Roman full_name: Hobza, Roman last_name: Hobza - first_name: Boris full_name: Vyskot, Boris last_name: Vyskot - first_name: Gabriel A. B. full_name: Marais, Gabriel A. B. last_name: Marais - first_name: Dmitry A. full_name: Filatov, Dmitry A. last_name: Filatov - first_name: John R. full_name: Pannell, John R. last_name: Pannell citation: ama: Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 2019;212(3):815-835. doi:10.1534/genetics.119.302045 apa: Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.119.302045 chicago: Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/genetics.119.302045. ieee: P. Veltsos et al., “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” Genetics, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019. ista: Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835. mla: Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:10.1534/genetics.119.302045. short: P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835. date_created: 2020-01-29T16:15:44Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-09-07T14:49:29Z day: '01' department: - _id: BeVi doi: 10.1534/genetics.119.302045 ec_funded: 1 external_id: isi: - '000474809300015' pmid: - '31113811' intvolume: ' 212' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1534/genetics.119.302045 month: '07' oa: 1 oa_version: Published Version page: 815-835 pmid: 1 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Genetics publication_identifier: eissn: - 1943-2631 issn: - 0016-6731 publication_status: published publisher: Genetics Society of America quality_controlled: '1' scopus_import: '1' status: public title: Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 212 year: '2019' ... --- _id: '7404' abstract: - lang: eng text: The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation. article_number: dev171397 article_processing_charge: No article_type: original author: - first_name: Tomke full_name: Stürner, Tomke last_name: Stürner - first_name: Anastasia full_name: Tatarnikova, Anastasia last_name: Tatarnikova - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Barbara full_name: Schaffran, Barbara last_name: Schaffran - first_name: Hermann full_name: Cuntz, Hermann last_name: Cuntz - first_name: Yun full_name: Zhang, Yun last_name: Zhang - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Sven full_name: Bogdan, Sven last_name: Bogdan - first_name: Vic full_name: Small, Vic last_name: Small - first_name: Gaia full_name: Tavosanis, Gaia last_name: Tavosanis citation: ama: Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 2019;146(7). doi:10.1242/dev.171397 apa: Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. The Company of Biologists. https://doi.org/10.1242/dev.171397 chicago: Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.171397. ieee: T. Stürner et al., “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” Development, vol. 146, no. 7. The Company of Biologists, 2019. ista: Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397. mla: Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development, vol. 146, no. 7, dev171397, The Company of Biologists, 2019, doi:10.1242/dev.171397. short: T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019). date_created: 2020-01-29T16:27:10Z date_published: 2019-04-04T00:00:00Z date_updated: 2023-09-07T14:47:00Z day: '04' department: - _id: MiSi doi: 10.1242/dev.171397 external_id: isi: - '000464583200006' pmid: - '30910826' intvolume: ' 146' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1242/dev.171397 month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Development publication_identifier: eissn: - 1477-9129 issn: - 0950-1991 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 146 year: '2019' ... --- _id: '7402' abstract: - lang: eng text: Graph planning gives rise to fundamental algorithmic questions such as shortest path, traveling salesman problem, etc. A classical problem in discrete planning is to consider a weighted graph and construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary, to represent the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time. Consequently, our polynomial-time algorithm for adversarial stopping time also computes an optimal plan among all possible plans. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: 34th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2019:1-13. doi:10.1109/lics.2019.8785706' apa: 'Chatterjee, K., & Doyen, L. (2019). Graph planning with expected finite horizon. In 34th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/lics.2019.8785706' chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” In 34th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. IEEE, 2019. https://doi.org/10.1109/lics.2019.8785706. ieee: K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” in 34th Annual ACM/IEEE Symposium on Logic in Computer Science, Vancouver, BC, Canada, 2019, pp. 1–13. ista: 'Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon. 34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.' mla: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13, doi:10.1109/lics.2019.8785706. short: K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13. conference: end_date: 2019-06-27 location: Vancouver, BC, Canada name: 'LICS: Symposium on Logic in Computer Science' start_date: 2019-06-24 date_created: 2020-01-29T16:18:33Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T14:48:11Z day: '01' department: - _id: KrCh doi: 10.1109/lics.2019.8785706 external_id: arxiv: - '1802.03642' isi: - '000805002800001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.03642 month: '06' oa: 1 oa_version: Preprint page: 1-13 publication: 34th Annual ACM/IEEE Symposium on Logic in Computer Science publication_identifier: isbn: - '9781728136080' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '11402' relation: later_version status: public scopus_import: '1' status: public title: Graph planning with expected finite horizon type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '7451' abstract: - lang: eng text: We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition. article_number: '150' article_processing_charge: No article_type: original author: - first_name: A. full_name: Vukics, A. last_name: Vukics - first_name: A. full_name: Dombi, A. last_name: Dombi - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: P. full_name: Domokos, P. last_name: Domokos citation: ama: Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 2019;3. doi:10.22331/q-2019-06-03-150 apa: Vukics, A., Dombi, A., Fink, J. M., & Domokos, P. (2019). Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/q-2019-06-03-150 chicago: Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. https://doi.org/10.22331/q-2019-06-03-150. ieee: A. Vukics, A. Dombi, J. M. Fink, and P. Domokos, “Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition,” Quantum, vol. 3. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. ista: Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 3, 150. mla: Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum, vol. 3, 150, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019, doi:10.22331/q-2019-06-03-150. short: A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019). date_created: 2020-02-05T09:57:57Z date_published: 2019-06-03T00:00:00Z date_updated: 2023-09-07T14:57:39Z day: '03' ddc: - '530' department: - _id: JoFi doi: 10.22331/q-2019-06-03-150 external_id: arxiv: - '1809.09737' isi: - '000469987500004' file: - access_level: open_access checksum: 26b9ba8f0155d183f1ee55295934a17f content_type: application/pdf creator: dernst date_created: 2020-02-11T09:25:23Z date_updated: 2020-07-14T12:47:58Z file_id: '7483' file_name: 2019_Quantum_Vukics.pdf file_size: 5805248 relation: main_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' intvolume: ' 3' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Quantum publication_identifier: issn: - 2521-327X publication_status: published publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften quality_controlled: '1' status: public title: Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 3 year: '2019' ... --- _id: '7468' abstract: - lang: eng text: We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems. article_number: 11138-11147 article_processing_charge: No author: - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Vol 2019-June. IEEE; 2019. doi:10.1109/CVPR.2019.01140' apa: 'Swoboda, P., & Kolmogorov, V. (2019). Map inference via block-coordinate Frank-Wolfe algorithm. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Vol. 2019–June). Long Beach, CA, United States: IEEE. https://doi.org/10.1109/CVPR.2019.01140' chicago: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Vol. 2019–June. IEEE, 2019. https://doi.org/10.1109/CVPR.2019.01140. ieee: P. Swoboda and V. Kolmogorov, “Map inference via block-coordinate Frank-Wolfe algorithm,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Long Beach, CA, United States, 2019, vol. 2019–June. ista: 'Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2019–June, 11138–11147.' mla: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, vol. 2019–June, 11138–11147, IEEE, 2019, doi:10.1109/CVPR.2019.01140. short: P. Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2019. conference: end_date: 2019-06-20 location: Long Beach, CA, United States name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2019-06-15 date_created: 2020-02-09T23:00:52Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T14:54:24Z day: '01' department: - _id: VlKo doi: 10.1109/CVPR.2019.01140 ec_funded: 1 external_id: arxiv: - '1806.05049' isi: - '000542649304076' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.05049 month: '06' oa: 1 oa_version: Preprint project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition publication_identifier: isbn: - '9781728132938' issn: - '10636919' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Map inference via block-coordinate Frank-Wolfe algorithm type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2019-June year: '2019' ... --- _id: '7479' abstract: - lang: eng text: "Multi-exit architectures, in which a stack of processing layers is interleaved with early output layers, allow the processing of a test example to stop early and thus save computation time and/or energy. In this work, we propose a new training procedure for multi-exit architectures based on the principle of knowledge distillation. The method encourage searly exits to mimic later, more accurate exits, by matching their output probabilities.\r\nExperiments on CIFAR100 and \ ImageNet show that distillation-based training significantly improves the accuracy of early exits while maintaining state-of-the-art accuracy for late \ ones. The method is particularly beneficial when training data is limited \ and it allows a straightforward extension to semi-supervised learning,i.e. making use of unlabeled data at training time. Moreover, it takes only afew lines to implement and incurs almost no computational overhead at training time, and none at all at test time." article_processing_charge: No author: - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Phuong M, Lampert C. Distillation-based training for multi-exit architectures. In: IEEE International Conference on Computer Vision. Vol 2019-October. IEEE; 2019:1355-1364. doi:10.1109/ICCV.2019.00144' apa: 'Phuong, M., & Lampert, C. (2019). Distillation-based training for multi-exit architectures. In IEEE International Conference on Computer Vision (Vol. 2019–October, pp. 1355–1364). Seoul, Korea: IEEE. https://doi.org/10.1109/ICCV.2019.00144' chicago: Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” In IEEE International Conference on Computer Vision, 2019–October:1355–64. IEEE, 2019. https://doi.org/10.1109/ICCV.2019.00144. ieee: M. Phuong and C. Lampert, “Distillation-based training for multi-exit architectures,” in IEEE International Conference on Computer Vision, Seoul, Korea, 2019, vol. 2019–October, pp. 1355–1364. ista: 'Phuong M, Lampert C. 2019. Distillation-based training for multi-exit architectures. IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision vol. 2019–October, 1355–1364.' mla: Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” IEEE International Conference on Computer Vision, vol. 2019–October, IEEE, 2019, pp. 1355–64, doi:10.1109/ICCV.2019.00144. short: M. Phuong, C. Lampert, in:, IEEE International Conference on Computer Vision, IEEE, 2019, pp. 1355–1364. conference: end_date: 2019-11-02 location: Seoul, Korea name: 'ICCV: International Conference on Computer Vision' start_date: 2019-10-27 date_created: 2020-02-11T09:06:57Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-09-08T11:11:12Z day: '01' ddc: - '000' department: - _id: ChLa doi: 10.1109/ICCV.2019.00144 ec_funded: 1 external_id: isi: - '000531438101047' file: - access_level: open_access checksum: 7b77fb5c2d27c4c37a7612ba46a66117 content_type: application/pdf creator: bphuong date_created: 2020-02-11T09:06:39Z date_updated: 2020-07-14T12:47:59Z file_id: '7480' file_name: main.pdf file_size: 735768 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 1355-1364 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: IEEE International Conference on Computer Vision publication_identifier: isbn: - '9781728148038' issn: - '15505499' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '9418' relation: dissertation_contains status: public scopus_import: '1' status: public title: Distillation-based training for multi-exit architectures type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2019-October year: '2019' ... --- _id: '7542' abstract: - lang: eng text: We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs. article_processing_charge: No author: - first_name: Chris full_name: Wendler, Chris last_name: Wendler - 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: Markus full_name: Püschel, Markus last_name: Püschel citation: ama: 'Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks. In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.' apa: 'Wendler, C., Alistarh, D.