[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Graphical games are a useful framework for modeling the interactions of (selfish) agents who are connected via an underlying topology and whose behaviors influence each other. They have wide applications ranging from computer science to economics and biology. Yet, even though an agent’s payoff only depends on the actions of their direct neighbors in graphical games, computing the Nash equilibria and making statements about the convergence time of \"natural\" local dynamics in particular can be highly challenging. In this work, we present a novel approach for classifying complexity of Nash equilibria in graphical games by establishing a connection to local graph algorithms, a subfield of distributed computing. In particular, we make the observation that the equilibria of graphical games are equivalent to locally verifiable labelings (LVL) in graphs; vertex labelings which are verifiable with constant-round local algorithms. This connection allows us to derive novel lower bounds on the convergence time to equilibrium of best-response dynamics in graphical games. Since we establish that distributed convergence can sometimes be provably slow, we also introduce and give bounds on an intuitive notion of \"time-constrained\" inefficiency of best responses. We exemplify how our results can be used in the implementation of mechanisms that ensure convergence of best responses to a Nash equilibrium. Our results thus also give insight into the convergence of strategy-proof algorithms for graphical games, which is still not well understood."}],"file_date_updated":"2024-02-26T09:04:58Z","doi":"10.4230/LIPIcs.OPODIS.2023.11","file":[{"content_type":"application/pdf","success":1,"date_updated":"2024-02-26T09:04:58Z","creator":"dernst","file_name":"2024_LIPICs_Hirvonen.pdf","access_level":"open_access","relation":"main_file","file_size":867363,"date_created":"2024-02-26T09:04:58Z","checksum":"4fc7eea6e4ba140b904781fc7df868ec","file_id":"15028"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"oa":1,"ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ieee":"J. Hirvonen, L. Schmid, K. Chatterjee, and S. Schmid, “On the convergence time in graphical games: A locality-sensitive approach,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","apa":"Hirvonen, J., Schmid, L., Chatterjee, K., & Schmid, S. (2024). On the convergence time in graphical games: A locality-sensitive approach. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11","ista":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. 2024. On the convergence time in graphical games: A locality-sensitive approach. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 11.","chicago":"Hirvonen, Juho, Laura Schmid, Krishnendu Chatterjee, and Stefan Schmid. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11.","short":"J. Hirvonen, L. Schmid, K. Chatterjee, S. Schmid, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Hirvonen, Juho, et al. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” 27th International Conference on Principles of Distributed Systems, vol. 286, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.11.","ama":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. On the convergence time in graphical games: A locality-sensitive approach. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.11"},"alternative_title":["LIPIcs"],"date_created":"2024-02-18T23:01:01Z","title":"On the convergence time in graphical games: A locality-sensitive approach","year":"2024","status":"public","department":[{"_id":"KrCh"}],"publication_status":"published","intvolume":" 286","publication":"27th International Conference on Principles of Distributed Systems","has_accepted_license":"1","volume":286,"scopus_import":"1","type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Juho","full_name":"Hirvonen, Juho","last_name":"Hirvonen"},{"first_name":"Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"publication_identifier":{"isbn":["9783959773089"],"issn":["18688969"]},"_id":"15006","article_number":"11","ddc":["000"],"article_processing_charge":"No","acknowledgement":"This work was partially funded by the Academy of Finland, grant 314888, the European Research Council CoG 863818 (ForM-SMArt), and the Austrian Science Fund (FWF) project I 4800-N (ADVISE). LS was supported by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324.","quality_controlled":"1","date_updated":"2024-02-26T09:16:12Z","license":"https://creativecommons.org/licenses/by/4.0/","day":"18","month":"01","conference":{"start_date":"2023-12-06","end_date":"2023-12-08","name":"OPODIS: Conference on Principles of Distributed Systems","location":"Tokyo, Japan"},"language":[{"iso":"eng"}],"date_published":"2024-01-18T00:00:00Z","external_id":{"arxiv":["2102.13457"]}},{"scopus_import":"1","type":"journal_article","volume":121,"has_accepted_license":"1","publisher":"Proceedings of the National Academy of Sciences","author":[{"orcid":"0000-0001-6160-9766","first_name":"Samo","full_name":"Curk, Samo","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","last_name":"Curk"},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"},{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"ddc":["570"],"article_number":"e2220075121","publication_identifier":{"eissn":["1091-6490"]},"_id":"15001","quality_controlled":"1","article_processing_charge":"Yes","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","pmid":1,"date_updated":"2024-02-26T08:45:56Z","day":"13","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"02","date_published":"2024-02-13T00:00:00Z","external_id":{"pmid":["38335256"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","file_size":7699487,"date_created":"2024-02-26T08:20:00Z","creator":"dernst","access_level":"open_access","file_name":"2024_PNAS_Curk.pdf","file_id":"15026","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","content_type":"application/pdf","success":1,"date_updated":"2024-02-26T08:20:00Z"}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2220075121","file_date_updated":"2024-02-26T08:20:00Z","article_type":"original","oa":1,"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"15027","relation":"research_data"}]},"date_created":"2024-02-18T23:01:00Z","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","citation":{"chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121","ieee":"S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121","mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"year":"2024","publication_status":"published","department":[{"_id":"AnSa"}],"status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":" 121","issue":"7"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.10220"}],"oa_version":"Preprint","citation":{"short":"E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters 132 (2024).","mla":"Petrova, Elena, et al. “Fractal States of the Schwinger Model.” Physical Review Letters, vol. 132, no. 5, 050401, American Physical Society, 2024, doi:10.1103/PhysRevLett.132.050401.","ama":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. Fractal states of the Schwinger model. Physical Review Letters. 2024;132(5). doi:10.1103/PhysRevLett.132.050401","apa":"Petrova, E., Tiunov, E. S., Bañuls, M. C., & Fedorov, A. K. (2024). Fractal states of the Schwinger model. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.132.050401","ieee":"E. Petrova, E. S. Tiunov, M. C. Bañuls, and A. K. Fedorov, “Fractal states of the Schwinger model,” Physical Review Letters, vol. 132, no. 5. American Physical Society, 2024.","ista":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. 2024. Fractal states of the Schwinger model. Physical Review Letters. 132(5), 050401.","chicago":"Petrova, Elena, Egor S. Tiunov, Mari Carmen Bañuls, and Aleksey K. Fedorov. “Fractal States of the Schwinger Model.” Physical Review Letters. American Physical Society, 2024. https://doi.org/10.1103/PhysRevLett.132.050401."},"date_created":"2024-02-18T23:01:00Z","title":"Fractal states of the Schwinger model","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The lattice Schwinger model, the discrete version of QED in \r\n1\r\n+\r\n1\r\n dimensions, is a well-studied test bench for lattice gauge theories. Here, we study the fractal properties of this model. We reveal the self-similarity of the ground state, which allows us to develop a recurrent procedure for finding the ground-state wave functions and predicting ground-state energies. We present the results of recurrently calculating ground-state wave functions using the fractal Ansatz and automized software package for fractal image processing. In certain parameter regimes, just a few terms are enough for our recurrent procedure to predict ground-state energies close to the exact ones for several hundreds of sites. Our findings pave the way to understanding the complexity of calculating many-body wave functions in terms of their fractal properties as well as finding new links between condensed matter and high-energy lattice models."}],"doi":"10.1103/PhysRevLett.132.050401","oa":1,"article_type":"original","intvolume":" 132","publication":"Physical Review Letters","issue":"5","year":"2024","department":[{"_id":"MaSe"}],"status":"public","publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"_id":"15002","article_number":"050401","article_processing_charge":"No","acknowledgement":"We thank A. Bargov, I. Khaymovich, and V. Tiunova for fruitful discussions and for useful comments. M. C. B. thanks S. Kühn for discussions about the phase structure of the model. A. K. F. thanks V. Gritsev and A. Garkun for insightful comments. E. V. P., E. S. T., and A. K. F. are\r\nsupported by the RSF Grant No. 20-42-05002 (studying the fractal Ansatz) and the Roadmap on Quantum Computing (Contract No. 868-1.3-15/15-2021, October 5, 2021; calculating on GS energies). A. K. F. thanks the Priority 2030 program at the NIST “MISIS” under the project No. K1-2022-027. M. C. B. was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868.","quality_controlled":"1","volume":132,"type":"journal_article","scopus_import":"1","publisher":"American Physical Society","author":[{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","full_name":"Petrova, Elena","last_name":"Petrova","first_name":"Elena"},{"last_name":"Tiunov","full_name":"Tiunov, Egor S.","first_name":"Egor S."},{"full_name":"Bañuls, Mari Carmen","last_name":"Bañuls","first_name":"Mari Carmen"},{"last_name":"Fedorov","full_name":"Fedorov, Aleksey K.","first_name":"Aleksey K."}],"month":"01","language":[{"iso":"eng"}],"date_published":"2024-01-30T00:00:00Z","external_id":{"arxiv":["2201.10220"]},"date_updated":"2024-02-26T08:03:31Z","day":"30"},{"publication":"Probability Theory and Related Fields","publication_status":"epub_ahead","department":[{"_id":"JuFi"}],"status":"public","year":"2024","date_created":"2023-02-02T10:45:15Z","title":"The critical variational setting for stochastic evolution equations","citation":{"ama":"Agresti A, Veraar M. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. 2024. doi:10.1007/s00440-023-01249-x","short":"A. Agresti, M. Veraar, Probability Theory and Related Fields (2024).","mla":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields, Springer Nature, 2024, doi:10.1007/s00440-023-01249-x.","ista":"Agresti A, Veraar M. 2024. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields.","chicago":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields. Springer Nature, 2024. https://doi.org/10.1007/s00440-023-01249-x.","ieee":"A. Agresti and M. Veraar, “The critical variational setting for stochastic evolution equations,” Probability Theory and Related Fields. Springer Nature, 2024.","apa":"Agresti, A., & Veraar, M. (2024). The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01249-x"},"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1007/s00440-023-01249-x","open_access":"1"}],"ec_funded":1,"article_type":"original","oa":1,"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"doi":"10.1007/s00440-023-01249-x","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation.","lang":"eng"}],"external_id":{"arxiv":["2206.00230"]},"date_published":"2024-02-02T00:00:00Z","language":[{"iso":"eng"}],"month":"02","day":"02","date_updated":"2024-02-26T09:39:07Z","quality_controlled":"1","acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819) . The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","article_processing_charge":"No","_id":"12485","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","last_name":"Agresti","orcid":"0000-0002-9573-2962","first_name":"Antonio"},{"last_name":"Veraar","full_name":"Veraar, Mark","first_name":"Mark"}],"publisher":"Springer Nature","scopus_import":"1","type":"journal_article"},{"publication":"15th Innovations in Theoretical Computer Science Conference","intvolume":" 287","year":"2024","publication_status":"published","status":"public","department":[{"_id":"MoHe"}],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"title":"Electrical flows for polylogarithmic competitive oblivious routing","date_created":"2024-02-18T23:01:02Z","alternative_title":["LIPIcs"],"citation":{"chicago":"Goranci, Gramoz, Monika H Henzinger, Harald Räcke, Sushant Sachdeva, and A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” In 15th Innovations in Theoretical Computer Science Conference, Vol. 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.55.","ista":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science Conference, LIPIcs, vol. 287, 55.","apa":"Goranci, G., Henzinger, M. H., Räcke, H., Sachdeva, S., & Sricharan, A. R. (2024). Electrical flows for polylogarithmic competitive oblivious routing. In 15th Innovations in Theoretical Computer Science Conference (Vol. 287). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.55","ieee":"G. Goranci, M. H. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical flows for polylogarithmic competitive oblivious routing,” in 15th Innovations in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287.","ama":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. Electrical flows for polylogarithmic competitive oblivious routing. In: 15th Innovations in Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ITCS.2024.55","short":"G. Goranci, M.H. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” 15th Innovations in Theoretical Computer Science Conference, vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ITCS.2024.55."},"file":[{"success":1,"date_updated":"2024-02-26T10:10:48Z","content_type":"application/pdf","file_id":"15030","checksum":"b89716aae6a5599f187897e39de1e53a","relation":"main_file","date_created":"2024-02-26T10:10:48Z","file_size":1054754,"creator":"dernst","file_name":"2024_LIPICs_Goranci.pdf","access_level":"open_access"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "}],"doi":"10.4230/LIPIcs.ITCS.2024.55","file_date_updated":"2024-02-26T10:10:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. \r\nIn this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth.","lang":"eng"}],"oa":1,"month":"01","external_id":{"arxiv":["2303.02491"]},"date_published":"2024-01-24T00:00:00Z","language":[{"iso":"eng"}],"conference":{"end_date":"2024-02-02","start_date":"2024-01-30","name":"ITCS: Innovations in Theoretical Computer Science Conference","location":"Berkeley, CA, United States"},"date_updated":"2024-02-26T10:12:19Z","day":"24","article_number":"55","ddc":["000"],"_id":"15008","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773096"]},"quality_controlled":"1","acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets), 2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398 and a Sloan Research Fellowship.","article_processing_charge":"No","type":"conference","scopus_import":"1","volume":287,"has_accepted_license":"1","author":[{"last_name":"Goranci","full_name":"Goranci, Gramoz","first_name":"Gramoz"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"full_name":"Sachdeva, Sushant","last_name":"Sachdeva","first_name":"Sushant"},{"last_name":"Sricharan","full_name":"Sricharan, A. R.","first_name":"A. R."}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"status":"public","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2024","intvolume":" 286","publication":"27th International Conference on Principles of Distributed Systems","oa":1,"abstract":[{"lang":"eng","text":"Traditional blockchains grant the miner of a block full control not only over which transactions but also their order. This constitutes a major flaw discovered with the introduction of decentralized finance and allows miners to perform MEV attacks. In this paper, we address the issue of sandwich attacks by providing a construction that takes as input a blockchain protocol and outputs a new blockchain protocol with the same security but in which sandwich attacks are not profitable. Furthermore, our protocol is fully decentralized with no trusted third parties or heavy cryptography primitives and carries a linear increase in latency and minimum computation overhead."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-02-26T10:16:57Z","doi":"10.4230/LIPIcs.OPODIS.2023.12","file":[{"checksum":"2993e810a45e8c8056106834b07aea92","file_id":"15031","file_name":"2024_LIPICs_Alpos.pdf","access_level":"open_access","creator":"dernst","file_size":1505994,"date_created":"2024-02-26T10:16:57Z","relation":"main_file","date_updated":"2024-02-26T10:16:57Z","success":1,"content_type":"application/pdf"}],"citation":{"chicago":"Alpos, Orestis, Ignacio Amores-Sesar, Christian Cachin, and Michelle X Yeo. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12.","ista":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. 2024. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 12.","apa":"Alpos, O., Amores-Sesar, I., Cachin, C., & Yeo, M. X. (2024). Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12","ieee":"O. Alpos, I. Amores-Sesar, C. Cachin, and M. X. Yeo, “Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","ama":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.12","short":"O. Alpos, I. Amores-Sesar, C. Cachin, M.X. Yeo, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Alpos, Orestis, et al. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” 27th International Conference on Principles of Distributed Systems, vol. 286, 12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.12."},"alternative_title":["LIPIcs"],"title":"Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks","date_created":"2024-02-18T23:01:02Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","day":"18","date_updated":"2024-02-26T10:18:18Z","conference":{"start_date":"2023-12-06","end_date":"2023-12-08","name":"OPODIS: Conference on Principles of Distributed Systems","location":"Tokyo, Japan"},"language":[{"iso":"eng"}],"date_published":"2024-01-18T00:00:00Z","external_id":{"arxiv":["2307.02954"]},"month":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Alpos","full_name":"Alpos, Orestis","first_name":"Orestis"},{"first_name":"Ignacio","full_name":"Amores-Sesar, Ignacio","last_name":"Amores-Sesar"},{"full_name":"Cachin, Christian","last_name":"Cachin","first_name":"Christian"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","last_name":"Yeo","first_name":"Michelle X"}],"has_accepted_license":"1","volume":286,"type":"conference","scopus_import":"1","article_processing_charge":"No","acknowledgement":"We would like to thank Krzysztof Pietrzak and Jovana Mićić for useful discussions. This work has been funded by the Swiss National Science Foundation (SNSF) under grant agreement Nr. 200021_188443 (Advanced Consensus Protocols).\r\n","quality_controlled":"1","publication_identifier":{"isbn":["9783959773089"],"issn":["1868-8969"]},"_id":"15007","article_number":"12","ddc":["000"]},{"article_processing_charge":"No","acknowledgement":"This project has received funding from the Euro-pean Research Council (ERC) under the EuropeanUnion’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The De-sign of Modern Fully Dynamic Data Structures (Mo-DynStruct)” and the Austrian Science Fund (FWF)project Z 422-N, project “Static and Dynamic Hierar-chical Graph Decompositions”, I 5982-N, and project“Fast Algorithms for a Reactive Network Layer (Re-actNet)”, P 33775-N, with additional funding from thenetidee SCIENCE Stiftung, 2020–2024.D. Sauplic has received funding from the Euro-pean Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreementNo 101034413.","quality_controlled":"1","_id":"14769","publication_identifier":{"eisbn":["9781611977929"]},"author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"full_name":"Saulpic, David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","last_name":"Saulpic","first_name":"David"},{"first_name":"Leonhard","last_name":"Sidl","full_name":"Sidl, Leonhard","id":"8b563fd0-b441-11ee-9101-a3891c61efa6"}],"publisher":"Society for Industrial & Applied Mathematics","type":"conference","scopus_import":"1","conference":{"start_date":"2024-01-07","end_date":"2024-01-08","name":"ALENEX: Workshop on Algorithm Engineering and Experiments","location":"Alexandria, VA, United States"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2310.18034"]},"date_published":"2024-01-04T00:00:00Z","month":"01","day":"04","date_updated":"2024-02-26T09:51:31Z","citation":{"mla":"Henzinger, Monika H., et al. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–33, doi:10.1137/1.9781611977929.17.","short":"M.H. Henzinger, D. Saulpic, L. Sidl, in:, 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–233.","ama":"Henzinger MH, Saulpic D, Sidl L. Experimental evaluation of fully dynamic k-means via coresets. In: 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. Society for Industrial & Applied Mathematics; 2024:220-233. doi:10.1137/1.9781611977929.17","ieee":"M. H. Henzinger, D. Saulpic, and L. Sidl, “Experimental evaluation of fully dynamic k-means via coresets,” in 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Alexandria, VA, United States, 2024, pp. 220–233.","apa":"Henzinger, M. H., Saulpic, D., & Sidl, L. (2024). Experimental evaluation of fully dynamic k-means via coresets. In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments (pp. 220–233). Alexandria, VA, United States: Society for Industrial & Applied Mathematics. https://doi.org/10.1137/1.9781611977929.17","chicago":"Henzinger, Monika H, David Saulpic, and Leonhard Sidl. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, 220–33. Society for Industrial & Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977929.17.","ista":"Henzinger MH, Saulpic D, Sidl L. 2024. Experimental evaluation of fully dynamic k-means via coresets. 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. ALENEX: Workshop on Algorithm Engineering and Experiments, 220–233."},"date_created":"2024-01-09T16:22:47Z","title":"Experimental evaluation of fully dynamic k-means via coresets","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.18034","open_access":"1"}],"ec_funded":1,"oa_version":"Preprint","oa":1,"page":"220-233","doi":"10.1137/1.9781611977929.17","abstract":[{"text":"For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020"},{"grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","status":"public","department":[{"_id":"MoHe"}],"publication_status":"published","year":"2024"},{"ddc":["570"],"article_number":"evae006","_id":"15009","publication_identifier":{"eissn":["1759-6653"]},"quality_controlled":"1","pmid":1,"article_processing_charge":"Yes","scopus_import":"1","type":"journal_article","volume":16,"has_accepted_license":"1","author":[{"last_name":"Bett","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"},{"first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"}],"publisher":"Oxford University Press","month":"01","external_id":{"pmid":["38245839"]},"date_published":"2024-01-20T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2024-02-26T09:59:30Z","day":"20","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"14705","relation":"research_data"}]},"date_created":"2024-02-18T23:01:02Z","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","citation":{"ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/evae006","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006.","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","apa":"Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024."},"file":[{"file_id":"15029","checksum":"106a40f10443b2e7ba66749844ebbdf1","relation":"main_file","file_size":5213306,"date_created":"2024-02-26T09:54:59Z","creator":"dernst","file_name":"2024_GBE_Bett.pdf","access_level":"open_access","success":1,"date_updated":"2024-02-26T09:54:59Z","content_type":"application/pdf"}],"doi":"10.1093/gbe/evae006","file_date_updated":"2024-02-26T09:54:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"article_type":"original","oa":1,"publication":"Genome Biology and Evolution","intvolume":" 16","issue":"1","year":"2024","publication_status":"published","department":[{"_id":"BeVi"}],"status":"public"},{"month":"02","language":[{"iso":"eng"}],"external_id":{"arxiv":["2307.07256"]},"date_published":"2024-02-01T00:00:00Z","date_updated":"2024-02-26T09:45:20Z","day":"01","_id":"15004","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"article_number":"023101","article_processing_charge":"No","acknowledgement":"We thank Bretislav Friedrich, Marjan Mirahmadi, Artem Volosniev, and Burkhard Schmidt for insightful discussions. M.L. acknowledges support by the European Research Council (ERC) under Starting Grant No. 801770 (ANGULON).","quality_controlled":"1","volume":109,"scopus_import":"1","type":"journal_article","author":[{"last_name":"Karle","full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","orcid":"0000-0002-6963-0129"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802"}],"publisher":"American Physical Society","intvolume":" 109","publication":"Physical Review A","issue":"2","year":"2024","status":"public","department":[{"_id":"MiLe"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.07256"}],"ec_funded":1,"oa_version":"Preprint","citation":{"mla":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A, vol. 109, no. 2, 023101, American Physical Society, 2024, doi:10.1103/PhysRevA.109.023101.","short":"V. Karle, M. Lemeshko, Physical Review A 109 (2024).","ama":"Karle V, Lemeshko M. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 2024;109(2). doi:10.1103/PhysRevA.109.023101","apa":"Karle, V., & Lemeshko, M. (2024). Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.023101","ieee":"V. Karle and M. Lemeshko, “Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics,” Physical Review A, vol. 109, no. 2. American Physical Society, 2024.","chicago":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.023101.","ista":"Karle V, Lemeshko M. 2024. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 109(2), 023101."},"title":"Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics","date_created":"2024-02-18T23:01:01Z","doi":"10.1103/PhysRevA.109.023101","abstract":[{"lang":"eng","text":"The impulsive limit (the “sudden approximation”) has been widely employed to describe the interaction between molecules and short, far-off-resonant laser pulses. This approximation assumes that the timescale of the laser-molecule interaction is significantly shorter than the internal rotational period of the molecule, resulting in the rotational motion being instantaneously “frozen” during the interaction. This simplified description of the laser-molecule interaction is incorporated in various theoretical models predicting rotational dynamics of molecules driven by short laser pulses. In this theoretical work, we develop an effective theory for ultrashort laser pulses by examining the full time-evolution operator and solving the time-dependent Schrödinger equation at the operator level. Our findings reveal a critical angular momentum, lcrit, at which the impulsive limit breaks down. In other words, the validity of the sudden approximation depends not only on the pulse duration but also on its intensity, since the latter determines how many angular momentum states are populated. We explore both ultrashort multicycle (Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce distinct effective potentials. We discuss the limitations of the impulsive limit and propose a method that rescales the effective matrix elements, enabling an improved and more accurate description of laser-molecule interactions."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"oa":1,"article_type":"original"},{"_id":"14705","related_material":{"record":[{"relation":"used_in_publication","id":"15009","status":"public"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"contributor":[{"first_name":"Vincent K","contributor_type":"researcher","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Ariana"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","contributor_type":"supervisor","orcid":"0000-0002-4579-8306"},{"contributor_type":"researcher","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"ddc":["576"],"oa_version":"Published Version","citation":{"ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705.","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705","short":"M.N. Elkrewi, (2024).","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705."},"article_processing_charge":"No","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","date_created":"2023-12-22T13:40:48Z","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","file_date_updated":"2023-12-22T14:14:06Z","doi":"10.15479/AT:ISTA:14705","type":"research_data","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"file":[{"file_size":847,"date_created":"2023-12-22T13:54:21Z","relation":"main_file","file_name":"readme.txt.txt","access_level":"open_access","creator":"melkrewi","file_id":"14707","checksum":"bdaf1392867786634ec5466d528c36ca","content_type":"text/plain","date_updated":"2023-12-22T13:54:21Z","success":1},{"success":1,"date_updated":"2023-12-22T14:14:06Z","content_type":"application/x-zip-compressed","checksum":"973e1cbdab923a71709782177980829f","file_id":"14708","creator":"melkrewi","file_name":"data_artemia_franciscana_genome.zip","access_level":"open_access","relation":"main_file","file_size":343632753,"date_created":"2023-12-22T14:14:06Z"}],"publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"}],"month":"01","date_published":"2024-01-02T00:00:00Z","year":"2024","date_updated":"2024-02-26T09:59:29Z","status":"public","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"day":"02"},{"type":"journal_article","volume":174,"has_accepted_license":"1","publisher":"Elsevier","author":[{"first_name":"Yosuke","full_name":"Shimura, Yosuke","last_name":"Shimura"},{"full_name":"Godfrin, Clement","last_name":"Godfrin","first_name":"Clement"},{"first_name":"Andriy","full_name":"Hikavyy, Andriy","last_name":"Hikavyy"},{"last_name":"Li","full_name":"Li, Roy","first_name":"Roy"},{"first_name":"Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"},{"full_name":"Favia, Paola","last_name":"Favia","first_name":"Paola"},{"first_name":"Han","last_name":"Han","full_name":"Han, Han"},{"full_name":"Wan, Danny","last_name":"Wan","first_name":"Danny"},{"first_name":"Kristiaan","full_name":"de Greve, Kristiaan","last_name":"de Greve"},{"first_name":"Roger","last_name":"Loo","full_name":"Loo, Roger"}],"ddc":["530"],"article_number":"108231","publication_identifier":{"issn":["1369-8001"]},"_id":"15018","quality_controlled":"1","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","article_processing_charge":"No","date_updated":"2024-02-26T10:36:35Z","day":"20","month":"02","date_published":"2024-02-20T00:00:00Z","language":[{"iso":"eng"}],"project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515"}],"abstract":[{"lang":"eng","text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.mssp.2024.108231","article_type":"original","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1016/j.mssp.2024.108231","open_access":"1"}],"title":"Compressively strained epitaxial Ge layers for quantum computing applications","date_created":"2024-02-22T14:10:40Z","citation":{"ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing, vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231.","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. Elsevier. https://doi.org/10.1016/j.mssp.2024.108231","ieee":"Y. Shimura et al., “Compressively strained epitaxial Ge layers for quantum computing applications,” Materials Science in Semiconductor Processing, vol. 174, no. 5. Elsevier, 2024."},"year":"2024","publication_status":"epub_ahead","status":"public","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"publication":"Materials Science in Semiconductor Processing","intvolume":" 174","issue":"5"},{"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v234/kurtic24a"}],"date_created":"2024-02-18T23:01:03Z","title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","citation":{"ieee":"E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in Proceedings of Machine Learning Research, Hongkong, China, 2024, vol. 234, pp. 542–553.","apa":"Kurtic, E., Hoefler, T., & Alistarh, D.-A. (2024). How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In Proceedings of Machine Learning Research (Vol. 234, pp. 542–553). Hongkong, China: ML Research Press.","chicago":"Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” In Proceedings of Machine Learning Research, 234:542–53. ML Research Press, 2024.","ista":"Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234, 542–553.","mla":"Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” Proceedings of Machine Learning Research, vol. 234, ML Research Press, 2024, pp. 542–53.","short":"E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning Research, ML Research Press, 2024, pp. 542–553.","ama":"Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In: Proceedings of Machine Learning Research. Vol 234. ML Research Press; 2024:542-553."},"alternative_title":["PMLR"],"abstract":[{"lang":"eng","text":"Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"542-553","oa":1,"publication":"Proceedings of Machine Learning Research","intvolume":" 234","year":"2024","publication_status":"published","department":[{"_id":"DaAl"}],"status":"public","publication_identifier":{"eissn":["2640-3498"]},"_id":"15011","quality_controlled":"1","article_processing_charge":"No","scopus_import":"1","type":"conference","volume":234,"publisher":"ML Research Press","author":[{"first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar","last_name":"Kurtic"},{"first_name":"Torsten","full_name":"Hoefler, Torsten","last_name":"Hoefler"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"month":"01","date_published":"2024-01-08T00:00:00Z","external_id":{"arxiv":["2312.13547"]},"conference":{"name":"CPAL: Conference on Parsimony and Learning","start_date":"2024-01-03","end_date":"2024-01-06","location":"Hongkong, China"},"language":[{"iso":"eng"}],"date_updated":"2024-02-26T10:30:52Z","day":"08"},{"author":[{"first_name":"Paul","orcid":"0000-0002-5728-9189","last_name":"Robin","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","full_name":"Robin, Paul"}],"publisher":"AIP Publishing","has_accepted_license":"1","volume":160,"type":"journal_article","scopus_import":"1","pmid":1,"acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","_id":"15024","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"ddc":["540"],"article_number":"064503","day":"14","date_updated":"2024-02-27T08:16:06Z","language":[{"iso":"eng"}],"external_id":{"pmid":["38349632"],"arxiv":["2311.11784"]},"date_published":"2024-02-14T00:00:00Z","month":"02","oa":1,"article_type":"original","doi":"10.1063/5.0188215","file_date_updated":"2024-02-27T08:12:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions.","lang":"eng"}],"file":[{"date_updated":"2024-02-27T08:12:52Z","success":1,"content_type":"application/pdf","file_id":"15034","checksum":"0a5e0ae70849bce674466fc054390ec0","date_created":"2024-02-27T08:12:52Z","file_size":5452738,"relation":"main_file","file_name":"2024_JourChemicalPhysics_Robin.pdf","access_level":"open_access","creator":"dernst"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"citation":{"ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","short":"P. Robin, Journal of Chemical Physics 160 (2024).","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215."},"title":"Correlation-induced viscous dissipation in concentrated electrolytes","date_created":"2024-02-25T23:00:55Z","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"EdHa"}],"status":"public","publication_status":"published","year":"2024","issue":"6","intvolume":" 160","publication":"Journal of Chemical Physics"},{"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation.","publication_identifier":{"issn":["1050-5164"]},"_id":"15025","publisher":"Institute of Mathematical Statistics","author":[{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2625-495X","first_name":"Benjamin","id":"b0cc634c-d549-11ee-96c8-87338c7ad808","full_name":"McKenna, Benjamin","last_name":"McKenna"}],"scopus_import":"1","type":"journal_article","volume":34,"date_published":"2024-02-01T00:00:00Z","external_id":{"arxiv":["2208.12206"]},"language":[{"iso":"eng"}],"month":"02","day":"01","date_updated":"2024-02-27T08:29:05Z","title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","date_created":"2024-02-25T23:00:56Z","citation":{"chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/23-AAP2000.","ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” Annals of Applied Probability, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","apa":"Erdös, L., & McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AAP2000","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 2024;34(1B):1623-1662. doi:10.1214/23-AAP2000","mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:10.1214/23-AAP2000.","short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662."},"oa_version":"Preprint","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.12206"}],"page":"1623-1662","oa":1,"article_type":"original","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble.","lang":"eng"}],"doi":"10.1214/23-AAP2000","issue":"1B","publication":"Annals of Applied Probability","intvolume":" 34","publication_status":"published","department":[{"_id":"LaEr"}],"status":"public","year":"2024"},{"type":"journal_article","has_accepted_license":"1","volume":13,"author":[{"last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","first_name":"Maciek","orcid":"0000-0001-6463-5257"},{"first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana","last_name":"Matijevic"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"publisher":"eLife Sciences Publications","ddc":["580"],"_id":"15033","publication_identifier":{"issn":["2050-084X"]},"quality_controlled":"1","article_processing_charge":"Yes","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","date_updated":"2024-02-28T12:29:43Z","day":"21","month":"02","date_published":"2024-02-21T00:00:00Z","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"doi":"10.7554/elife.68993","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"article_type":"original","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.7554/eLife.68993","open_access":"1"}],"ec_funded":1,"date_created":"2024-02-27T07:10:11Z","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","citation":{"ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.68993.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.","apa":"Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68993","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife Sciences Publications, 2024."},"year":"2024","publication_status":"epub_ahead","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"department":[{"_id":"JiFr"}],"status":"public","publication":"eLife","intvolume":" 13"},{"doi":"10.1016/j.cub.2024.01.017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.","lang":"eng"}],"article_type":"original","oa":1,"page":"902-909.e6","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.26.564092","open_access":"1"}],"oa_version":"Preprint","citation":{"ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017.","ieee":"E. Csata et al., “Fungal infection alters collective nutritional intake of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6. doi:10.1016/j.cub.2024.01.017","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:10.1016/j.cub.2024.01.017."},"date_created":"2023-10-31T13:30:20Z","title":"Fungal infection alters collective nutritional intake of ant colonies","year":"2024","status":"public","department":[{"_id":"SyCr"}],"publication_status":"published","intvolume":" 34","publication":"Current Biology","issue":"4","volume":34,"scopus_import":"1","type":"journal_article","author":[{"full_name":"Csata, Eniko","last_name":"Csata","first_name":"Eniko"},{"first_name":"Alfonso","last_name":"Perez-Escudero","full_name":"Perez-Escudero, Alfonso"},{"first_name":"Emmanuel","full_name":"Laury, Emmanuel","last_name":"Laury"},{"first_name":"Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","full_name":"Leitner, Hanna","last_name":"Leitner"},{"first_name":"Gerard","last_name":"Latil","full_name":"Latil, Gerard"},{"last_name":"Heinze","full_name":"Heinze, Juerge","first_name":"Juerge"},{"full_name":"Simpson, Stephen","last_name":"Simpson","first_name":"Stephen"},{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"},{"last_name":"Dussutour","full_name":"Dussutour, Audrey","first_name":"Audrey"}],"publisher":"Elsevier","_id":"14479","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"pmid":1,"article_processing_charge":"No","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","quality_controlled":"1","date_updated":"2024-03-04T07:14:41Z","day":"26","month":"02","language":[{"iso":"eng"}],"external_id":{"pmid":["38307022"]},"date_published":"2024-02-26T00:00:00Z"},{"title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","date_created":"2024-03-01T11:39:33Z","citation":{"ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024, doi:10.1007/s00601-024-01880-x.","ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems. Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.","apa":"Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. Springer Nature. https://doi.org/10.1007/s00601-024-01880-x","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer Nature, 2024."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"article_type":"original","file":[{"checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","file_id":"15049","file_name":"2024_FewBodySys_Varshney.pdf","access_level":"open_access","creator":"dernst","file_size":436712,"date_created":"2024-03-04T07:07:10Z","relation":"main_file","date_updated":"2024-03-04T07:07:10Z","success":1,"content_type":"application/pdf"}],"file_date_updated":"2024-03-04T07:07:10Z","doi":"10.1007/s00601-024-01880-x","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport.","lang":"eng"}],"publication":"Few-Body Systems","intvolume":" 65","publication_status":"published","keyword":["Atomic and Molecular Physics","and Optics"],"department":[{"_id":"MiLe"}],"status":"public","year":"2024","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","article_number":"12","ddc":["530"],"_id":"15045","publication_identifier":{"issn":["1432-5411"]},"author":[{"first_name":"Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul"},{"orcid":"0000-0001-9666-3543","first_name":"Areg","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan"},{"last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"publisher":"Springer Nature","type":"journal_article","scopus_import":"1","volume":65,"has_accepted_license":"1","external_id":{"arxiv":["2401.08454"]},"date_published":"2024-02-17T00:00:00Z","language":[{"iso":"eng"}],"month":"02","day":"17","date_updated":"2024-03-04T07:08:16Z"},{"author":[{"full_name":"Jin, Shuwei","last_name":"Jin","first_name":"Shuwei"},{"last_name":"Dai","full_name":"Dai, Kunlun","first_name":"Kunlun"},{"full_name":"Verstraten, Joris","last_name":"Verstraten","first_name":"Joris"},{"full_name":"Dixmerias, Maxime","last_name":"Dixmerias","first_name":"Maxime"},{"first_name":"Ragheed","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"first_name":"Christophe","last_name":"Salomon","full_name":"Salomon, Christophe"},{"first_name":"Bruno","full_name":"Peaudecerf, Bruno","last_name":"Peaudecerf"},{"first_name":"Tim","full_name":"de Jongh, Tim","last_name":"de Jongh"},{"full_name":"Yefsah, Tarik","last_name":"Yefsah","first_name":"Tarik"}],"publisher":"American Physical Society","volume":6,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","article_processing_charge":"Yes","acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","quality_controlled":"1","_id":"15053","publication_identifier":{"issn":["2643-1564"]},"ddc":["530"],"article_number":"013158","day":"13","date_updated":"2024-03-04T07:55:29Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2304.08433"]},"date_published":"2024-02-13T00:00:00Z","month":"02","oa":1,"article_type":"original","file_date_updated":"2024-03-04T07:53:08Z","doi":"10.1103/physrevresearch.6.013158","abstract":[{"text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","date_updated":"2024-03-04T07:53:08Z","success":1,"file_size":4025988,"date_created":"2024-03-04T07:53:08Z","relation":"main_file","file_name":"2024_PhysicalReviewResearch_Jin.pdf","access_level":"open_access","creator":"dernst","file_id":"15054","checksum":"ba2ae3e3a011f8897d3803c9366a67e2"}],"citation":{"ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013158.","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158.","chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.","ieee":"S. Jin et al., “Multipurpose platform for analog quantum simulation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158"},"title":"Multipurpose platform for analog quantum simulation","date_created":"2024-03-04T07:42:52Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["General Physics and Astronomy"],"department":[{"_id":"MiLe"}],"status":"public","publication_status":"published","year":"2024","issue":"1","intvolume":" 6","publication":"Physical Review Research"},{"date_created":"2024-03-03T23:00:50Z","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","citation":{"short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. The Company of Biologists. https://doi.org/10.1242/dev.202316","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"id":"14926","status":"public","relation":"research_data"}]},"ec_funded":1,"page":"1-18","article_type":"original","oa":1,"file":[{"relation":"main_file","date_created":"2024-03-04T07:24:43Z","file_size":14839986,"creator":"dernst","file_name":"2024_Development_Schauer.pdf","access_level":"open_access","file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","content_type":"application/pdf","success":1,"date_updated":"2024-03-04T07:24:43Z"}],"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2024-03-04T07:24:43Z","doi":"10.1242/dev.202316","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"issue":"4","publication":"Development","intvolume":" 151","publication_status":"published","status":"public","department":[{"_id":"CaHe"},{"_id":"Bio"}],"year":"2024","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","ddc":["570"],"_id":"15048","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"author":[{"full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","orcid":"0000-0001-7659-9142","first_name":"Alexandra"},{"first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha"},{"first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"publisher":"The Company of Biologists","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":151,"date_published":"2024-02-01T00:00:00Z","language":[{"iso":"eng"}],"month":"02","day":"01","date_updated":"2024-03-04T07:28:25Z"},{"type":"software","file":[{"date_updated":"2024-02-02T14:40:31Z","success":1,"content_type":"application/octet-stream","checksum":"df7f358ae19a176cf710c0a802ce31b1","file_id":"14927","file_name":"README.md","access_level":"open_access","creator":"rhauschild","date_created":"2024-02-02T14:40:31Z","file_size":736,"relation":"main_file"},{"date_created":"2024-02-02T14:40:31Z","file_size":3543,"relation":"main_file","access_level":"open_access","file_name":"Supplementary_file_1.zip","creator":"rhauschild","file_id":"14928","checksum":"10194cc11619eccd8f4b24472e465b7f","content_type":"application/x-zip-compressed","date_updated":"2024-02-02T14:40:31Z","success":1}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-02-02T14:40:31Z","doi":"10.15479/AT:ISTA:14926","publisher":"ISTA","author":[{"orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild"}],"oa":1,"tmp":{"short":"MIT","legal_code_url":"https://opensource.org/licenses/MIT","name":"The MIT License"},"ddc":["570"],"related_material":{"record":[{"id":"15048","status":"public","relation":"used_in_publication"}]},"_id":"14926","title":"Matlab script for analysis of clone dispersal","date_created":"2024-02-02T14:42:26Z","citation":{"short":"R. Hauschild, (2024).","mla":"Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. ISTA, 2024, doi:10.15479/AT:ISTA:14926.