-A., & Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada: Neural Information Processing Systems Foundation.' chicago: Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation, 2019. ieee: 'C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.' ista: 'Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks. NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.' mla: Wendler, Chris, et al. Powerset Convolutional Neural Networks. Vol. 32, Neural Information Processing Systems Foundation, 2019, pp. 927–38. short: C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing Systems Foundation, 2019, pp. 927–938. conference: end_date: 2019-12-14 location: Vancouver, Canada name: 'NIPS: Conference on Neural Information Processing Systems' start_date: 2019-12-08 date_created: 2020-02-28T10:03:24Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-08T11:13:52Z day: '01' department: - _id: DaAl ec_funded: 1 external_id: arxiv: - '1909.02253' isi: - '000534424300084' intvolume: ' 32' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks month: '12' oa: 1 oa_version: Published Version page: 927-938 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' status: public title: Powerset convolutional neural networks type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2019' ... --- _id: '7640' abstract: - lang: eng text: We propose a new model for detecting visual relationships, such as "person riding motorcycle" or "bottle on table". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results. article_number: 1749-1753 article_processing_charge: No author: - first_name: Alexander full_name: Kolesnikov, Alexander id: 2D157DB6-F248-11E8-B48F-1D18A9856A87 last_name: Kolesnikov - first_name: Alina full_name: Kuznetsova, Alina last_name: Kuznetsova - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Vittorio full_name: Ferrari, Vittorio last_name: Ferrari citation: ama: 'Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships using box attention. In: Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00217' apa: 'Kolesnikov, A., Kuznetsova, A., Lampert, C., & Ferrari, V. (2019). Detecting visual relationships using box attention. In Proceedings of the 2019 International Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00217' chicago: Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio Ferrari. “Detecting Visual Relationships Using Box Attention.” In Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00217. ieee: A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual relationships using box attention,” in Proceedings of the 2019 International Conference on Computer Vision Workshop, Seoul, South Korea, 2019. ista: 'Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual relationships using box attention. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 1749–1753.' mla: Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.” Proceedings of the 2019 International Conference on Computer Vision Workshop, 1749–1753, IEEE, 2019, doi:10.1109/ICCVW.2019.00217. short: A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019. conference: end_date: 2019-10-28 location: Seoul, South Korea name: 'ICCVW: International Conference on Computer Vision Workshop' start_date: 2019-10-27 date_created: 2020-04-05T22:00:51Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-09-08T11:18:37Z day: '01' department: - _id: ChLa doi: 10.1109/ICCVW.2019.00217 ec_funded: 1 external_id: arxiv: - '1807.02136' isi: - '000554591601098' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.02136 month: '10' oa: 1 oa_version: Preprint project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: Proceedings of the 2019 International Conference on Computer Vision Workshop publication_identifier: isbn: - '9781728150239' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Detecting visual relationships using box attention type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '8184' abstract: - lang: eng text: "Denote by ∆N the N-dimensional simplex. A map f : ∆N → Rd is an almost r-embedding if fσ1∩. . .∩fσr = ∅ whenever σ1, . . . , σr are pairwise disjoint faces. A counterexample to the topological Tverberg conjecture asserts that if r is not a prime power and d ≥ 2r + 1, then there is an almost r-embedding ∆(d+1)(r−1) → Rd. This was improved by Blagojevi´c–Frick–Ziegler using a simple construction of higher-dimensional counterexamples by taking k-fold join power of lower-dimensional ones. We improve this further (for d large compared to r): If r is not a prime power and N := (d+ 1)r−r l\r\nd + 2 r + 1 m−2, then there is an almost r-embedding ∆N → Rd. For the r-fold van Kampen–Flores conjecture we also produce counterexamples which are stronger than previously known. Our proof is based on generalizations of the Mabillard–Wagner theorem on construction of almost r-embeddings from equivariant maps, and of the Ozaydin theorem on existence of equivariant maps. " acknowledgement: We would like to thank F. Frick for helpful discussions article_number: '1908.08731' article_processing_charge: No author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: R. full_name: Karasev, R. last_name: Karasev - first_name: A. full_name: Skopenkov, A. last_name: Skopenkov citation: ama: Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv. apa: Avvakumov, S., Karasev, R., & Skopenkov, A. (n.d.). Stronger counterexamples to the topological Tverberg conjecture. arXiv. arXiv. chicago: Avvakumov, Sergey, R. Karasev, and A. Skopenkov. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv. arXiv, n.d. ieee: S. Avvakumov, R. Karasev, and A. Skopenkov, “Stronger counterexamples to the topological Tverberg conjecture,” arXiv. arXiv. ista: Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv, 1908.08731. mla: Avvakumov, Sergey, et al. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv, 1908.08731, arXiv. short: S. Avvakumov, R. Karasev, A. Skopenkov, ArXiv (n.d.). date_created: 2020-07-30T10:45:34Z date_published: 2019-08-23T00:00:00Z date_updated: 2023-09-08T11:20:02Z day: '23' department: - _id: UlWa external_id: arxiv: - '1908.08731' isi: - '000986519600004' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.08731 month: '08' oa: 1 oa_version: Preprint project: - _id: 26611F5C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31312 name: Algorithms for Embeddings and Homotopy Theory publication: arXiv publication_status: submitted publisher: arXiv related_material: record: - id: '8156' relation: dissertation_contains status: public status: public title: Stronger counterexamples to the topological Tverberg conjecture type: preprint user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '6430' abstract: - lang: eng text: "A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key \U0001D45D\U0001D458′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under \U0001D45D\U0001D458′ without having to know the underlying message, while transformations from \U0001D45D\U0001D458′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14)." alternative_title: - LNCS article_processing_charge: No author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:10.1007/978-3-030-17259-6_11' apa: 'Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-030-17259-6_11' chicago: Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17259-6_11. ieee: 'G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.' ista: 'Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.' mla: Fuchsbauer, Georg, et al. Adaptively Secure Proxy Re-Encryption. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:10.1007/978-3-030-17259-6_11. short: G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346. conference: end_date: 2019-04-17 location: Beijing, China name: 'PKC: Public-Key Cryptograhy' start_date: 2019-04-14 date_created: 2019-05-13T08:13:46Z date_published: 2019-04-06T00:00:00Z date_updated: 2023-09-08T11:33:20Z day: '06' department: - _id: KrPi doi: 10.1007/978-3-030-17259-6_11 ec_funded: 1 intvolume: ' 11443' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/426 month: '04' oa: 1 oa_version: Preprint page: 317-346 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: eissn: - '16113349' isbn: - '9783030172589' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10035' relation: dissertation_contains status: public scopus_import: '1' status: public title: Adaptively secure proxy re-encryption type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11443 year: '2019' ... --- _id: '6069' abstract: - lang: eng text: Electron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments. article_number: '937' article_processing_charge: No author: - first_name: Jonathan full_name: Mayzel, Jonathan last_name: Mayzel - first_name: Victor full_name: Steinberg, Victor last_name: Steinberg - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 citation: ama: Mayzel J, Steinberg V, Varshney A. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 2019;10. doi:10.1038/s41467-019-08916-5 apa: Mayzel, J., Steinberg, V., & Varshney, A. (2019). Stokes flow analogous to viscous electron current in graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08916-5 chicago: Mayzel, Jonathan, Victor Steinberg, and Atul Varshney. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08916-5. ieee: J. Mayzel, V. Steinberg, and A. Varshney, “Stokes flow analogous to viscous electron current in graphene,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Mayzel J, Steinberg V, Varshney A. 2019. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 10, 937. mla: Mayzel, Jonathan, et al. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications, vol. 10, 937, Springer Nature, 2019, doi:10.1038/s41467-019-08916-5. short: J. Mayzel, V. Steinberg, A. Varshney, Nature Communications 10 (2019). date_created: 2019-03-05T13:18:30Z date_published: 2019-02-26T00:00:00Z date_updated: 2023-09-08T11:39:02Z day: '26' ddc: - '530' - '532' department: - _id: BjHo doi: 10.1038/s41467-019-08916-5 ec_funded: 1 external_id: isi: - '000459704600001' file: - access_level: open_access checksum: 61192fc49e0d44907c2a4fe384e4b97f content_type: application/pdf creator: dernst date_created: 2019-03-05T13:33:04Z date_updated: 2020-07-14T12:47:18Z file_id: '6070' file_name: 2019_NatureComm_Mayzel.pdf file_size: 2646391 relation: main_file file_date_updated: 2020-07-14T12:47:18Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Stokes flow analogous to viscous electron current in 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2019' ... --- _id: '6014' abstract: - lang: eng text: Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity. article_number: '652' article_processing_charge: No article_type: original author: - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 - first_name: Victor full_name: Steinberg, Victor last_name: Steinberg citation: ama: Varshney A, Steinberg V. Elastic alfven waves in elastic turbulence. Nature Communications. 2019;10. doi:10.1038/s41467-019-08551-0 apa: Varshney, A., & Steinberg, V. (2019). Elastic alfven waves in elastic turbulence. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08551-0 chicago: Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08551-0. ieee: A. Varshney and V. Steinberg, “Elastic alfven waves in elastic turbulence,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Varshney A, Steinberg V. 2019. Elastic alfven waves in elastic turbulence. Nature Communications. 10, 652. mla: Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications, vol. 10, 652, Springer Nature, 2019, doi:10.1038/s41467-019-08551-0. short: A. Varshney, V. Steinberg, Nature Communications 10 (2019). date_created: 2019-02-15T07:10:46Z date_published: 2019-02-08T00:00:00Z date_updated: 2023-09-08T11:39:54Z day: '08' ddc: - '530' department: - _id: BjHo doi: 10.1038/s41467-019-08551-0 ec_funded: 1 external_id: arxiv: - '1902.03763' isi: - '000458175300001' file: - access_level: open_access checksum: d3acf07eaad95ec040d8e8565fc9ac37 content_type: application/pdf creator: dernst date_created: 2019-02-15T07:15:00Z date_updated: 2020-07-14T12:47:17Z file_id: '6015' file_name: 2019_NatureComm_Varshney.pdf file_size: 1331490 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Elastic alfven waves in elastic 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2019' ... --- _id: '6451' abstract: - lang: eng text: Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis. article_processing_charge: No author: - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Panagiota A. full_name: Sotiropoulou, Panagiota A. last_name: Sotiropoulou - first_name: Gerwin full_name: Heller, Gerwin last_name: Heller - first_name: Beate M. full_name: Lichtenberger, Beate M. last_name: Lichtenberger - first_name: Martin full_name: Holcmann, Martin last_name: Holcmann - first_name: Bahar full_name: Camurdanoglu, Bahar last_name: Camurdanoglu - first_name: Temenuschka full_name: Baykuscheva-Gentscheva, Temenuschka last_name: Baykuscheva-Gentscheva - first_name: Cedric full_name: Blanpain, Cedric last_name: Blanpain - first_name: Maria full_name: Sibilia, Maria last_name: Sibilia citation: ama: Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 2019;15:243-256. doi:10.1016/j.isci.2019.04.018 apa: Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.04.018 chicago: Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.04.018. ieee: N. Amberg et al., “EGFR controls hair shaft differentiation in a p53-independent manner,” iScience, vol. 15. Elsevier, pp. 243–256, 2019. ista: Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256. mla: Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience, vol. 15, Elsevier, 2019, pp. 243–56, doi:10.1016/j.isci.2019.04.018. short: N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256. date_created: 2019-05-14T11:47:40Z date_published: 2019-05-31T00:00:00Z date_updated: 2023-09-08T11:38:04Z day: '31' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.isci.2019.04.018 external_id: isi: - '000470104600022' file: - access_level: open_access checksum: a9ad2296726c9474ad5860c9c2f53622 content_type: application/pdf creator: dernst date_created: 2019-05-14T11:51:51Z date_updated: 2020-07-14T12:47:30Z file_id: '6452' file_name: 2019_iScience_Amberg.pdf file_size: 8365970 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 243-256 publication: iScience publication_identifier: issn: - 2589-0042 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: EGFR controls hair shaft differentiation in a p53-independent manner 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 15 year: '2019' ...