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. ISTA. https://doi.org/10.15479/AT:ISTA:14926","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” ISTA, 2024. https://doi.org/10.15479/AT:ISTA:14926.","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, ISTA, 10.15479/AT:ISTA:14926."},"year":"2024","date_updated":"2024-03-04T07:28:25Z","day":"02","license":"https://opensource.org/licenses/MIT","status":"public","department":[{"_id":"Bio"}],"month":"02","date_published":"2024-02-02T00:00:00Z"},{"issue":"8","intvolume":" 10","publication":"Science Advances","status":"public","department":[{"_id":"CaMu"}],"publication_status":"published","year":"2024","citation":{"ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801.","apa":"Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” Science Advances, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 2024;10(8). doi:10.1126/sciadv.adj6801","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801."},"title":"Intensification of daily tropical precipitation extremes from more organized convection","date_created":"2024-03-03T23:00:50Z","ec_funded":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","description":"News on ISTA Website","relation":"press_release"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","article_type":"original","oa":1,"abstract":[{"lang":"eng","text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1126/sciadv.adj6801","file_date_updated":"2024-03-04T07:34:00Z","file":[{"access_level":"open_access","file_name":"2024_ScienceAdv_Bao.pdf","creator":"dernst","date_created":"2024-03-04T07:34:00Z","file_size":800926,"relation":"main_file","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_id":"15051","content_type":"application/pdf","date_updated":"2024-03-04T07:34:00Z","success":1}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"date_published":"2024-02-23T00:00:00Z","external_id":{"pmid":["38394192"]},"month":"02","day":"23","date_updated":"2024-03-05T09:26:47Z","article_processing_charge":"Yes","acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","pmid":1,"quality_controlled":"1","publication_identifier":{"eissn":["2375-2548"]},"_id":"15047","article_number":"eadj6801","ddc":["550"],"publisher":"American Association for the Advancement of Science","author":[{"first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei","last_name":"Bao"},{"last_name":"Stevens","full_name":"Stevens, Bjorn","first_name":"Bjorn"},{"first_name":"Lukas","full_name":"Kluft, Lukas","last_name":"Kluft"},{"first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"has_accepted_license":"1","volume":10,"scopus_import":"1","type":"journal_article"},{"year":"2024","status":"public","department":[{"_id":"SiHi"},{"_id":"RySh"}],"publication_status":"published","intvolume":" 112","publication":"Neuron","issue":"2","abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-02-06T13:56:15Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.1016/j.neuron.2023.11.009","project":[{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"file":[{"success":1,"date_updated":"2024-02-06T13:56:15Z","content_type":"application/pdf","file_id":"14944","checksum":"32b3788f7085cf44a84108d8faaff3ce","relation":"main_file","file_size":5942467,"date_created":"2024-02-06T13:56:15Z","creator":"dernst","file_name":"2024_Neuron_Cheung.pdf","access_level":"open_access"}],"article_type":"original","oa":1,"page":"230-246.e11","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009","ieee":"G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11."},"title":"Multipotent progenitors instruct ontogeny of the superior colliculus","date_created":"2023-04-27T09:41:48Z","date_updated":"2024-03-05T09:43:02Z","day":"17","month":"01","language":[{"iso":"eng"}],"date_published":"2024-01-17T00:00:00Z","external_id":{"pmid":["38096816"]},"volume":112,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","publisher":"Elsevier","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","first_name":"Giselle T"},{"orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner"},{"last_name":"Krausgruber","full_name":"Krausgruber, Thomas","first_name":"Thomas"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen"},{"id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","full_name":"Schrammel, Martin","last_name":"Schrammel","first_name":"Martin"},{"first_name":"Natalie Y","last_name":"Özgen","full_name":"Özgen, Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090"},{"full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","last_name":"Ivec","first_name":"Alexis"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"publication_identifier":{"issn":["0896-6273"]},"_id":"12875","ddc":["570"],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","pmid":1,"quality_controlled":"1"},{"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses."}],"doi":"10.1038/s41594-023-01201-6","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"oa":1,"article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41594-023-01201-6"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website","relation":"press_release"}]},"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","date_created":"2024-02-12T09:59:45Z","citation":{"mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology."},"year":"2024","publication_status":"epub_ahead","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"status":"public","keyword":["Molecular Biology","Structural Biology"],"publication":"Nature Structural & Molecular Biology","type":"journal_article","has_accepted_license":"1","publisher":"Springer Nature","author":[{"orcid":"0000-0002-3616-8580","first_name":"Julia","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler"},{"first_name":"Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse"},{"last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","first_name":"Andreas"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"first_name":"Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","full_name":"Bauer, Lukas W","last_name":"Bauer"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"ddc":["570"],"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"_id":"14979","quality_controlled":"1","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","article_processing_charge":"Yes (in subscription journal)","pmid":1,"date_updated":"2024-03-05T09:27:47Z","day":"05","month":"02","date_published":"2024-02-05T00:00:00Z","external_id":{"pmid":["38316877"]},"language":[{"iso":"eng"}]},{"publication":"Nature Physics","publication_status":"epub_ahead","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"status":"public","year":"2024","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","date_created":"2024-01-21T23:00:57Z","citation":{"ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1.","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1","ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1038/s41567-023-02302-1","open_access":"1"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/","description":"News on ISTA Website","relation":"press_release"}]},"oa":1,"article_type":"original","project":[{"_id":"2646861A-B435-11E9-9278-68D0E5697425","grant_number":"I03601","name":"Control of embryonic cleavage pattern","call_identifier":"FWF"}],"doi":"10.1038/s41567-023-02302-1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces."}],"date_published":"2024-01-09T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"09","date_updated":"2024-03-05T09:33:38Z","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","_id":"14846","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"author":[{"orcid":"0000-0002-5223-3346","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo"},{"first_name":"Rushikesh","last_name":"Shinde","full_name":"Shinde, Rushikesh"},{"first_name":"Madison","orcid":"0000-0002-8176-4824","last_name":"Bolger-Munro","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","full_name":"Bolger-Munro, Madison"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","first_name":"Matilda"},{"last_name":"Szep","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Gregory","first_name":"Gregory"},{"first_name":"Irene","last_name":"Steccari","full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E"},{"first_name":"David","last_name":"Labrousse Arias","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","full_name":"Labrousse Arias, David"},{"orcid":"0000-0002-9438-4783","first_name":"Vanessa","full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"first_name":"Andrew","full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"publisher":"Springer Nature","type":"journal_article","scopus_import":"1","has_accepted_license":"1"},{"publication_identifier":{"issn":["2663 - 337X"]},"_id":"15020","ddc":["576","519"],"article_processing_charge":"No","supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"has_accepted_license":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Michal","full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik"}],"month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-23T00:00:00Z","date_updated":"2024-03-06T14:22:52Z","day":"23","ec_funded":1,"related_material":{"record":[{"id":"7553","status":"public","relation":"part_of_dissertation"},{"id":"12081","status":"public","relation":"part_of_dissertation"},{"id":"7606","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","citation":{"ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024."},"alternative_title":["ISTA Thesis"],"date_created":"2024-02-23T14:02:04Z","title":"Genetic information and biological optimization","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal."}],"degree_awarded":"PhD","file_date_updated":"2024-02-23T14:20:16Z","doi":"10.15479/at:ista:15020","acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"file":[{"relation":"main_file","date_created":"2024-02-23T13:50:53Z","file_size":7102089,"creator":"mhledik","file_name":"hledik thesis pdfa 2b.pdf","access_level":"open_access","file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","content_type":"application/pdf","success":1,"date_updated":"2024-02-23T13:50:53Z"},{"date_updated":"2024-02-23T14:20:16Z","content_type":"application/zip","file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a","date_created":"2024-02-23T13:50:54Z","file_size":14014790,"relation":"source_file","access_level":"closed","file_name":"hledik thesis source.zip","creator":"mhledik"}],"oa":1,"page":"158","year":"2024","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"status":"public","keyword":["Theoretical biology","Optimality","Evolution","Information"],"publication_status":"published"},{"title":"Eva Benkova","date_created":"2024-01-21T23:00:56Z","citation":{"ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039.","apa":"Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp. R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","ama":"Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039","short":"E. Benková, Eva Benkova, Elsevier, 2024.","mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039."},"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2023.11.039"}],"page":"R3-R5","oa":1,"doi":"10.1016/j.cub.2023.11.039","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability."}],"issue":"1","publication":"Current Biology","intvolume":" 34","publication_status":"published","status":"public","department":[{"_id":"EvBe"}],"year":"2024","quality_controlled":"1","article_processing_charge":"No","_id":"14842","publication_identifier":{"eissn":["1879-0445"]},"author":[{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"publisher":"Elsevier","type":"other_academic_publication","volume":34,"date_published":"2024-01-08T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"08","date_updated":"2024-03-12T12:19:12Z"},{"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","pmid":1,"quality_controlled":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"15084","ddc":["570"],"article_number":"e2301449121","publisher":"Proceedings of the National Academy of Sciences","author":[{"orcid":"0000-0002-3509-1948","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"orcid":"0000-0003-0863-4481","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep","last_name":"Bhandari"},{"full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","last_name":"Önal","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C"},{"full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","first_name":"Carolina"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","last_name":"Le Monnier","first_name":"Elodie"},{"first_name":"Utsa","last_name":"Roy","full_name":"Roy, Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"first_name":"Yukihiro","last_name":"Nakamura","full_name":"Nakamura, Yukihiro"},{"first_name":"Tetsushi","full_name":"Sadakata, Tetsushi","last_name":"Sadakata"},{"first_name":"Makoto","full_name":"Sanbo, Makoto","last_name":"Sanbo"},{"first_name":"Masumi","last_name":"Hirabayashi","full_name":"Hirabayashi, Masumi"},{"full_name":"Rhee, JeongSeop","last_name":"Rhee","first_name":"JeongSeop"},{"first_name":"Nils","last_name":"Brose","full_name":"Brose, Nils"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"has_accepted_license":"1","volume":121,"type":"journal_article","language":[{"iso":"eng"}],"date_published":"2024-02-20T00:00:00Z","external_id":{"pmid":["38346189"]},"month":"02","day":"20","date_updated":"2024-03-12T13:44:18Z","citation":{"ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 121(8), e2301449121.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no. 8. Proceedings of the National Academy of Sciences, 2024.","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 2024;121(8). doi:10.1073/pnas.2301449121","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121 (2024).","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121."},"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","date_created":"2024-03-05T09:23:55Z","ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"13173","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","relation":"press_release","description":"News on ISTA Website"}]},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","article_type":"original","oa":1,"abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-03-12T13:42:42Z","doi":"10.1073/pnas.2301449121","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"file":[{"content_type":"application/pdf","date_updated":"2024-03-12T13:42:42Z","success":1,"file_name":"2024_PNAS_Koppensteiner.pdf","access_level":"open_access","creator":"dernst","date_created":"2024-03-12T13:42:42Z","file_size":13648221,"relation":"main_file","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","file_id":"15110"}],"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"issue":"8","intvolume":" 121","publication":"Proceedings of the National Academy of Sciences","department":[{"_id":"RySh"},{"_id":"PeJo"}],"status":"public","publication_status":"published","year":"2024"},{"author":[{"first_name":"Valentin","full_name":"Hübner, Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","last_name":"Hübner"},{"first_name":"Manuel","full_name":"Staab, Manuel","last_name":"Staab"},{"first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Maria","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"publisher":"Proceedings of the National Academy of Sciences","volume":121,"has_accepted_license":"1","type":"journal_article","pmid":1,"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","quality_controlled":"1","_id":"15083","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"ddc":["000"],"article_number":"e2315558121","day":"05","date_updated":"2024-03-12T13:29:25Z","language":[{"iso":"eng"}],"external_id":{"pmid":["38408249"]},"date_published":"2024-03-05T00:00:00Z","month":"03","article_type":"original","oa":1,"file_date_updated":"2024-03-12T13:12:22Z","doi":"10.1073/pnas.2315558121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation.","lang":"eng"}],"file":[{"success":1,"date_updated":"2024-03-12T13:12:22Z","content_type":"application/pdf","file_id":"15109","checksum":"068520e3efd4d008bb9177e8aedb7d22","relation":"main_file","date_created":"2024-03-12T13:12:22Z","file_size":2203220,"creator":"dernst","file_name":"2024_PNAS_Huebner.pdf","access_level":"open_access"}],"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences, vol. 121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121.","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences 121 (2024).","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National Academy of Sciences, 2024.","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.","ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 121(10), e2315558121."},"title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","date_created":"2024-03-05T09:18:49Z","related_material":{"record":[{"relation":"research_data","id":"15108","status":"public"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/"}]},"ec_funded":1,"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"department":[{"_id":"KrCh"}],"status":"public","publication_status":"published","year":"2024","issue":"10","intvolume":" 121","publication":"Proceedings of the National Academy of Sciences"},{"author":[{"full_name":"Hübner, Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","last_name":"Hübner","first_name":"Valentin"},{"first_name":"Maria","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"oa":1,"publisher":"Zenodo","type":"research_data_reference","doi":"10.5281/ZENODO.10639167","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below.","lang":"eng"}],"date_created":"2024-03-12T13:02:58Z","title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","citation":{"ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.","short":"V. Hübner, M. Kleshnina, (2024).","chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024."},"article_processing_charge":"No","oa_version":"Published Version","ddc":["000"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"used_in_publication","id":"15083","status":"public"}]},"_id":"15108","main_file_link":[{"url":"https://10.5281/zenodo.10639167","open_access":"1"}],"day":"09","department":[{"_id":"KrCh"}],"status":"public","date_updated":"2024-03-12T13:29:26Z","year":"2024","date_published":"2024-02-09T00:00:00Z","month":"02"},{"date_updated":"2024-03-13T09:01:20Z","day":"22","month":"02","date_published":"2024-02-22T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","volume":17,"has_accepted_license":"1","author":[{"last_name":"Schmidt","full_name":"Schmidt, Hauke","first_name":"Hauke"},{"full_name":"Rast, Sebastian","last_name":"Rast","first_name":"Sebastian"},{"first_name":"Jiawei","last_name":"Bao","full_name":"Bao, Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"},{"last_name":"Cassim","full_name":"Cassim, Amrit","first_name":"Amrit"},{"first_name":"Shih Wei","full_name":"Fang, Shih Wei","last_name":"Fang"},{"first_name":"Diego","last_name":"Jimenez-De La Cuesta","full_name":"Jimenez-De La Cuesta, Diego"},{"first_name":"Paul","full_name":"Keil, Paul","last_name":"Keil"},{"last_name":"Kluft","full_name":"Kluft, Lukas","first_name":"Lukas"},{"full_name":"Kroll, Clarissa","last_name":"Kroll","first_name":"Clarissa"},{"first_name":"Theresa","last_name":"Lang","full_name":"Lang, Theresa"},{"first_name":"Ulrike","full_name":"Niemeier, Ulrike","last_name":"Niemeier"},{"last_name":"Schneidereit","full_name":"Schneidereit, Andrea","first_name":"Andrea"},{"first_name":"Andrew I.L.","full_name":"Williams, Andrew I.L.","last_name":"Williams"},{"first_name":"Bjorn","last_name":"Stevens","full_name":"Stevens, Bjorn"}],"publisher":"European Geosciences Union","ddc":["550"],"_id":"15097","publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"quality_controlled":"1","acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","article_processing_charge":"Yes (via OA deal)","year":"2024","publication_status":"published","department":[{"_id":"CaMu"}],"status":"public","publication":"Geoscientific Model Development","intvolume":" 17","issue":"4","file":[{"access_level":"open_access","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","creator":"dernst","date_created":"2024-03-13T08:59:21Z","file_size":13364601,"relation":"main_file","checksum":"270d2340402729b0532f7072ea914cae","file_id":"15111","content_type":"application/pdf","date_updated":"2024-03-13T08:59:21Z","success":1}],"doi":"10.5194/gmd-17-1563-2024","file_date_updated":"2024-03-13T08:59:21Z","abstract":[{"lang":"eng","text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1563-1584","article_type":"original","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"date_created":"2024-03-10T23:00:53Z","title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","citation":{"ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584."}},{"main_file_link":[{"url":"https://doi.org/10.1017/prm.2024.7","open_access":"1"}],"ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"apa":"Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2024.7","ieee":"B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024.","ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.","chicago":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.","short":"B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2024).","mla":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015, Cambridge University Press, 2024, doi:10.1017/prm.2024.7.","ama":"Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7"},"date_created":"2023-01-16T11:45:22Z","title":"Common valuations of division polynomials","doi":"10.1017/prm.2024.7","abstract":[{"lang":"eng","text":"In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_type":"original","oa":1,"publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","year":"2024","keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"department":[{"_id":"TiBr"}],"status":"public","publication_status":"epub_ahead","_id":"12311","publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"ddc":["510"],"article_number":"2203.02015","article_processing_charge":"Yes (via OA deal)","acknowledgement":"Silverman, and Paul Voutier for the comments on the earlier version of this paper. The first author acknowledges the support by Dioscuri programme initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. The second author has been supported by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in arithmetic’ and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","quality_controlled":"1","has_accepted_license":"1","type":"journal_article","scopus_import":"1","author":[{"first_name":"Bartosz","last_name":"Naskręcki","full_name":"Naskręcki, Bartosz"},{"orcid":"0000-0002-0854-0306","first_name":"Matteo","full_name":"Verzobio, Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","last_name":"Verzobio"}],"publisher":"Cambridge University Press","month":"02","language":[{"iso":"eng"}],"external_id":{"arxiv":["2203.02015"]},"date_published":"2024-02-26T00:00:00Z","date_updated":"2024-03-13T11:55:21Z","day":"26"},{"has_accepted_license":"1","scopus_import":"1","type":"journal_article","author":[{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"}],"publisher":"Cell Press","_id":"15099","publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"ddc":["570"],"pmid":1,"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","quality_controlled":"1","date_updated":"2024-03-13T12:08:57Z","day":"22","month":"02","language":[{"iso":"eng"}],"external_id":{"pmid":["38395682"]},"date_published":"2024-02-22T00:00:00Z","doi":"10.1016/j.tig.2024.01.002","abstract":[{"text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"article_type":"review","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tig.2024.01.002"}],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024).","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002."},"date_created":"2024-03-10T23:00:54Z","title":"Diverse pathways to speciation revealed by marine snails","year":"2024","status":"public","department":[{"_id":"NiBa"}],"publication_status":"epub_ahead","publication":"Trends in Genetics"},{"quality_controlled":"1","acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"_id":"15098","publisher":"Springer Nature","author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","last_name":"Agresti","orcid":"0000-0002-9573-2962","first_name":"Antonio"},{"full_name":"Luongo, Eliseo","last_name":"Luongo","first_name":"Eliseo"}],"type":"journal_article","scopus_import":"1","date_published":"2024-02-27T00:00:00Z","external_id":{"arxiv":["2306.11081"]},"language":[{"iso":"eng"}],"month":"02","day":"27","date_updated":"2024-03-13T12:20:23Z","title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","date_created":"2024-03-10T23:00:54Z","citation":{"chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0.","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen.","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen. Springer Nature, 2024.","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0","ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024. doi:10.1007/s00208-024-02812-0","short":"A. Agresti, E. Luongo, Mathematische Annalen (2024).","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, Springer Nature, 2024, doi:10.1007/s00208-024-02812-0."},"oa_version":"Published Version","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-024-02812-0"}],"article_type":"original","oa":1,"project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force."}],"doi":"10.1007/s00208-024-02812-0","publication":"Mathematische Annalen","publication_status":"epub_ahead","status":"public","department":[{"_id":"JuFi"}],"year":"2024"},{"month":"01","conference":{"name":"SODA: Symposium on Discrete Algorigthms","start_date":"2024-01-07","end_date":"2024-01-10","location":"Alexandria, VA, USA"},"language":[{"iso":"eng"}],"date_published":"2024-01-04T00:00:00Z","external_id":{"arxiv":["2311.01115"]},"date_updated":"2024-03-15T12:59:53Z","editor":[{"first_name":"David P.","last_name":"Woodruff","full_name":"Woodruff, David P."}],"day":"04","publication_identifier":{"eisbn":["9781611977912"]},"_id":"15093","acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","article_processing_charge":"No","quality_controlled":"1","type":"conference","publisher":"Society for Industrial and Applied Mathematics","author":[{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Ost, Lara","last_name":"Ost","first_name":"Lara"}],"publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","year":"2024","department":[{"_id":"HeEd"},{"_id":"MoHe"}],"status":"public","publication_status":"published","ec_funded":1,"related_material":{"record":[{"status":"for_moderation","id":"15094","relation":"dissertation_contains"}]},"main_file_link":[{"url":"https://arxiv.org/abs/2311.01115","open_access":"1"}],"oa_version":"Preprint","citation":{"ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11"},"date_created":"2024-03-08T10:27:39Z","title":"Dynamically maintaining the persistent homology of time series","abstract":[{"lang":"eng","text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1137/1.9781611977912.11","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF"},{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020"},{"grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"oa":1,"page":"243 - 295"},{"date_updated":"2024-03-15T12:59:53Z","year":"2024","status":"public","department":[{"_id":"HeEd"}],"publication_status":"submitted","day":"07","month":"02","publication":"arXiv","language":[{"iso":"eng"}],"external_id":{"arxiv":["2212.03128"]},"date_published":"2024-02-07T00:00:00Z","abstract":[{"text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","author":[{"last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832"},{"first_name":"Ondrej","last_name":"Draganov","full_name":"Draganov, Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza","first_name":"Morteza"}],"oa":1,"related_material":{"record":[{"status":"for_moderation","id":"15094","relation":"dissertation_contains"}]},"_id":"15091","main_file_link":[{"url":"https://arxiv.org/abs/2212.03128","open_access":"1"}],"article_number":"2212.03128","oa_version":"Preprint","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"article_processing_charge":"No","citation":{"short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d."},"title":"Chromatic alpha complexes","date_created":"2024-03-08T10:13:59Z"},{"editor":[{"last_name":"Margadant","full_name":"Margadant, Coert","first_name":"Coert"}],"day":"19","series_title":"MIMB","date_updated":"2023-02-03T10:58:56Z","date_published":"2023-01-19T00:00:00Z","external_id":{"pmid":["36653709"]},"language":[{"iso":"eng"}],"month":"01","publisher":"Springer Nature","author":[{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."}],"scopus_import":"1","type":"book_chapter","has_accepted_license":"1","volume":2608,"quality_controlled":"1","article_processing_charge":"No","pmid":1,"ddc":["570"],"publication_identifier":{"eissn":["1940-6029"],"isbn":["9781071628867"],"eisbn":["9781071628874"]},"_id":"12428","publication_status":"published","department":[{"_id":"EdHa"}],"status":"public","year":"2023","publication":"Cell Migration in Three Dimensions","intvolume":" 2608","page":"183-205","oa":1,"file":[{"date_created":"2023-02-03T10:56:39Z","file_size":826598,"relation":"main_file","access_level":"open_access","file_name":"2023_MIMB_Hannezo.pdf","creator":"dernst","file_id":"12500","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","content_type":"application/pdf","date_updated":"2023-02-03T10:56:39Z","success":1}],"abstract":[{"text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-02-03T10:56:39Z","doi":"10.1007/978-1-0716-2887-4_12","date_created":"2023-01-29T23:00:58Z","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","alternative_title":["Methods in Molecular Biology"],"citation":{"apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"issue":"1","publication":"Physical Review Research","intvolume":" 5","publication_status":"published","status":"public","department":[{"_id":"MiLe"}],"year":"2023","date_created":"2023-02-10T09:02:26Z","title":"Dissipative dynamics of an impurity with spin-orbit coupling","citation":{"mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"oa":1,"article_type":"original","project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"file":[{"file_id":"12546","checksum":"6068b62874c0099628a108bb9c5c6bd2","relation":"main_file","file_size":865150,"date_created":"2023-02-13T10:38:10Z","creator":"dernst","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","access_level":"open_access","success":1,"date_updated":"2023-02-13T10:38:10Z","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-02-13T10:38:10Z","doi":"10.1103/physrevresearch.5.013029","date_published":"2023-01-20T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"20","date_updated":"2023-02-20T07:02:00Z","quality_controlled":"1","acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","article_processing_charge":"No","article_number":"013029","ddc":["530"],"publication_identifier":{"issn":["2643-1564"]},"_id":"12534","publisher":"American Physical Society","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","first_name":"Areg"},{"full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","orcid":"0000-0001-6110-2359","first_name":"Alberto"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"type":"journal_article","scopus_import":"1","volume":5,"has_accepted_license":"1"},{"status":"public","department":[{"_id":"ScienComp"}],"keyword":["Genetics"],"publication_status":"published","year":"2023","intvolume":" 55","publication":"Nature Genetics","article_type":"review","oa":1,"page":"333-345","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.","lang":"eng"}],"doi":"10.1038/s41588-022-01260-3","file_date_updated":"2023-02-27T07:46:45Z","file":[{"content_type":"application/pdf","date_updated":"2023-02-27T07:46:45Z","success":1,"access_level":"open_access","file_name":"2023_NatureGenetics_Zeller.pdf","creator":"dernst","file_size":21484855,"date_created":"2023-02-27T07:46:45Z","relation":"main_file","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","file_id":"12688"}],"citation":{"apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3"},"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","date_created":"2023-01-12T12:09:09Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","day":"01","date_updated":"2023-02-27T07:48:24Z","language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","month":"02","publisher":"Springer Nature","author":[{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"last_name":"Yeung","id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake","first_name":"Jake","orcid":"0000-0003-1732-1559"},{"full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza","first_name":"Helena"},{"first_name":"Buys Anton","last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton"},{"last_name":"Bhardwaj","full_name":"Bhardwaj, Vivek","first_name":"Vivek"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"first_name":"Reinier","last_name":"van der Linden","full_name":"van der Linden, Reinier"},{"first_name":"Alexander","last_name":"van Oudenaarden","full_name":"van Oudenaarden, Alexander"}],"volume":55,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"_id":"12158","ddc":["570","000"]},{"day":"01","date_updated":"2023-02-27T09:01:16Z","date_published":"2023-02-01T00:00:00Z","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2023-01-22","end_date":"2023-01-25","location":"Florence, Italy"},"language":[{"iso":"eng"}],"month":"02","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","first_name":"Tobias"},{"last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","orcid":"0000-0001-5103-038X"},{"first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"}],"publisher":"Society for Industrial and Applied Mathematics","type":"conference","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","_id":"12676","publication_identifier":{"isbn":["9781611977554"]},"publication_status":"published","status":"public","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"year":"2023","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","page":"4590-4605","oa":1,"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1137/1.9781611977554.ch173","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"title":"Faster algorithm for turn-based stochastic games with bounded treewidth","date_created":"2023-02-24T12:20:47Z","citation":{"ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173."},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"ec_funded":1},{"date_created":"2023-03-19T23:00:58Z","title":"Fast and scalable channels in Kotlin Coroutines","quality_controlled":"1","article_processing_charge":"No","citation":{"ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 107–18. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118."},"oa_version":"Preprint","_id":"12735","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04986","open_access":"1"}],"publication_identifier":{"isbn":["9798400700156"]},"page":"107-118","oa":1,"author":[{"last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","first_name":"Nikita"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"publisher":"Association for Computing Machinery","type":"conference","scopus_import":"1","doi":"10.1145/3572848.3577481","abstract":[{"lang":"eng","text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2211.04986"]},"date_published":"2023-02-25T00:00:00Z","language":[{"iso":"eng"}],"conference":{"location":"Montreal, QC, Canada","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","start_date":"2023-02-25","end_date":"2023-03-01"},"month":"02","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"25","publication_status":"published","status":"public","department":[{"_id":"DaAl"}],"date_updated":"2023-03-20T07:29:28Z","year":"2023"},{"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","month":"02","date_published":"2023-02-25T00:00:00Z","language":[{"iso":"eng"}],"conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2023-03-01","start_date":"2023-02-25","location":"Montreal, QB, Canada"},"year":"2023","date_updated":"2023-03-20T07:57:27Z","day":"25","publication_status":"published","status":"public","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"oa_version":"Published Version","publication_identifier":{"isbn":["9798400700156"]},"main_file_link":[{"url":"https://doi.org/10.1145/3572848.3577512","open_access":"1"}],"_id":"12736","quality_controlled":"1","date_created":"2023-03-19T23:00:58Z","title":"Unexpected scaling in path copying trees","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","article_processing_charge":"No","citation":{"apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512"},"type":"conference_poster","abstract":[{"text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/3572848.3577512","page":"438-440","publisher":"Association for Computing Machinery","author":[{"full_name":"Aksenov, Vitaly","last_name":"Aksenov","first_name":"Vitaly"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown"},{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","first_name":"Alexander"},{"first_name":"Ilya","full_name":"Kokorin, Ilya","last_name":"Kokorin"}],"oa":1},{"language":[{"iso":"eng"}],"conference":{"location":"Hamburg, Germany","start_date":"2023-03-07","end_date":"2023-03-09","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"external_id":{"arxiv":["2301.01744"]},"date_published":"2023-03-01T00:00:00Z","month":"03","day":"01","date_updated":"2023-03-27T06:46:27Z","article_processing_charge":"No","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","quality_controlled":"1","_id":"12760","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772662"]},"ddc":["000"],"article_number":"36","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"first_name":"Stefan","last_name":"Neumann","full_name":"Neumann, Stefan"},{"first_name":"Harald","last_name":"Räcke","full_name":"Räcke, Harald"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","has_accepted_license":"1","volume":254,"type":"conference","scopus_import":"1","intvolume":" 254","publication":"40th International Symposium on Theoretical Aspects of Computer Science","department":[{"_id":"MoHe"}],"status":"public","publication_status":"published","year":"2023","alternative_title":["LIPIcs"],"citation":{"chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.","ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","mla":"Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” 40th International Symposium on Theoretical Aspects of Computer Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.STACS.2023.36.","short":"M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"date_created":"2023-03-26T22:01:07Z","title":"Dynamic maintenance of monotone dynamic programs and applications","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"doi":"10.4230/LIPIcs.STACS.2023.36","file_date_updated":"2023-03-27T06:37:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack.","lang":"eng"}],"file":[{"relation":"main_file","file_size":872706,"date_created":"2023-03-27T06:37:22Z","creator":"dernst","file_name":"2023_LIPICS_HenzingerM.pdf","access_level":"open_access","file_id":"12769","checksum":"22141ab8bc55188e2dfff665e5daecbd","content_type":"application/pdf","success":1,"date_updated":"2023-03-27T06:37:22Z"}]},{"date_published":"2023-03-10T00:00:00Z","language":[{"iso":"eng"}],"month":"03","day":"10","date_updated":"2023-04-05T10:59:04Z","supervisor":[{"last_name":"Jösch","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"}],"article_processing_charge":"No","ddc":["599","573"],"publication_identifier":{"issn":["2663-337X"]},"_id":"12716","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","full_name":"Burnett, Laura","first_name":"Laura","orcid":"0000-0002-8937-410X"}],"type":"dissertation","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"status":"public","year":"2023","date_created":"2023-03-08T15:19:45Z","title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","alternative_title":["ISTA Thesis"],"citation":{"ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716"},"oa_version":"Published Version","ec_funded":1,"page":"178","oa":1,"project":[{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502"}],"file":[{"access_level":"closed","file_name":"Burnett_Thesis_2023.docx","creator":"lburnett","file_size":23029260,"date_created":"2023-03-08T15:08:46Z","relation":"source_file","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_id":"12717","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-03-08T15:08:46Z"},{"content_type":"application/pdf","success":1,"date_updated":"2023-03-08T15:08:46Z","relation":"main_file","file_size":11959869,"date_created":"2023-03-08T15:08:46Z","creator":"lburnett","file_name":"Burnett_Thesis_2023_pdfA.pdf","access_level":"open_access","file_id":"12718","checksum":"cebc77705288bf4382db9b3541483cd0"}],"abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"doi":"10.15479/at:ista:12716","file_date_updated":"2023-03-08T15:08:46Z"},{"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"file":[{"content_type":"application/pdf","date_updated":"2023-04-25T06:58:36Z","success":1,"file_size":16096413,"date_created":"2023-04-25T06:58:36Z","relation":"main_file","file_name":"2023_LNCS_Chalupa.pdf","access_level":"open_access","creator":"dernst","file_id":"12864","checksum":"120d2c2a38384058ad0630fdf8288312"}],"abstract":[{"lang":"eng","text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-031-30820-8_32","file_date_updated":"2023-04-25T06:58:36Z","page":"535-540","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"date_created":"2023-04-20T08:22:53Z","title":"Bubaak: Runtime monitoring of program verifiers","citation":{"ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In Tools and Algorithms for the Construction and Analysis of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540."},"alternative_title":["LNCS"],"year":"2023","publication_status":"published","department":[{"_id":"ToHe"}],"status":"public","publication":"Tools and Algorithms for the Construction and Analysis of Systems","intvolume":" 13994","type":"conference","has_accepted_license":"1","volume":13994,"publisher":"Springer Nature","author":[{"last_name":"Chalupa","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"ddc":["000"],"publication_identifier":{"eisbn":["9783031308208"],"isbn":["9783031308192"],"issn":["0302-9743"],"eissn":["1611-3349"]},"_id":"12854","quality_controlled":"1","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","article_processing_charge":"No","date_updated":"2023-04-25T07:02:43Z","day":"20","month":"04","date_published":"2023-04-20T00:00:00Z","conference":{"location":"Paris, France","end_date":"2023-04-27","start_date":"2023-04-22","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"language":[{"iso":"eng"}]},{"oa_version":"Preprint","article_number":"2303.14555","main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"_id":"12846","date_created":"2023-04-18T19:16:06Z","title":"Area formula for spherical polygons via prequantization","citation":{"short":"A. Chern, S. Ishida, ArXiv (n.d.).","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555."},"article_processing_charge":"No","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","type":"preprint","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.48550/arXiv.2303.14555","oa":1,"author":[{"first_name":"Albert","last_name":"Chern","full_name":"Chern, Albert"},{"first_name":"Sadashige","last_name":"Ishida","full_name":"Ishida, Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"}],"publication":"arXiv","month":"03","date_published":"2023-03-25T00:00:00Z","external_id":{"arxiv":["2303.14555"]},"language":[{"iso":"eng"}],"year":"2023","date_updated":"2023-04-25T06:51:21Z","day":"25","publication_status":"submitted","status":"public","department":[{"_id":"GradSch"},{"_id":"ChWo"}]},{"publisher":"Springer Nature","author":[{"full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa","first_name":"Marek"},{"first_name":"Fabian","orcid":"0000-0003-1548-0177","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian"},{"first_name":"Stefanie","last_name":"Muroya Lei","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"volume":13991,"has_accepted_license":"1","type":"conference","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031308260"],"isbn":["9783031308253"],"eissn":["1611-3349"]},"_id":"12856","ddc":["000"],"day":"20","date_updated":"2023-04-25T07:19:07Z","language":[{"iso":"eng"}],"conference":{"location":"Paris, France","end_date":"2023-04-27","start_date":"2023-04-22","name":"FASE: Fundamental Approaches to Software Engineering"},"date_published":"2023-04-20T00:00:00Z","month":"04","oa":1,"page":"260-281","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-04-25T07:16:36Z","doi":"10.1007/978-3-031-30826-0_15","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"file":[{"success":1,"date_updated":"2023-04-25T07:16:36Z","content_type":"application/pdf","checksum":"17a7c8e08be609cf2408d37ea55e322c","file_id":"12865","creator":"dernst","access_level":"open_access","file_name":"2023_LNCS_ChalupaM.pdf","relation":"main_file","file_size":580828,"date_created":"2023-04-25T07:16:36Z"}],"alternative_title":["LNCS"],"citation":{"ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15"},"date_created":"2023-04-20T08:29:42Z","title":"Vamos: Middleware for best-effort third-party monitoring","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"12407","status":"public"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","department":[{"_id":"ToHe"}],"status":"public","publication_status":"published","year":"2023","intvolume":" 13991","publication":"Fundamental Approaches to Software Engineering"},{"author":[{"first_name":"Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"first_name":"Fabian","orcid":"0000-0003-1548-0177","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei","first_name":"Stefanie"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"publisher":"Institute of Science and Technology Austria","type":"technical_report","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","ddc":["005"],"_id":"12407","publication_identifier":{"eissn":["2664-1690"]},"day":"27","date_updated":"2023-04-25T07:19:06Z","date_published":"2023-01-27T00:00:00Z","language":[{"iso":"eng"}],"month":"01","page":"38","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2023-01-27T03:18:34Z","success":1,"file_size":662409,"date_created":"2023-01-27T03:18:34Z","relation":"main_file","access_level":"open_access","file_name":"main.pdf","creator":"fmuehlbo","file_id":"12408","checksum":"55426e463fdeafe9777fc3ff635154c7"}],"project":[{"call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"doi":"10.15479/AT:ISTA:12407","file_date_updated":"2023-01-27T03:18:34Z","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","date_created":"2023-01-27T03:18:08Z","alternative_title":["IST Austria Technical Report"],"citation":{"ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407","mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"later_version","id":"12856","status":"public"}]},"ec_funded":1,"publication_status":"published","keyword":["runtime monitoring","best effort","third party"],"department":[{"_id":"ToHe"}],"status":"public","year":"2023"},{"language":[{"iso":"eng"}],"conference":{"location":"Orlando, FL, United States","start_date":"2023-06-20","end_date":"2023-06-23","name":"STOC: Symposium on Theory of Computing"},"date_published":"2023-06-02T00:00:00Z","external_id":{"arxiv":["2303.04014"]},"month":"06","day":"02","date_updated":"2023-05-22T08:15:19Z","acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073.","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"isbn":["9781450399135"]},"_id":"13048","publisher":"Association for Computing Machinery","author":[{"last_name":"Lieutier","full_name":"Lieutier, André","first_name":"André"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken"}],"type":"conference","publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","department":[{"_id":"HeEd"}],"status":"public","publication_status":"published","year":"2023","citation":{"ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: Proceedings of the 55th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2023:1768-1776. doi:10.1145/3564246.3585113","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–76, doi:10.1145/3564246.3585113.","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776.","chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In Proceedings of the 55th Annual ACM Symposium on Theory of Computing, 1768–76. Association for Computing Machinery, 2023. https://doi.org/10.1145/3564246.3585113.","ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Orlando, FL, United States, 2023, pp. 1768–1776.","apa":"Lieutier, A., & Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In Proceedings of the 55th Annual ACM Symposium on Theory of Computing (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3564246.3585113"},"date_created":"2023-05-22T08:02:02Z","title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/2303.04014","open_access":"1"}],"oa_version":"Preprint","oa":1,"page":"1768-1776","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.","lang":"eng"}],"doi":"10.1145/3564246.3585113","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}]},{"author":[{"first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste"},{"first_name":"Adrian","full_name":"Vladu, Adrian","last_name":"Vladu"},{"first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar","last_name":"Kurtic"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"}],"oa":1,"abstract":[{"text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}],"type":"conference","project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations .","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d.","ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda ."},"article_processing_charge":"No","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","quality_controlled":"1","title":"CrAM: A Compression-Aware Minimizer","date_created":"2023-05-23T11:36:18Z","ec_funded":1,"related_material":{"record":[{"status":"public","id":"13074","relation":"dissertation_contains"}]},"_id":"13053","main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"oa_version":"Preprint","status":"public","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publication_status":"accepted","year":"2023","date_updated":"2023-06-01T12:54:45Z","conference":{"end_date":"2023-05-05","start_date":"2023-05-01","name":"ICLR: International Conference on Learning Representations","location":"Kigali, Rwanda "},"language":[{"iso":"eng"}],"date_published":"2023-05-01T00:00:00Z","external_id":{"arxiv":["2207.14200"]},"publication":"11th International Conference on Learning Representations ","month":"05"},{"date_published":"2023-05-02T00:00:00Z","conference":{"location":"Atlanta, GA, United States","name":"PKC: Public-Key Cryptography","start_date":"2023-05-07","end_date":"2023-05-10"},"language":[{"iso":"eng"}],"month":"05","day":"02","date_updated":"2023-06-19T08:03:37Z","quality_controlled":"1","acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","article_processing_charge":"No","_id":"13143","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031313677"],"eissn":["1611-3349"]},"author":[{"first_name":"Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","full_name":"Hoffmann, Charlotte","last_name":"Hoffmann"},{"last_name":"Hubáček","full_name":"Hubáček, Pavel","first_name":"Pavel"},{"last_name":"Kamath","full_name":"Kamath, Chethan","first_name":"Chethan"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","scopus_import":"1","type":"conference","volume":13940,"publication":"Public-Key Cryptography - PKC 2023","intvolume":" 13940","publication_status":"published","status":"public","department":[{"_id":"KrPi"}],"year":"2023","title":"Certifying giant nonprimes","date_created":"2023-06-18T22:00:47Z","alternative_title":["LNCS"],"citation":{"mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553.","ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: Public-Key Cryptography - PKC 2023. Vol 13940. Springer Nature; 2023:530-553. doi:10.1007/978-3-031-31368-4_19","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in Public-Key Cryptography - PKC 2023, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Pietrzak, K. Z. (2023). Certifying giant nonprimes. In Public-Key Cryptography - PKC 2023 (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-31368-4_19","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In Public-Key Cryptography - PKC 2023, 13940:530–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-31368-4_19."},"oa_version":"Submitted Version","main_file_link":[{"url":"https://eprint.iacr.org/2023/238","open_access":"1"}],"page":"530-553","oa":1,"doi":"10.1007/978-3-031-31368-4_19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality.","lang":"eng"}]},{"publisher":"Springer Nature","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde"}],"type":"conference","scopus_import":"1","has_accepted_license":"1","volume":13993,"quality_controlled":"1","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","article_processing_charge":"No","ddc":["000"],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308222"],"eissn":["1611-3349"]},"_id":"13142","day":"22","date_updated":"2023-06-19T08:30:54Z","date_published":"2023-04-22T00:00:00Z","language":[{"iso":"eng"}],"conference":{"location":"Paris, France","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","start_date":"2023-04-22"},"month":"04","page":"3-25","oa":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"file":[{"success":1,"date_updated":"2023-06-19T08:29:30Z","content_type":"application/pdf","file_id":"13150","checksum":"3d8a8bb24d211bc83360dfc2fd744307","relation":"main_file","file_size":528455,"date_created":"2023-06-19T08:29:30Z","creator":"dernst","file_name":"2023_LNCS_Chatterjee.pdf","access_level":"open_access"}],"abstract":[{"text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-06-19T08:29:30Z","doi":"10.1007/978-3-031-30823-9_1","date_created":"2023-06-18T22:00:47Z","title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","alternative_title":["LNCS"],"citation":{"mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” Tools and Algorithms for the Construction and Analysis of Systems , vol. 13993, Springer Nature, 2023, pp. 3–25, doi:10.1007/978-3-031-30823-9_1.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems . Vol 13993. Springer Nature; 2023:3-25. doi:10.1007/978-3-031-30823-9_1","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in Tools and Algorithms for the Construction and Analysis of Systems , Paris, France, 2023, vol. 13993, pp. 3–25.","apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_1","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In Tools and Algorithms for the Construction and Analysis of Systems , 13993:3–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_1."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"publication_status":"published","status":"public","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2023","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","intvolume":" 13993"},{"intvolume":" 13994","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","status":"public","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2023","citation":{"chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228.","apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15.","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228."},"alternative_title":["LNCS"],"date_created":"2023-06-18T22:00:47Z","title":"Computing adequately permissive assumptions for synthesis","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"page":"211-228","doi":"10.1007/978-3-031-30820-8_15","file_date_updated":"2023-06-19T08:43:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive.","lang":"eng"}],"file":[{"success":1,"date_updated":"2023-06-19T08:43:21Z","content_type":"application/pdf","file_id":"13151","checksum":"60dcafc1b4f6f070be43bad3fe877974","relation":"main_file","date_created":"2023-06-19T08:43:21Z","file_size":521425,"creator":"dernst","file_name":"2023_LNCS_Anand.pdf","access_level":"open_access"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2023-04-22","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Paris, France"},"date_published":"2023-04-20T00:00:00Z","month":"04","day":"20","date_updated":"2023-06-19T08:49:46Z","article_processing_charge":"No","quality_controlled":"1","_id":"13141","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308192"],"eissn":["1611-3349"]},"ddc":["000"],"author":[{"first_name":"Ashwani","full_name":"Anand, Ashwani","last_name":"Anand"},{"last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","full_name":"Mallik, Kaushik","first_name":"Kaushik","orcid":"0000-0001-9864-7475"},{"first_name":"Satya Prakash","full_name":"Nayak, Satya Prakash","last_name":"Nayak"},{"full_name":"Schmuck, Anne Kathrin","last_name":"Schmuck","first_name":"Anne Kathrin"}],"publisher":"Springer Nature","volume":13994,"has_accepted_license":"1","type":"conference","scopus_import":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","date_created":"2023-04-14T14:56:04Z","citation":{"ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826."},"alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2023-04-20T09:26:51Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"5f589a9af025f7eeebfd0c186209913e","file_id":"12857","creator":"vpokusae","file_name":"Thesis_Pokusaeva.docx","access_level":"closed","relation":"source_file","date_created":"2023-04-20T09:14:38Z","file_size":14507243},{"content_type":"application/pdf","success":1,"date_updated":"2023-04-20T09:14:44Z","relation":"main_file","date_created":"2023-04-20T09:14:44Z","file_size":10090711,"creator":"vpokusae","file_name":"Thesis_Pokusaeva.pdf","access_level":"open_access","file_id":"12858","checksum":"bbeed76db45a996b4c91a9abe12ce0ec"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","file_date_updated":"2023-04-20T09:26:51Z","doi":"10.15479/at:ista:12826","page":"106","oa":1,"year":"2023","publication_status":"published","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"status":"public","ddc":["570","571"],"publication_identifier":{"issn":["2663 - 337X"]},"_id":"12826","supervisor":[{"first_name":"Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","type":"dissertation","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0001-7660-444X","first_name":"Victoria","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva"}],"month":"04","date_published":"2023-04-18T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-06-23T09:47:36Z","day":"18"},{"volume":85,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","author":[{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","first_name":"Georg F"}],"publisher":"Springer Nature","_id":"12086","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"ddc":["510"],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","quality_controlled":"1","date_updated":"2023-06-27T12:53:43Z","day":"01","isi":1,"month":"01","language":[{"iso":"eng"}],"external_id":{"isi":["000846967100001"]},"date_published":"2023-01-01T00:00:00Z","doi":"10.1007/s00453-022-01027-6","file_date_updated":"2023-01-20T10:02:48Z","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.","lang":"eng"}],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00342"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"file":[{"relation":"main_file","file_size":911017,"date_created":"2023-01-20T10:02:48Z","creator":"dernst","file_name":"2023_Algorithmica_Edelsbrunner.pdf","access_level":"open_access","file_id":"12322","checksum":"71685ca5121f4c837f40c3f8eb50c915","content_type":"application/pdf","success":1,"date_updated":"2023-01-20T10:02:48Z"}],"oa":1,"article_type":"original","page":"277-295","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023."},"title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","date_created":"2022-09-11T22:01:57Z","year":"2023","department":[{"_id":"HeEd"}],"status":"public","publication_status":"published","intvolume":" 85","publication":"Algorithmica"},{"file":[{"relation":"main_file","date_created":"2023-01-20T10:45:06Z","file_size":422612,"creator":"dernst","access_level":"open_access","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","file_id":"12325","checksum":"1f34f3e2cb521033de6154f274ea3a4e","content_type":"application/pdf","success":1,"date_updated":"2023-01-20T10:45:06Z"}],"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208"},{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-01-20T10:45:06Z","doi":"10.1007/s00028-022-00859-7","oa":1,"article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","date_created":"2023-01-08T23:00:53Z","citation":{"mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9."},"year":"2023","publication_status":"published","department":[{"_id":"JaMa"}],"status":"public","publication":"Journal of Evolution Equations","intvolume":" 23","issue":"1","scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":23,"publisher":"Springer Nature","author":[{"last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo","orcid":"0000-0002-9881-6870"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior"}],"article_number":"9","ddc":["510"],"publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"_id":"12104","quality_controlled":"1","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","article_processing_charge":"Yes (via OA deal)","date_updated":"2023-06-28T11:54:35Z","day":"01","month":"01","isi":1,"date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000906214600004"]},"language":[{"iso":"eng"}]},{"ddc":["000"],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031308284"]},"_id":"12467","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","type":"conference","scopus_import":"1","volume":13992,"has_accepted_license":"1","publisher":"Springer Nature","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"},{"first_name":"Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien"},{"last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E"}],"month":"04","date_published":"2023-04-21T00:00:00Z","external_id":{"arxiv":["2301.11175"]},"conference":{"start_date":"2023-04-22","end_date":"2023-04-27","name":"FOSSACS: Foundations of Software Science and Computation Structures","location":"Paris, France"},"language":[{"iso":"eng"}],"date_updated":"2023-07-14T11:20:27Z","day":"21","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"title":"Quantitative safety and liveness","date_created":"2023-01-31T07:23:56Z","citation":{"short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17."},"alternative_title":["LNCS"],"file":[{"content_type":"application/pdf","date_updated":"2023-01-31T07:22:21Z","success":1,"file_size":449027,"date_created":"2023-01-31T07:22:21Z","relation":"main_file","access_level":"open_access","file_name":"qsl.pdf","creator":"esarac","file_id":"12468","checksum":"981025aed580b6b27c426cb8856cf63e"},{"content_type":"application/pdf","success":1,"date_updated":"2023-06-19T10:28:09Z","creator":"dernst","access_level":"open_access","file_name":"2023_LNCS_HenzingerT.pdf","relation":"main_file","file_size":1048171,"date_created":"2023-06-19T10:28:09Z","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","file_id":"13153"}],"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"file_date_updated":"2023-06-19T10:28:09Z","doi":"10.1007/978-3-031-30829-1_17","page":"349-370","oa":1,"publication":"26th International Conference Foundations of Software Science and Computation Structures","intvolume":" 13992","year":"2023","publication_status":"published","status":"public","department":[{"_id":"GradSch"},{"_id":"ToHe"}]},{"date_updated":"2023-07-17T08:43:19Z","day":"06","month":"06","date_published":"2023-06-06T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":7,"author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","first_name":"Nikita"},{"last_name":"Khalanskiy","full_name":"Khalanskiy, Dmitry","first_name":"Dmitry"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"publisher":"Association for Computing Machinery ","article_number":"116","ddc":["000"],"_id":"13179","publication_identifier":{"eissn":["2475-1421"]},"quality_controlled":"1","article_processing_charge":"No","year":"2023","publication_status":"published","department":[{"_id":"DaAl"}],"status":"public","publication":"Proceedings of the ACM on Programming Languages","intvolume":" 7","file":[{"file_id":"13187","checksum":"5dba6e73f0ed79adbdae14d165bc2f68","date_created":"2023-07-03T13:09:39Z","file_size":1266773,"relation":"main_file","file_name":"2023_ACMProgram.Lang._Koval.pdf","access_level":"open_access","creator":"alisjak","date_updated":"2023-07-03T13:09:39Z","success":1,"content_type":"application/pdf"}],"doi":"10.1145/3591230","file_date_updated":"2023-07-03T13:09:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives.","lang":"eng"}],"article_type":"original","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"title":"CQS: A formally-verified framework for fair and abortable synchronization","date_created":"2023-07-02T22:00:43Z","citation":{"ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230","chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery , 2023. https://doi.org/10.1145/3591230.","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages, vol. 7, 116, Association for Computing Machinery , 2023, doi:10.1145/3591230.","ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230"}},{"month":"05","date_published":"2023-05-26T00:00:00Z","external_id":{"arxiv":["2203.06881"]},"language":[{"iso":"eng"}],"date_updated":"2023-07-17T08:39:19Z","day":"26","publication_identifier":{"eissn":["1944-4184"],"issn":["1944-4176"]},"_id":"13180","quality_controlled":"1","article_processing_charge":"No","scopus_import":"1","type":"journal_article","volume":16,"publisher":"Mathematical Sciences Publishers","author":[{"orcid":"0000-0002-8314-0177","first_name":"Timothy D","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning"},{"id":"3572849A-F248-11E8-B48F-1D18A9856A87","full_name":"Lyczak, Julian","last_name":"Lyczak","first_name":"Julian"},{"first_name":"Roman","last_name":"Sarapin","full_name":"Sarapin, Roman"}],"publication":"Involve","intvolume":" 16","issue":"2","year":"2023","publication_status":"published","department":[{"_id":"TiBr"}],"status":"public","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2203.06881","open_access":"1"}],"date_created":"2023-07-02T22:00:43Z","title":"Local solubility for a family of quadrics over a split quadric surface","citation":{"apa":"Browning, T. D., Lyczak, J., & Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. Involve. Mathematical Sciences Publishers. https://doi.org/10.2140/involve.2023.16.331","ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” Involve, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/involve.2023.16.331.","ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:10.2140/involve.2023.16.331.","ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. Involve. 2023;16(2):331-342. doi:10.2140/involve.2023.16.331"},"abstract":[{"text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.2140/involve.2023.16.331","page":"331-342","oa":1,"article_type":"original"},{"intvolume":" 13904","publication":"International Conference on Integer Programming and Combinatorial Optimization","year":"2023","status":"public","department":[{"_id":"MoHe"}],"publication_status":"published","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.09217","open_access":"1"}],"oa_version":"Preprint","citation":{"chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” In International Conference on Integer Programming and Combinatorial Optimization, 13904:453–65. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32726-1_32.","ista":"Zheng DW, Henzinger MH. 2023. Multiplicative auction algorithm for approximate maximum weight bipartite matching. International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 13904, 453–465.","apa":"Zheng, D. W., & Henzinger, M. H. (2023). Multiplicative auction algorithm for approximate maximum weight bipartite matching. In International Conference on Integer Programming and Combinatorial Optimization (Vol. 13904, pp. 453–465). Madison, WI, United States: Springer Nature. https://doi.org/10.1007/978-3-031-32726-1_32","ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” in International Conference on Integer Programming and Combinatorial Optimization, Madison, WI, United States, 2023, vol. 13904, pp. 453–465.","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. In: International Conference on Integer Programming and Combinatorial Optimization. Vol 13904. Springer Nature; 2023:453-465. doi:10.1007/978-3-031-32726-1_32","short":"D.W. Zheng, M.H. Henzinger, in:, International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2023, pp. 453–465.","mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” International Conference on Integer Programming and Combinatorial Optimization, vol. 13904, Springer Nature, 2023, pp. 453–65, doi:10.1007/978-3-031-32726-1_32."},"alternative_title":["LNCS"],"title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","date_created":"2023-07-16T22:01:11Z","abstract":[{"text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-031-32726-1_32","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"oa":1,"page":"453-465","month":"05","language":[{"iso":"eng"}],"conference":{"location":"Madison, WI, United States","start_date":"2023-06-21","end_date":"2023-06-23","name":"IPCO: Integer Programming and Combinatorial Optimization"},"date_published":"2023-05-22T00:00:00Z","external_id":{"arxiv":["2301.09217"]},"date_updated":"2023-07-18T07:08:51Z","day":"22","publication_identifier":{"isbn":["9783031327254"],"issn":["0302-9743"],"eissn":["1611-3349"]},"_id":"13236","article_processing_charge":"No","acknowledgement":"The first author thanks to Chandra Chekuri for useful discussions about this paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","quality_controlled":"1","volume":13904,"type":"conference","scopus_import":"1","publisher":"Springer Nature","author":[{"first_name":"Da Wei","last_name":"Zheng","full_name":"Zheng, Da Wei"},{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"}]},{"year":"2023","date_updated":"2023-07-18T09:32:16Z","day":"01","publication_status":"accepted","status":"public","department":[{"_id":"ScienComp"}],"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","month":"07","date_published":"2023-07-01T00:00:00Z","conference":{"end_date":"2023-06-15","start_date":"2023-06-12","name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia"},"language":[{"iso":"eng"}],"type":"conference_abstract","file":[{"success":1,"date_updated":"2023-07-18T09:28:30Z","content_type":"application/pdf","checksum":"0ab6173cd5c5634ed773cd37ff012681","file_id":"13250","creator":"dernst","access_level":"open_access","file_name":"2023_ASHPC_Elefante.pdf","relation":"main_file","date_created":"2023-07-18T09:28:30Z","file_size":380354}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","file_date_updated":"2023-07-18T09:28:30Z","page":"42-42","publisher":"EuroCC","author":[{"first_name":"Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano"},{"full_name":"Stadlbauer, Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","last_name":"Stadlbauer","first_name":"Stephan"},{"full_name":"Alexander, Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Alexander","first_name":"Michael F"},{"first_name":"Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ddc":["000"],"oa_version":"Submitted Version","_id":"13162","quality_controlled":"1","date_created":"2023-06-23T11:03:18Z","title":"Cryo-EM software packages: A sys-admins point of view","article_processing_charge":"No","citation":{"mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :42-42.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 42–42.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC, n.d.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42."}},{"publication_status":"inpress","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"status":"public","year":"2023","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","page":"59-59","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2023-07-18T09:18:55Z","success":1,"file_size":316959,"date_created":"2023-07-18T09:18:55Z","relation":"main_file","access_level":"open_access","file_name":"2023_ASHPC_Schloegl.pdf","creator":"dernst","file_id":"13249","checksum":"ec8e4295d54171032cdd1b01423eb4a6"}],"file_date_updated":"2023-07-18T09:18:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-06-23T11:01:23Z","title":"Running Windows-applications on a Linux HPC cluster using WINE","citation":{"chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59."},"oa_version":"Submitted Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"01","date_updated":"2023-07-18T09:30:54Z","date_published":"2023-07-01T00:00:00Z","language":[{"iso":"eng"}],"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","end_date":"2023-06-15","start_date":"2023-06-13","location":"Maribor, Slovenia"},"month":"07","author":[{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano","first_name":"Stefano"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin"}],"publisher":"EuroCC","type":"conference_abstract","has_accepted_license":"1","quality_controlled":"1","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","article_processing_charge":"No","ddc":["000"],"_id":"13161"},{"status":"public","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"keyword":["General Materials Science","Physical and Theoretical Chemistry"],"publication_status":"published","year":"2023","issue":"27","intvolume":" 14","publication":"The Journal of Physical Chemistry Letters","oa":1,"article_type":"original","page":"6309-6314","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.","lang":"eng"}],"file_date_updated":"2023-07-19T06:55:39Z","doi":"10.1021/acs.jpclett.3c01158","file":[{"file_id":"13253","checksum":"c0c040063f06a51b9c463adc504f1a23","relation":"main_file","file_size":2121252,"date_created":"2023-07-19T06:55:39Z","creator":"dernst","file_name":"2023_JourPhysChemistry_Wei.pdf","access_level":"open_access","success":1,"date_updated":"2023-07-19T06:55:39Z","content_type":"application/pdf"}],"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"citation":{"ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158.","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314."},"date_created":"2023-07-18T11:13:17Z","title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","day":"05","date_updated":"2023-07-19T06:59:19Z","language":[{"iso":"eng"}],"date_published":"2023-07-05T00:00:00Z","external_id":{"arxiv":["2304.14198"],"isi":["001022811500001"]},"isi":1,"month":"07","publisher":"American Chemical Society","author":[{"id":"0c5ff007-2600-11ee-b896-98bd8d663294","full_name":"Wei, Yujing","last_name":"Wei","orcid":"0000-0001-8913-9719","first_name":"Yujing"},{"orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev"},{"first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan","last_name":"Lorenc"},{"full_name":"Zhumekenov, Ayan A.","last_name":"Zhumekenov","first_name":"Ayan A."},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0002-7183-5203","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev"}],"has_accepted_license":"1","volume":14,"type":"journal_article","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication_identifier":{"eissn":["1948-7185"]},"_id":"13251","ddc":["530"]},{"year":"2023","status":"public","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published","intvolume":" 261","publication":"50th International Colloquium on Automata, Languages, and Programming","abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.4230/LIPIcs.ICALP.2023.129","file_date_updated":"2023-07-24T15:11:05Z","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"file":[{"checksum":"5d4c8932ef3450615a53b9bb15d92eb2","file_id":"13293","creator":"esarac","access_level":"open_access","file_name":"icalp23.pdf","relation":"main_file","file_size":859379,"date_created":"2023-07-24T15:11:05Z","success":1,"date_updated":"2023-07-24T15:11:05Z","content_type":"application/pdf"}],"oa":1,"page":"129:1--129:20","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["LIPIcs"],"citation":{"ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129"},"date_created":"2023-07-24T15:11:41Z","title":"Regular methods for operator precedence languages","date_updated":"2023-07-31T08:38:38Z","day":"05","month":"07","language":[{"iso":"eng"}],"conference":{"end_date":"2023-07-14","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany"},"date_published":"2023-07-05T00:00:00Z","external_id":{"arxiv":["2305.03447"]},"has_accepted_license":"1","volume":261,"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724"},{"first_name":"Pavol","last_name":"Kebis","full_name":"Kebis, Pavol"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","first_name":"Naci E"}],"publication_identifier":{"isbn":["9783959772785"],"eissn":["1868-8969"]},"_id":"13292","ddc":["000"],"article_processing_charge":"Yes","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","quality_controlled":"1"},{"author":[{"last_name":"Tucci","full_name":"Tucci, Gennaro","first_name":"Gennaro"},{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","full_name":"De Nicola, Stefano","last_name":"De Nicola","orcid":"0000-0002-4842-6671","first_name":"Stefano"},{"first_name":"Sascha","full_name":"Wald, Sascha","last_name":"Wald"},{"first_name":"Andrea","last_name":"Gambassi","full_name":"Gambassi, Andrea"}],"publisher":"SciPost Foundation","has_accepted_license":"1","volume":6,"type":"journal_article","acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","article_processing_charge":"No","quality_controlled":"1","_id":"13277","publication_identifier":{"issn":["2666-9366"]},"article_number":"029","ddc":["530"],"day":"14","date_updated":"2023-07-31T09:03:28Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2211.01923"]},"date_published":"2023-04-14T00:00:00Z","month":"04","oa":1,"article_type":"original","doi":"10.21468/scipostphyscore.6.2.029","file_date_updated":"2023-07-31T09:02:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results."}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"file":[{"file_id":"13329","checksum":"b472bc82108747eda5d52adf9e2ac7f3","date_created":"2023-07-31T09:02:27Z","file_size":523236,"relation":"main_file","file_name":"2023_SciPostPhysCore_Tucci.pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-07-31T09:02:27Z","success":1,"content_type":"application/pdf"}],"citation":{"apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029.","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029"},"title":"Stochastic representation of the quantum quartic oscillator","date_created":"2023-07-24T10:47:46Z","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"department":[{"_id":"MaSe"}],"status":"public","publication_status":"published","year":"2023","issue":"2","intvolume":" 6","publication":"SciPost Physics Core"},{"publication":"SciPost Physics Codebases","year":"2023","publication_status":"published","department":[{"_id":"MiLe"}],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"id":"13275","status":"public","relation":"research_data"}]},"title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","date_created":"2023-07-24T10:47:15Z","citation":{"ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12."},"file":[{"success":1,"date_updated":"2023-07-31T09:09:23Z","content_type":"application/pdf","checksum":"f583a70fe915d2208c803f5afb426daa","file_id":"13330","creator":"dernst","access_level":"open_access","file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","relation":"main_file","file_size":551418,"date_created":"2023-07-31T09:09:23Z"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-07-31T09:09:23Z","doi":"10.21468/scipostphyscodeb.12","article_type":"original","oa":1,"month":"04","date_published":"2023-04-19T00:00:00Z","external_id":{"arxiv":["2202.04603"]},"language":[{"iso":"eng"}],"date_updated":"2023-07-31T09:16:02Z","day":"19","ddc":["530"],"article_number":"12","publication_identifier":{"issn":["2949-804X"]},"_id":"13276","quality_controlled":"1","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","article_processing_charge":"No","type":"journal_article","has_accepted_license":"1","publisher":"SciPost Foundation","author":[{"first_name":"Lukas","full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}]},{"date_created":"2023-07-24T10:46:23Z","title":"Codebase release 1.0 for FermiFCI","article_processing_charge":"No","citation":{"apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0.","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0.","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0"},"ddc":["530"],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0","open_access":"1"}],"_id":"13275","related_material":{"record":[{"relation":"used_in_publication","id":"13276","status":"public"}]},"ec_funded":1,"oa":1,"author":[{"full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller","first_name":"Lukas"},{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"publisher":"SciPost Foundation","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"type":"research_data_reference","doi":"10.21468/scipostphyscodeb.12-r1.0","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"date_published":"2023-04-19T00:00:00Z","month":"04","day":"19","status":"public","department":[{"_id":"MiLe"}],"date_updated":"2023-07-31T09:16:02Z","year":"2023"},{"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","ddc":["000"],"_id":"13262","publication_identifier":{"isbn":["9781450395458"]},"author":[{"last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander","first_name":"Alexander"},{"id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","full_name":"Hashemi, Diba","last_name":"Hashemi","first_name":"Diba"},{"first_name":"Giorgi","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Association for Computing Machinery","type":"conference","scopus_import":"1","has_accepted_license":"1","external_id":{"arxiv":["2304.09331"]},"date_published":"2023-06-17T00:00:00Z","language":[{"iso":"eng"}],"conference":{"location":"Orlando, FL, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2023-06-17","end_date":"2023-06-19"},"month":"06","day":"17","date_updated":"2023-07-31T10:54:32Z","title":"Provably-efficient and internally-deterministic parallel Union-Find","date_created":"2023-07-23T22:01:12Z","citation":{"apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"page":"261-271","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2023-07-31T10:53:08Z","success":1,"access_level":"open_access","file_name":"2023_SPAA_Fedorov.pdf","creator":"dernst","file_size":2087937,"date_created":"2023-07-31T10:53:08Z","relation":"main_file","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","file_id":"13334"}],"doi":"10.1145/3558481.3591082","file_date_updated":"2023-07-31T10:53:08Z","abstract":[{"lang":"eng","text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","publication_status":"published","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"status":"public","year":"2023"},{"day":"01","date_updated":"2023-08-01T12:25:44Z","language":[{"iso":"eng"}],"external_id":{"isi":["000815663700001"]},"date_published":"2023-02-01T00:00:00Z","isi":1,"month":"02","author":[{"last_name":"De Jode","full_name":"De Jode, Aurélien","first_name":"Aurélien"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Sean","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle"}],"publisher":"Wiley","volume":16,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","article_processing_charge":"No","quality_controlled":"1","_id":"11479","publication_identifier":{"eissn":["1752-4571"]},"ddc":["576"],"status":"public","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publication_status":"published","year":"2023","issue":"2","intvolume":" 16","publication":"Evolutionary Applications","article_type":"original","oa":1,"page":"542-559","doi":"10.1111/eva.13428","file_date_updated":"2023-02-27T07:10:17Z","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"date_updated":"2023-02-27T07:10:17Z","content_type":"application/pdf","checksum":"d4d6fa9ddf36643af994a6a757919afb","file_id":"12685","creator":"dernst","access_level":"open_access","file_name":"2023_EvolutionaryApplications_DeJode.pdf","relation":"main_file","file_size":2269822,"date_created":"2023-02-27T07:10:17Z"}],"citation":{"apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428"},"date_created":"2022-07-03T22:01:33Z","title":"Ten years of demographic modelling of divergence and speciation in the sea","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"}},{"external_id":{"isi":["001003345000051"]},"date_published":"2023-01-10T00:00:00Z","language":[{"iso":"eng"}],"month":"01","isi":1,"day":"10","date_updated":"2023-08-01T12:31:40Z","quality_controlled":"1","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","article_processing_charge":"No","ddc":["510"],"article_number":"468","_id":"12329","publication_identifier":{"eissn":["2045-2322"]},"author":[{"full_name":"Gómez, Arturo","last_name":"Gómez","first_name":"Arturo"},{"first_name":"Goncalo","full_name":"Oliveira, Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","last_name":"Oliveira"}],"publisher":"Springer Nature","type":"journal_article","scopus_import":"1","volume":13,"has_accepted_license":"1","publication":"Scientific Reports","intvolume":" 13","publication_status":"published","department":[{"_id":"TaHa"}],"status":"public","year":"2023","date_created":"2023-01-22T23:00:55Z","title":"New approaches to epidemic modeling on networks","citation":{"ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9.","apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"article_type":"original","file":[{"file_size":2167792,"date_created":"2023-01-23T07:53:23Z","relation":"main_file","access_level":"open_access","file_name":"2023_ScientificReports_Gomez.pdf","creator":"dernst","file_id":"12336","checksum":"a8b83739f4a951e83e0b2a778f03b327","content_type":"application/pdf","date_updated":"2023-01-23T07:53:23Z","success":1}],"file_date_updated":"2023-01-23T07:53:23Z","doi":"10.1038/s41598-022-19827-9","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection."}]},{"citation":{"apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048"},"title":"Integral points of bounded height on a log Fano threefold","date_created":"2021-01-22T09:31:09Z","main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"oa_version":"Preprint","article_type":"original","oa":1,"page":"6780-6808","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors.","lang":"eng"}],"doi":"10.1093/imrn/rnac048","issue":"8","intvolume":" 2023","publication":"International Mathematics Research Notices","status":"public","department":[{"_id":"TiBr"}],"publication_status":"published","year":"2023","article_processing_charge":"No","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","quality_controlled":"1","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"_id":"9034","publisher":"Oxford Academic","author":[{"orcid":"0000-0001-7302-8256","first_name":"Florian Alexander","full_name":"Wilsch, Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425","last_name":"Wilsch"}],"volume":2023,"type":"journal_article","language":[{"iso":"eng"}],"date_published":"2023-04-01T00:00:00Z","external_id":{"isi":["000773116000001"],"arxiv":["1901.08503"]},"isi":1,"month":"04","day":"01","date_updated":"2023-08-01T12:23:55Z"},{"ddc":["570"],"article_number":"1119002","_id":"12469","publication_identifier":{"eissn":["1664-302X"]},"quality_controlled":"1","pmid":1,"acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","article_processing_charge":"Yes (via OA deal)","type":"journal_article","scopus_import":"1","volume":14,"has_accepted_license":"1","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"orcid":"0000-0002-3712-925X","first_name":"Matthias","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst"},{"first_name":"Anna V","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse"},{"last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana","first_name":"Jaana"},{"last_name":"Oh","full_name":"Oh, Jinook","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","first_name":"Jinook","orcid":"0000-0001-7425-2372"},{"last_name":"Tolonen","full_name":"Tolonen, Lassi","first_name":"Lassi"},{"full_name":"Eder, Thomas","last_name":"Eder","first_name":"Thomas"},{"last_name":"Rattei","full_name":"Rattei, Thomas","first_name":"Thomas"},{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"publisher":"Frontiers","month":"03","isi":1,"external_id":{"pmid":["PPR559293 "],"isi":["000961542100001"]},"date_published":"2023-03-16T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-08-01T12:39:58Z","day":"16","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"date_created":"2023-01-31T08:13:40Z","title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","citation":{"ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002"},"file":[{"access_level":"open_access","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","creator":"dernst","date_created":"2023-04-17T07:49:09Z","file_size":4866332,"relation":"main_file","checksum":"cd52292963acce1111634d9fac08c699","file_id":"12843","content_type":"application/pdf","date_updated":"2023-04-17T07:49:09Z","success":1}],"project":[{"call_identifier":"FWF","name":"Viral pathogens and social immunity in ants","grant_number":"M02076","_id":"25DF61D8-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2023-04-17T07:49:09Z","doi":"10.3389/fmicb.2023.1119002","abstract":[{"lang":"eng","text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"article_type":"original","publication":"Frontiers in Microbiology","intvolume":" 14","year":"2023","publication_status":"published","department":[{"_id":"SyCr"}],"status":"public"},{"article_processing_charge":"No","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","quality_controlled":"1","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"_id":"12287","ddc":["510"],"publisher":"Springer Nature","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"first_name":"Ramsay","full_name":"Dyer, Ramsay","last_name":"Dyer"},{"full_name":"Ghosh, Arijit","last_name":"Ghosh","first_name":"Arijit"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"has_accepted_license":"1","volume":69,"scopus_import":"1","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000862193600001"]},"isi":1,"month":"01","day":"01","date_updated":"2023-08-01T12:47:32Z","citation":{"apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7"},"title":"Local criteria for triangulating general manifolds","date_created":"2023-01-16T10:04:06Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","article_type":"original","oa":1,"page":"156-191","abstract":[{"text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-02-02T11:01:10Z","doi":"10.1007/s00454-022-00431-7","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses","grant_number":"M03073"}],"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-02-02T11:01:10Z","creator":"dernst","access_level":"open_access","file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","relation":"main_file","date_created":"2023-02-02T11:01:10Z","file_size":582850,"checksum":"46352e0ee71e460848f88685ca852681","file_id":"12488"}],"intvolume":" 69","publication":"Discrete & Computational Geometry","department":[{"_id":"HeEd"}],"status":"public","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"publication_status":"published","year":"2023"},{"date_updated":"2023-08-01T12:55:32Z","day":"01","isi":1,"month":"02","language":[{"iso":"eng"}],"external_id":{"isi":["000926043100001"]},"date_published":"2023-02-01T00:00:00Z","has_accepted_license":"1","volume":51,"scopus_import":"1","type":"journal_article","author":[{"first_name":"Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"last_name":"Javoor","full_name":"Javoor, Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"publisher":"Portland Press","_id":"12421","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"ddc":["570"],"acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","article_processing_charge":"No","quality_controlled":"1","year":"2023","keyword":["Biochemistry"],"status":"public","department":[{"_id":"FlSc"}],"publication_status":"published","intvolume":" 51","publication":"Biochemical Society Transactions","issue":"1","doi":"10.1042/bst20220221","file_date_updated":"2023-03-16T07:58:16Z","abstract":[{"lang":"eng","text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-03-16T07:58:16Z","relation":"main_file","date_created":"2023-03-16T07:58:16Z","file_size":10045006,"creator":"dernst","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","access_level":"open_access","file_id":"12728","checksum":"4e7069845e3dad22bb44fb71ec624c60"}],"article_type":"original","oa":1,"page":"87-99","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221"},"date_created":"2023-01-27T10:08:19Z","title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM"},{"citation":{"ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023)."},"date_created":"2023-01-08T23:00:53Z","title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"article_type":"original","file_date_updated":"2023-02-02T12:34:54Z","doi":"10.1017/jfm.2022.1001","abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","date_updated":"2023-02-02T12:34:54Z","success":1,"access_level":"open_access","file_name":"2023_JourFluidMechanics_Marensi.pdf","creator":"dernst","file_size":1931647,"date_created":"2023-02-02T12:34:54Z","relation":"main_file","checksum":"9224f987caefe5dd85a70814d3cce65c","file_id":"12489"}],"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"intvolume":" 954","publication":"Journal of Fluid Mechanics","department":[{"_id":"BjHo"}],"status":"public","publication_status":"published","year":"2023","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","_id":"12105","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"ddc":["530"],"article_number":"A10","author":[{"full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","first_name":"Elena"},{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","last_name":"Yalniz","orcid":"0000-0002-8490-9312","first_name":"Gökhan"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754"},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","orcid":"0000-0003-0423-5010","first_name":"Nazmi B"}],"publisher":"Cambridge University Press","volume":954,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","language":[{"iso":"eng"}],"external_id":{"isi":["000903336600001"],"arxiv":["2101.07516"]},"date_published":"2023-01-10T00:00:00Z","isi":1,"month":"01","day":"10","date_updated":"2023-08-01T12:53:23Z"},{"department":[{"_id":"NiBa"}],"status":"public","publication_status":"published","year":"2023","issue":"1","intvolume":" 77","publication":"Evolution: International journal of organic evolution","article_type":"original","oa":1,"page":"318-328","doi":"10.1093/evolut/qpac004","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004."},"date_created":"2023-02-05T23:00:59Z","title":"A multivariate view of the speciation continuum","main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"oa_version":"Published Version","day":"01","date_updated":"2023-08-01T12:58:30Z","language":[{"iso":"eng"}],"external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"date_published":"2023-01-01T00:00:00Z","isi":1,"month":"01","author":[{"first_name":"Daniel I.","full_name":"Bolnick, Daniel I.","last_name":"Bolnick"},{"last_name":"Hund","full_name":"Hund, Amanda K.","first_name":"Amanda K."},{"last_name":"Nosil","full_name":"Nosil, Patrik","first_name":"Patrik"},{"full_name":"Peng, Foen","last_name":"Peng","first_name":"Foen"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"full_name":"Subramanian, Swapna","last_name":"Subramanian","first_name":"Swapna"},{"first_name":"Jochen B.W.","last_name":"Wolf","full_name":"Wolf, Jochen B.W."},{"first_name":"Roman","full_name":"Yukilevich, Roman","last_name":"Yukilevich"}],"publisher":"Oxford University Press","volume":77,"scopus_import":"1","type":"journal_article","pmid":1,"article_processing_charge":"No","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","quality_controlled":"1","_id":"12514","publication_identifier":{"eissn":["1558-5646"]}},{"author":[{"first_name":"Mohammad","full_name":"Forghani, Mohammad","last_name":"Forghani"},{"first_name":"Christophe","last_name":"Claramunt","full_name":"Claramunt, Christophe"},{"full_name":"Karimipour, Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","last_name":"Karimipour","orcid":"0000-0001-6746-4174","first_name":"Farid"},{"first_name":"Georg","last_name":"Heiler","full_name":"Heiler, Georg"}],"publisher":"Institute of Electrical and Electronics Engineers","type":"conference","has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","article_number":"00093","ddc":["600"],"_id":"12548","publication_identifier":{"eisbn":["9798350346091"],"eissn":["2375-9259"]},"day":"08","date_updated":"2023-08-01T13:15:48Z","external_id":{"isi":["000971492200145"]},"date_published":"2023-02-08T00:00:00Z","language":[{"iso":"eng"}],"conference":{"location":"Orlando, FL, United States","start_date":"2022-11-28","end_date":"2022-12-01","name":"ICDMW: Conference on Data Mining Workshops"},"month":"02","isi":1,"oa":1,"file":[{"file_id":"12549","checksum":"c253bee25e6dfe484f96662daa119cb6","relation":"main_file","file_size":1183339,"date_created":"2023-02-14T07:58:26Z","creator":"fkarimip","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","access_level":"open_access","success":1,"date_updated":"2023-02-14T07:58:26Z","content_type":"application/pdf"}],"file_date_updated":"2023-02-14T07:58:26Z","doi":"10.1109/icdmw58026.2022.00093","abstract":[{"lang":"eng","text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","date_created":"2023-02-14T07:56:21Z","citation":{"ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093."},"oa_version":"Submitted Version","publication_status":"published","department":[{"_id":"HeEd"}],"status":"public","year":"2023","publication":"2022 IEEE International Conference on Data Mining Workshops"},{"date_updated":"2023-08-01T13:11:30Z","day":"01","isi":1,"month":"01","language":[{"iso":"eng"}],"external_id":{"arxiv":["2003.11351"],"isi":["000955000000001"]},"date_published":"2023-01-01T00:00:00Z","volume":52,"type":"journal_article","scopus_import":"1","author":[{"full_name":"Krokhin, Andrei","last_name":"Krokhin","first_name":"Andrei"},{"first_name":"Jakub","orcid":"0000-0003-1245-3456","last_name":"Opršal","full_name":"Opršal, Jakub","id":"ec596741-c539-11ec-b829-c79322a91242"},{"full_name":"Wrochna, Marcin","last_name":"Wrochna","first_name":"Marcin"},{"full_name":"Živný, Stanislav","last_name":"Živný","first_name":"Stanislav"}],"publisher":"Society for Industrial & Applied Mathematics","_id":"12563","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","article_processing_charge":"No","quality_controlled":"1","year":"2023","keyword":["General Mathematics","General Computer Science"],"status":"public","department":[{"_id":"UlWa"}],"publication_status":"published","intvolume":" 52","publication":"SIAM Journal on Computing","issue":"1","doi":"10.1137/20m1378223","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"oa":1,"article_type":"original","page":"38-79","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"ec_funded":1,"oa_version":"Preprint","citation":{"ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223.","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223."},"title":"Topology and adjunction in promise constraint satisfaction","date_created":"2023-02-16T07:03:52Z"},{"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","date_created":"2023-02-12T23:00:59Z","citation":{"ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608"},"doi":"10.1103/PhysRevE.107.014608","abstract":[{"lang":"eng","text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","oa":1,"publication":"Physical Review E","intvolume":" 107","issue":"1","year":"2023","publication_status":"published","status":"public","department":[{"_id":"GradSch"}],"article_number":"014608","_id":"12545","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","scopus_import":"1","type":"journal_article","volume":107,"author":[{"last_name":"Rojas Vega","full_name":"Rojas Vega, Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","first_name":"Mauricio Nicolas"},{"first_name":"Pablo","full_name":"De Castro, Pablo","last_name":"De Castro"},{"first_name":"Rodrigo","full_name":"Soto, Rodrigo","last_name":"Soto"}],"publisher":"American Physical Society","month":"01","isi":1,"external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"date_published":"2023-01-24T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-08-01T13:09:45Z","day":"24"},{"article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"_id":"12427","publisher":"American Mathematical Society","author":[{"first_name":"Francesca","last_name":"Balestrieri","full_name":"Balestrieri, Francesca","id":"3ACCD756-F248-11E8-B48F-1D18A9856A87"}],"volume":151,"type":"journal_article","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000898440000001"]},"isi":1,"month":"01","day":"01","date_updated":"2023-08-01T13:03:32Z","citation":{"ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239","chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239.","ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914.","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239.","short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914.","ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239"},"title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","date_created":"2023-01-29T23:00:58Z","main_file_link":[{"url":"https://hal.science/hal-03013498/","open_access":"1"}],"oa_version":"Preprint","article_type":"original","oa":1,"page":"907-914","abstract":[{"lang":"eng","text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1090/proc/15239","issue":"3","intvolume":" 151","publication":"Proceedings of the American Mathematical Society","department":[{"_id":"TiBr"}],"status":"public","publication_status":"published","year":"2023"},{"department":[{"_id":"PeJo"}],"status":"public","publication_status":"published","year":"2023","issue":"3","intvolume":" 24","publication":"International Journal of Molecular Sciences","oa":1,"article_type":"original","file_date_updated":"2023-02-20T07:09:27Z","doi":"10.3390/ijms24032128","abstract":[{"text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"date_updated":"2023-02-20T07:09:27Z","content_type":"application/pdf","file_id":"12569","checksum":"69a35dcd3e0249f902ab881b06ee2e58","relation":"main_file","date_created":"2023-02-20T07:09:27Z","file_size":2823025,"creator":"dernst","file_name":"2023_IJMS_Mrestani.pdf","access_level":"open_access"}],"citation":{"ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128.","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128"},"date_created":"2023-02-19T23:00:56Z","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"21","date_updated":"2023-08-01T13:16:36Z","language":[{"iso":"eng"}],"external_id":{"isi":["000930324700001"]},"date_published":"2023-01-21T00:00:00Z","isi":1,"month":"01","author":[{"last_name":"Mrestani","full_name":"Mrestani, Achmed","first_name":"Achmed"},{"last_name":"Lichter","full_name":"Lichter, Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","first_name":"Katharina"},{"full_name":"Sirén, Anna Leena","last_name":"Sirén","first_name":"Anna Leena"},{"last_name":"Heckmann","full_name":"Heckmann, Manfred","first_name":"Manfred"},{"first_name":"Mila M.","last_name":"Paul","full_name":"Paul, Mila M."},{"last_name":"Pauli","full_name":"Pauli, Martin","first_name":"Martin"}],"publisher":"MDPI","has_accepted_license":"1","volume":24,"scopus_import":"1","type":"journal_article","article_processing_charge":"No","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","quality_controlled":"1","_id":"12567","publication_identifier":{"eissn":["1422-0067"]},"article_number":"2128","ddc":["570"]},{"day":"28","date_updated":"2023-08-01T13:17:20Z","external_id":{"isi":["000934262700001"]},"date_published":"2023-02-28T00:00:00Z","language":[{"iso":"eng"}],"month":"02","isi":1,"author":[{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"first_name":"Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel"}],"publisher":"Elsevier","type":"journal_article","scopus_import":"1","volume":948,"has_accepted_license":"1","quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","article_processing_charge":"Yes (via OA deal)","ddc":["000"],"article_number":"113733","_id":"12566","publication_identifier":{"issn":["0304-3975"]},"publication_status":"published","department":[{"_id":"DaAl"}],"status":"public","year":"2023","issue":"2","publication":"Theoretical Computer Science","intvolume":" 948","oa":1,"article_type":"original","file":[{"file_id":"12570","checksum":"b27c5290f2f1500c403494364ee39c9f","file_size":602333,"date_created":"2023-02-20T07:30:20Z","relation":"main_file","access_level":"open_access","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","creator":"dernst","date_updated":"2023-02-20T07:30:20Z","success":1,"content_type":"application/pdf"}],"project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","grant_number":"840605","call_identifier":"H2020"}],"file_date_updated":"2023-02-20T07:30:20Z","doi":"10.1016/j.tcs.2023.113733","abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Wait-free approximate agreement on graphs","date_created":"2023-02-19T23:00:55Z","citation":{"ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1},{"day":"19","date_updated":"2023-08-01T13:19:47Z","language":[{"iso":"eng"}],"date_published":"2023-01-19T00:00:00Z","external_id":{"isi":["000915418100026"]},"isi":1,"month":"01","publisher":"Annual Reviews","author":[{"first_name":"Yves","last_name":"Dubief","full_name":"Dubief, Yves"},{"last_name":"Terrapon","full_name":"Terrapon, Vincent E.","first_name":"Vincent E."},{"last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"has_accepted_license":"1","volume":55,"type":"journal_article","scopus_import":"1","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1545-4479"],"issn":["0066-4189"]},"_id":"12681","ddc":["530"],"status":"public","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2023","issue":"1","intvolume":" 55","publication":"Annual Review of Fluid Mechanics","article_type":"original","oa":1,"page":"675-705","abstract":[{"lang":"eng","text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-02-27T09:23:02Z","doi":"10.1146/annurev-fluid-032822-025933","file":[{"date_updated":"2023-02-27T09:23:02Z","success":1,"content_type":"application/pdf","file_id":"12690","checksum":"2666aa3af2a25252d35eb8681d3edff7","file_size":4036706,"date_created":"2023-02-27T09:23:02Z","relation":"main_file","file_name":"2023_AnnReviewFluidMech_Dubief.pdf","access_level":"open_access","creator":"dernst"}],"citation":{"ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","apa":"Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.","short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933"},"title":"Elasto-inertial turbulence","date_created":"2023-02-26T23:01:01Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"date_created":"2023-02-26T23:01:01Z","title":"Transition to turbulence in pipe flow","citation":{"ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957.","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023.","apa":"Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"page":"575-602","article_type":"original","oa":1,"project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960"}],"file":[{"file_id":"12691","checksum":"f99ef30f76cabc9e5e1946b380c16db4","file_size":4769537,"date_created":"2023-02-27T09:35:52Z","relation":"main_file","file_name":"2023_AnnReviewFluidMech_Avila.pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-02-27T09:35:52Z","success":1,"content_type":"application/pdf"}],"doi":"10.1146/annurev-fluid-120720-025957","file_date_updated":"2023-02-27T09:35:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed."}],"publication":"Annual Review of Fluid Mechanics","intvolume":" 55","publication_status":"published","status":"public","department":[{"_id":"BjHo"}],"year":"2023","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","ddc":["530"],"_id":"12682","publication_identifier":{"issn":["0066-4189"]},"author":[{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"full_name":"Barkley, Dwight","last_name":"Barkley","first_name":"Dwight"},{"last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"publisher":"Annual Reviews","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":55,"external_id":{"isi":["000915418100023"]},"date_published":"2023-01-19T00:00:00Z","language":[{"iso":"eng"}],"month":"01","isi":1,"day":"19","date_updated":"2023-08-01T13:20:30Z"},{"publication_status":"published","status":"public","department":[{"_id":"AnSa"}],"year":"2023","publication":"Soft Matter","intvolume":" 19","page":"1695-1704","article_type":"original","oa":1,"file":[{"checksum":"af95aa18b9b01e32fb8f13477c0e2687","file_id":"12711","file_name":"2023_SoftMatter_Araujo.pdf","access_level":"open_access","creator":"cchlebak","date_created":"2023-03-07T09:19:41Z","file_size":3581939,"relation":"main_file","date_updated":"2023-03-07T09:19:41Z","success":1,"content_type":"application/pdf"}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"file_date_updated":"2023-03-07T09:19:41Z","doi":"10.1039/d2sm01562e","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.","lang":"eng"}],"date_created":"2023-03-05T23:01:06Z","title":"Steering self-organisation through confinement","citation":{"chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e.","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","ieee":"N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"day":"06","date_updated":"2023-08-01T13:28:39Z","external_id":{"arxiv":["2204.10059"],"isi":["000940388100001"]},"date_published":"2023-02-06T00:00:00Z","language":[{"iso":"eng"}],"month":"02","isi":1,"author":[{"first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M.","last_name":"Araújo"},{"last_name":"Janssen","full_name":"Janssen, Liesbeth M.C.","first_name":"Liesbeth M.C."},{"first_name":"Thomas","last_name":"Barois","full_name":"Barois, Thomas"},{"full_name":"Boffetta, Guido","last_name":"Boffetta","first_name":"Guido"},{"last_name":"Cohen","full_name":"Cohen, Itai","first_name":"Itai"},{"full_name":"Corbetta, Alessandro","last_name":"Corbetta","first_name":"Alessandro"},{"full_name":"Dauchot, Olivier","last_name":"Dauchot","first_name":"Olivier"},{"full_name":"Dijkstra, Marjolein","last_name":"Dijkstra","first_name":"Marjolein"},{"full_name":"Durham, William M.","last_name":"Durham","first_name":"William M."},{"last_name":"Dussutour","full_name":"Dussutour, Audrey","first_name":"Audrey"},{"first_name":"Simon","last_name":"Garnier","full_name":"Garnier, Simon"},{"first_name":"Hanneke","full_name":"Gelderblom, Hanneke","last_name":"Gelderblom"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"full_name":"Isa, Lucio","last_name":"Isa","first_name":"Lucio"},{"full_name":"Koenderink, Gijsje H.","last_name":"Koenderink","first_name":"Gijsje H."},{"full_name":"Löwen, Hartmut","last_name":"Löwen","first_name":"Hartmut"},{"first_name":"Ralf","full_name":"Metzler, Ralf","last_name":"Metzler"},{"last_name":"Polin","full_name":"Polin, Marco","first_name":"Marco"},{"last_name":"Royall","full_name":"Royall, C. Patrick","first_name":"C. Patrick"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"},{"first_name":"Anupam","last_name":"Sengupta","full_name":"Sengupta, Anupam"},{"first_name":"Cécile","full_name":"Sykes, Cécile","last_name":"Sykes"},{"last_name":"Trianni","full_name":"Trianni, Vito","first_name":"Vito"},{"last_name":"Tuval","full_name":"Tuval, Idan","first_name":"Idan"},{"first_name":"Nicolas","full_name":"Vogel, Nicolas","last_name":"Vogel"},{"first_name":"Julia M.","full_name":"Yeomans, Julia M.","last_name":"Yeomans"},{"full_name":"Zuriguel, Iker","last_name":"Zuriguel","first_name":"Iker"},{"last_name":"Marin","full_name":"Marin, Alvaro","first_name":"Alvaro"},{"full_name":"Volpe, Giorgio","last_name":"Volpe","first_name":"Giorgio"}],"publisher":"Royal Society of Chemistry","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":19,"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","ddc":["540"],"_id":"12708","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]}},{"doi":"10.1038/s41467-023-36841-1","file_date_updated":"2023-03-07T10:58:00Z","abstract":[{"text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"cchlebak","file_name":"2023_NatComm_Cheng.pdf","access_level":"open_access","relation":"main_file","file_size":1946443,"date_created":"2023-03-07T10:58:00Z","checksum":"5ff61ad21511950c15abb73b18613883","file_id":"12713","content_type":"application/pdf","success":1,"date_updated":"2023-03-07T10:58:00Z"}],"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"oa":1,"article_type":"original","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1"},"date_created":"2023-03-05T23:01:04Z","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","year":"2023","department":[{"_id":"BiCh"}],"status":"public","publication_status":"published","intvolume":" 14","publication":"Nature Communications","volume":14,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","author":[{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632"},{"first_name":"Sebastien","last_name":"Hamel","full_name":"Hamel, Sebastien"},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","full_name":"Bethkenhagen, Mandy","last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129","first_name":"Mandy"}],"publisher":"Springer Nature","_id":"12702","publication_identifier":{"eissn":["2041-1723"]},"ddc":["540"],"article_number":"1104","pmid":1,"acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","article_processing_charge":"No","quality_controlled":"1","date_updated":"2023-08-01T13:36:11Z","day":"27","isi":1,"month":"02","language":[{"iso":"eng"}],"external_id":{"pmid":["36843123"],"isi":["000939678300002"]},"date_published":"2023-02-27T00:00:00Z"},{"abstract":[{"text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1186/s13073-023-01161-y","file_date_updated":"2023-03-14T10:29:47Z","file":[{"file_id":"12722","checksum":"833b837910c4db42fb5f0f34125f77a7","date_created":"2023-03-14T10:29:47Z","file_size":4275987,"relation":"main_file","file_name":"2023_GenomeMed_Bernabeu.pdf","access_level":"open_access","creator":"cchlebak","date_updated":"2023-03-14T10:29:47Z","success":1,"content_type":"application/pdf"}],"article_type":"original","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y","ieee":"E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12.","chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y.","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.","short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023).","ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y"},"title":"Refining epigenetic prediction of chronological and biological age","date_created":"2023-03-12T23:01:02Z","year":"2023","department":[{"_id":"MaRo"}],"status":"public","publication_status":"published","intvolume":" 15","publication":"Genome Medicine","has_accepted_license":"1","volume":15,"scopus_import":"1","type":"journal_article","publisher":"Springer Nature","author":[{"last_name":"Bernabeu","full_name":"Bernabeu, Elena","first_name":"Elena"},{"last_name":"Mccartney","full_name":"Mccartney, Daniel L.","first_name":"Daniel L."},{"full_name":"Gadd, Danni A.","last_name":"Gadd","first_name":"Danni A."},{"first_name":"Robert F.","full_name":"Hillary, Robert F.","last_name":"Hillary"},{"first_name":"Ake T.","full_name":"Lu, Ake T.","last_name":"Lu"},{"last_name":"Murphy","full_name":"Murphy, Lee","first_name":"Lee"},{"full_name":"Wrobel, Nicola","last_name":"Wrobel","first_name":"Nicola"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"first_name":"Sarah E.","full_name":"Harris, Sarah E.","last_name":"Harris"},{"first_name":"David","last_name":"Liewald","full_name":"Liewald, David"},{"full_name":"Hayward, Caroline","last_name":"Hayward","first_name":"Caroline"},{"first_name":"Cathie","last_name":"Sudlow","full_name":"Sudlow, Cathie"},{"last_name":"Cox","full_name":"Cox, Simon R.","first_name":"Simon R."},{"last_name":"Evans","full_name":"Evans, Kathryn L.","first_name":"Kathryn L."},{"full_name":"Horvath, Steve","last_name":"Horvath","first_name":"Steve"},{"last_name":"Mcintosh","full_name":"Mcintosh, Andrew M.","first_name":"Andrew M."},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"},{"first_name":"Catalina A.","full_name":"Vallejos, Catalina A.","last_name":"Vallejos"},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."}],"publication_identifier":{"eissn":["1756-994X"]},"_id":"12719","article_number":"12","ddc":["570"],"acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","article_processing_charge":"No","quality_controlled":"1","date_updated":"2023-08-01T13:38:12Z","day":"28","isi":1,"month":"02","language":[{"iso":"eng"}],"date_published":"2023-02-28T00:00:00Z","external_id":{"isi":["000940286600001"]}},{"day":"01","date_updated":"2023-08-01T13:36:50Z","language":[{"iso":"eng"}],"date_published":"2023-03-01T00:00:00Z","external_id":{"arxiv":["2204.07373"],"isi":["000936534100012"]},"isi":1,"month":"03","publisher":"Institute of Electrical and Electronics Engineers","author":[{"first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner"},{"last_name":"Amini","full_name":"Amini, Alexander","first_name":"Alexander"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"volume":8,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["2377-3766"]},"_id":"12704","ddc":["000"],"status":"public","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2023","issue":"3","intvolume":" 8","publication":"IEEE Robotics and Automation Letters","article_type":"original","oa":1,"page":"1595-1602","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.","lang":"eng"}],"file_date_updated":"2023-03-07T12:22:23Z","doi":"10.1109/LRA.2023.3240930","file":[{"success":1,"date_updated":"2023-03-07T12:22:23Z","content_type":"application/pdf","checksum":"5a75dcd326ea66685de2b1aaec259e85","file_id":"12714","creator":"cchlebak","access_level":"open_access","file_name":"2023_IEEERobAutLetters_Lechner.pdf","relation":"main_file","file_size":944052,"date_created":"2023-03-07T12:22:23Z"}],"citation":{"mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930."},"title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","date_created":"2023-03-05T23:01:04Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"11366"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"oa_version":"Preprint","citation":{"apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901","ieee":"A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901"},"title":"Spin-electric coupling in lead halide perovskites","date_created":"2023-03-14T13:11:59Z","doi":"10.1103/physrevlett.130.106901","abstract":[{"lang":"eng","text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"article_type":"original","intvolume":" 130","publication":"Physical Review Letters","issue":"10","year":"2023","keyword":["General Physics and Astronomy"],"status":"public","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication_status":"published","_id":"12723","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_number":"106901","article_processing_charge":"No","quality_controlled":"1","volume":130,"type":"journal_article","scopus_import":"1","author":[{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"},{"first_name":"Abhishek","full_name":"Shiva Kumar, Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","last_name":"Shiva Kumar"},{"first_name":"Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"last_name":"Ashourishokri","full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes"},{"first_name":"Ayan A.","full_name":"Zhumekenov, Ayan A.","last_name":"Zhumekenov"},{"first_name":"Osman M.","full_name":"Bakr, Osman M.","last_name":"Bakr"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Zhanybek","orcid":"0000-0002-7183-5203","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"publisher":"American Physical Society","isi":1,"month":"03","language":[{"iso":"eng"}],"external_id":{"arxiv":["2203.09443"],"isi":["000982435900002"]},"date_published":"2023-03-10T00:00:00Z","date_updated":"2023-08-01T13:39:04Z","day":"10"},{"language":[{"iso":"eng"}],"date_published":"2023-03-15T00:00:00Z","external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"isi":1,"month":"03","day":"15","date_updated":"2023-08-01T13:39:47Z","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"_id":"12724","article_number":"125201","publisher":"American Physical Society","author":[{"first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"},{"last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek"},{"first_name":"Dusan","last_name":"Lorenc","full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Younes","last_name":"Ashourishokri","full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334"},{"first_name":"Ayan","full_name":"Zhumekenov, Ayan","last_name":"Zhumekenov"},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","first_name":"Zhanybek"}],"volume":107,"type":"journal_article","scopus_import":"1","issue":"12","intvolume":" 107","publication":"Physical Review B","status":"public","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication_status":"published","year":"2023","citation":{"ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201.","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201","ieee":"A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023."},"title":"Effective model for studying optical properties of lead halide perovskites","date_created":"2023-03-14T13:13:05Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"oa_version":"Preprint","article_type":"original","oa":1,"abstract":[{"text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/physrevb.107.125201"},{"department":[{"_id":"PeJo"}],"status":"public","publication_status":"published","year":"2023","issue":"3 March","intvolume":" 18","publication":"PLoS ONE","oa":1,"article_type":"original","file_date_updated":"2023-03-27T06:51:09Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1371/journal.pone.0277148","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739"}],"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-03-27T06:51:09Z","creator":"dernst","access_level":"open_access","file_name":"2023_PLoSOne_Rothman.pdf","relation":"main_file","date_created":"2023-03-27T06:51:09Z","file_size":7290413,"checksum":"2380331ec27cc87808826fc64419ac1c","file_id":"12770"}],"citation":{"ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no. 3 March. Public Library of Science, 2023.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0277148","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148"},"date_created":"2023-03-26T22:01:07Z","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"17","date_updated":"2023-08-01T13:46:39Z","language":[{"iso":"eng"}],"external_id":{"isi":["001024737400001"]},"date_published":"2023-03-17T00:00:00Z","isi":1,"month":"03","author":[{"first_name":"Jason Seth","full_name":"Rothman, Jason Seth","last_name":"Rothman"},{"first_name":"Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Holderith","full_name":"Holderith, Noemi","first_name":"Noemi"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"},{"full_name":"Angus Silver, R.","last_name":"Angus Silver","first_name":"R."}],"publisher":"Public Library of Science","volume":18,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","article_processing_charge":"No","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","quality_controlled":"1","_id":"12759","publication_identifier":{"eissn":["1932-6203"]},"article_number":"e0277148","ddc":["570"]},{"day":"17","date_updated":"2023-08-01T13:45:54Z","external_id":{"isi":["000968083500010"]},"date_published":"2023-03-17T00:00:00Z","language":[{"iso":"eng"}],"month":"03","isi":1,"author":[{"last_name":"Hurtig","full_name":"Hurtig, Fredrik","first_name":"Fredrik"},{"full_name":"Burgers, Thomas C.Q.","last_name":"Burgers","first_name":"Thomas C.Q."},{"last_name":"Cezanne","full_name":"Cezanne, Alice","first_name":"Alice"},{"first_name":"Xiuyun","full_name":"Jiang, Xiuyun","last_name":"Jiang"},{"last_name":"Mol","full_name":"Mol, Frank N.","first_name":"Frank N."},{"last_name":"Traparić","full_name":"Traparić, Jovan","first_name":"Jovan"},{"first_name":"Andre Arashiro","full_name":"Pulschen, Andre Arashiro","last_name":"Pulschen"},{"full_name":"Nierhaus, Tim","last_name":"Nierhaus","first_name":"Tim"},{"last_name":"Tarrason-Risa","full_name":"Tarrason-Risa, Gabriel","first_name":"Gabriel"},{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"last_name":"Löwe","full_name":"Löwe, Jan","first_name":"Jan"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"first_name":"Rifka","last_name":"Vlijm","full_name":"Vlijm, Rifka"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"}],"publisher":"American Association for the Advancement of Science","type":"journal_article","scopus_import":"1","volume":9,"has_accepted_license":"1","quality_controlled":"1","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","article_processing_charge":"No","article_number":"eade5224","ddc":["570"],"_id":"12756","publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","status":"public","department":[{"_id":"AnSa"}],"year":"2023","issue":"11","publication":"Science Advances","intvolume":" 9","article_type":"original","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2023-03-27T06:24:49Z","success":1,"date_created":"2023-03-27T06:24:49Z","file_size":1826471,"relation":"main_file","access_level":"open_access","file_name":"2023_ScienceAdvances_Hurtig.pdf","creator":"dernst","file_id":"12768","checksum":"6d7dbe9ed86a116c8a002d62971202c5"}],"project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"file_date_updated":"2023-03-27T06:24:49Z","doi":"10.1126/sciadv.ade5224","abstract":[{"lang":"eng","text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","date_created":"2023-03-26T22:01:06Z","citation":{"ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224","ieee":"F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science Advances, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.ade5224."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1},{"date_updated":"2023-08-01T13:47:14Z","day":"16","isi":1,"month":"03","language":[{"iso":"eng"}],"external_id":{"isi":["000985134400106"]},"date_published":"2023-03-16T00:00:00Z","volume":18,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","author":[{"full_name":"Pak, Marina A.","last_name":"Pak","first_name":"Marina A."},{"first_name":"Karina A.","full_name":"Markhieva, Karina A.","last_name":"Markhieva"},{"last_name":"Novikova","full_name":"Novikova, Mariia S.","first_name":"Mariia S."},{"first_name":"Dmitry S.","last_name":"Petrov","full_name":"Petrov, Dmitry S."},{"first_name":"Ilya S.","full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev"},{"id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","full_name":"Maksimova, Ekaterina","last_name":"Maksimova","first_name":"Ekaterina"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"first_name":"Dmitry N.","full_name":"Ivankov, Dmitry N.","last_name":"Ivankov"}],"publisher":"Public Library of Science","_id":"12758","publication_identifier":{"eissn":["1932-6203"]},"ddc":["570"],"article_number":"e0282689","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","article_processing_charge":"No","quality_controlled":"1","year":"2023","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"status":"public","publication_status":"published","intvolume":" 18","publication":"PLoS ONE","issue":"3","doi":"10.1371/journal.pone.0282689","file_date_updated":"2023-03-27T07:09:08Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding.","lang":"eng"}],"file":[{"content_type":"application/pdf","date_updated":"2023-03-27T07:09:08Z","success":1,"file_size":856625,"date_created":"2023-03-27T07:09:08Z","relation":"main_file","access_level":"open_access","file_name":"2023_PLoSOne_Pak.pdf","creator":"dernst","file_id":"12771","checksum":"0281bdfccf8d76c4e08dd011c603f6b6"}],"oa":1,"article_type":"original","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689"},"title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","date_created":"2023-03-26T22:01:07Z"},{"abstract":[{"text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1042/BCJ20210285","page":"319-333","article_type":"review","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","date_created":"2023-03-26T22:01:06Z","citation":{"ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023."},"year":"2023","publication_status":"published","status":"public","department":[{"_id":"LeSa"}],"publication":"The Biochemical Journal","intvolume":" 480","issue":"5","scopus_import":"1","type":"journal_article","volume":480,"has_accepted_license":"1","publisher":"Portland Press","author":[{"first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"ddc":["570"],"publication_identifier":{"eissn":["1470-8728"],"issn":["0264-6021"]},"_id":"12757","quality_controlled":"1","article_processing_charge":"No","pmid":1,"date_updated":"2023-08-01T13:45:12Z","day":"15","month":"03","isi":1,"date_published":"2023-03-15T00:00:00Z","external_id":{"pmid":["36920092"],"isi":["000957065700001"]},"language":[{"iso":"eng"}]},{"ec_funded":1,"related_material":{"link":[{"url":"https://doi.org/10.6084/m9.figshare.21261771.v1","relation":"research_data"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.","apa":"Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rspa.2022.0685","ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271. The Royal Society, 2023.","ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685","mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:10.1098/rspa.2022.0685.","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023)."},"date_created":"2023-04-02T22:01:09Z","title":"Coexistence times in the Moran process with environmental heterogeneity","abstract":[{"lang":"eng","text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-04-03T06:25:29Z","doi":"10.1098/rspa.2022.0685","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"file":[{"success":1,"date_updated":"2023-04-03T06:25:29Z","content_type":"application/pdf","checksum":"13953d349fbefcb5d21ccc6b303297eb","file_id":"12796","creator":"dernst","access_level":"open_access","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","relation":"main_file","date_created":"2023-04-03T06:25:29Z","file_size":827784}],"oa":1,"article_type":"original","intvolume":" 479","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","issue":"2271","year":"2023","status":"public","department":[{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"eissn":["1471-2946"],"issn":["1364-5021"]},"_id":"12787","article_number":"20220685","ddc":["000"],"acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","article_processing_charge":"No","quality_controlled":"1","has_accepted_license":"1","volume":479,"type":"journal_article","scopus_import":"1","publisher":"The Royal Society","author":[{"first_name":"Jakub","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda"},{"first_name":"Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaveh","full_name":"Kaveh, Kamran","first_name":"Kamran"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"month":"03","language":[{"iso":"eng"}],"date_published":"2023-03-29T00:00:00Z","external_id":{"isi":["000957125500002"]},"date_updated":"2023-08-01T13:58:34Z","day":"29"},{"oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/PhysRevLett.130.103202","project":[{"call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202","mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:10.1103/PhysRevLett.130.103202.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202.","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of periodically kicked molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.130.103202"},"title":"Topological charges of periodically kicked molecules","date_created":"2023-04-02T22:01:10Z","ec_funded":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/","relation":"press_release","description":"News on the ISTA website"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.07067"}],"oa_version":"Preprint","status":"public","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2023","issue":"10","intvolume":" 130","publication":"Physical Review Letters","publisher":"American Physical Society","author":[{"last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker","first_name":"Volker"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","first_name":"Areg"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"}],"volume":130,"type":"journal_article","scopus_import":"1","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"_id":"12788","article_number":"103202","day":"10","date_updated":"2023-08-01T14:02:06Z","language":[{"iso":"eng"}],"date_published":"2023-03-10T00:00:00Z","external_id":{"arxiv":["2206.07067"],"isi":["000957635500003"]},"isi":1,"month":"03"},{"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","article_number":"104502","_id":"12790","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"author":[{"orcid":"0000-0001-9666-3543","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"last_name":"Holder","full_name":"Holder, Tobias","first_name":"Tobias"},{"first_name":"Erez","last_name":"Berg","full_name":"Berg, Erez"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827"}],"publisher":"American Physical Society","scopus_import":"1","type":"journal_article","volume":107,"external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"date_published":"2023-03-01T00:00:00Z","language":[{"iso":"eng"}],"month":"03","isi":1,"day":"01","date_updated":"2023-08-01T13:59:29Z","date_created":"2023-04-02T22:01:10Z","title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","citation":{"ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” Physical Review B, vol. 107, no. 10. American Physical Society, 2023.","apa":"Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502.","chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.","short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.","ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502"},"oa_version":"Preprint","related_material":{"link":[{"url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/","relation":"press_release","description":"News on the ISTA website"}]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.02492","open_access":"1"}],"oa":1,"article_type":"original","doi":"10.1103/PhysRevB.107.104502","abstract":[{"text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"10","publication":"Physical Review B","intvolume":" 107","publication_status":"published","status":"public","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"year":"2023"},{"date_published":"2023-03-20T00:00:00Z","external_id":{"arxiv":["2301.07769"],"isi":["000956387200001"]},"language":[{"iso":"eng"}],"month":"03","isi":1,"day":"20","date_updated":"2023-08-01T14:03:47Z","quality_controlled":"1","acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","article_processing_charge":"No","article_number":"16","publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"_id":"12791","publisher":"Springer Nature","author":[{"full_name":"Clark Di Leoni, Patricio","last_name":"Clark Di Leoni","first_name":"Patricio"},{"id":"cd100965-0804-11ed-9c55-f4878ff4e877","full_name":"Agasthya, Lokahith N","last_name":"Agasthya","first_name":"Lokahith N"},{"first_name":"Michele","last_name":"Buzzicotti","full_name":"Buzzicotti, Michele"},{"first_name":"Luca","full_name":"Biferale, Luca","last_name":"Biferale"}],"scopus_import":"1","type":"journal_article","volume":46,"issue":"3","publication":"The European Physical Journal E","intvolume":" 46","publication_status":"published","status":"public","department":[{"_id":"CaMu"}],"year":"2023","date_created":"2023-04-02T22:01:11Z","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","citation":{"ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer Nature, 2023.","apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00276-9","chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.","ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9"},"oa_version":"Preprint","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2301.07769","open_access":"1"}],"oa":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra."}],"doi":"10.1140/epje/s10189-023-00276-9"},{"title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","date_created":"2023-04-16T22:01:07Z","citation":{"chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016","ieee":"K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"page":"582-596.e7","article_type":"original","oa":1,"file":[{"file_size":7925886,"date_created":"2023-04-17T07:41:25Z","relation":"main_file","access_level":"open_access","file_name":"2023_DevelopmentalCell_Huljev.pdf","creator":"dernst","file_id":"12842","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","content_type":"application/pdf","date_updated":"2023-04-17T07:41:25Z","success":1}],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429"}],"abstract":[{"lang":"eng","text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.devcel.2023.02.016","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"file_date_updated":"2023-04-17T07:41:25Z","issue":"7","publication":"Developmental Cell","intvolume":" 58","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"Bio"}],"status":"public","year":"2023","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","ddc":["570"],"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"_id":"12830","publisher":"Elsevier","author":[{"full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev","first_name":"Karla"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503","first_name":"Diana C"},{"first_name":"Friedrich","last_name":"Preusser","full_name":"Preusser, Friedrich"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene","last_name":"Steccari","first_name":"Irene"},{"orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"last_name":"Naik","full_name":"Naik, Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","first_name":"Suyash","orcid":"0000-0001-8421-5508"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"scopus_import":"1","type":"journal_article","volume":58,"has_accepted_license":"1","date_published":"2023-04-10T00:00:00Z","external_id":{"isi":["000982111800001"]},"language":[{"iso":"eng"}],"month":"04","isi":1,"day":"10","date_updated":"2023-08-01T14:10:38Z"},{"oa":1,"article_type":"original","doi":"10.1063/5.0135893","file_date_updated":"2023-04-17T07:28:38Z","abstract":[{"lang":"eng","text":"The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"date_updated":"2023-04-17T07:28:38Z","content_type":"application/pdf","checksum":"8d801babea4df48e08895c76571bb19e","file_id":"12841","creator":"dernst","file_name":"2023_JourChemicalPhysics_Zeng.pdf","access_level":"open_access","relation":"main_file","file_size":7388057,"date_created":"2023-04-17T07:28:38Z"}],"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"citation":{"mla":"Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:10.1063/5.0135893.","short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023).","ama":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13). doi:10.1063/5.0135893","ieee":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” The Journal of Chemical Physics, vol. 158, no. 13. American Institute of Physics, 2023.","apa":"Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893","ista":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301.","chicago":"Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893."},"date_created":"2023-04-16T22:01:07Z","title":"Variational theory of angulons and their rotational spectroscopy","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2023","issue":"13","intvolume":" 158","publication":"The Journal of Chemical Physics","author":[{"full_name":"Zeng, Zhongda","last_name":"Zeng","first_name":"Zhongda"},{"first_name":"Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"first_name":"Tao","last_name":"Shi","full_name":"Shi, Tao"},{"first_name":"Richard","last_name":"Schmidt","full_name":"Schmidt, Richard"}],"publisher":"American Institute of Physics","has_accepted_license":"1","volume":158,"scopus_import":"1","type":"journal_article","acknowledgement":"We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503).","article_processing_charge":"No","quality_controlled":"1","_id":"12831","publication_identifier":{"eissn":["1089-7690"]},"ddc":["530"],"article_number":"134301","day":"07","date_updated":"2023-08-01T14:08:47Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2211.08070"],"isi":["000970038800001"]},"date_published":"2023-04-07T00:00:00Z","isi":1,"month":"04"},{"file":[{"relation":"main_file","file_size":1958523,"date_created":"2023-04-17T08:36:53Z","creator":"dernst","file_name":"2023_PhysReviewX_Ljubotina.pdf","access_level":"open_access","file_id":"12845","checksum":"ee060cea609af79bba7af74b1ce28078","content_type":"application/pdf","success":1,"date_updated":"2023-04-17T08:36:53Z"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"file_date_updated":"2023-04-17T08:36:53Z","doi":"10.1103/PhysRevX.13.011033","abstract":[{"text":"Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"title":"Superdiffusive energy transport in kinetically constrained models","date_created":"2023-04-16T22:01:09Z","citation":{"ama":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).","mla":"Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:10.1103/PhysRevX.13.011033.","chicago":"Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033.","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033.","ieee":"M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” Physical Review X, vol. 13, no. 1. American Physical Society, 2023.","apa":"Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033"},"year":"2023","publication_status":"published","status":"public","department":[{"_id":"MaSe"}],"publication":"Physical Review X","intvolume":" 13","issue":"1","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":13,"author":[{"last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","first_name":"Marko"},{"full_name":"Desaules, Jean Yves","last_name":"Desaules","first_name":"Jean Yves"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"}],"publisher":"American Physical Society","ddc":["530"],"article_number":"011033","_id":"12839","publication_identifier":{"eissn":["2160-3308"]},"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54].","date_updated":"2023-08-01T14:11:28Z","day":"07","month":"03","isi":1,"external_id":{"isi":["000957625700001"]},"date_published":"2023-03-07T00:00:00Z","language":[{"iso":"eng"}]}]