[{"date_published":"2021-02-03T00:00:00Z","external_id":{"isi":["000658724600010"],"arxiv":["1905.03588"]},"type":"journal_article","publisher":"International Federation for Computational Logic","month":"02","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["510"],"keyword":["computer science","computer science and game theory","logic in computer science"],"quality_controlled":"1","page":"10:1-10:23","day":"03","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","oa":1,"volume":17,"author":[{"first_name":"Milad","last_name":"Aghajohari","full_name":"Aghajohari, Milad"},{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToHe"}],"publication":"Logical Methods in Computer Science","date_updated":"2023-08-17T06:56:42Z","arxiv":1,"intvolume":" 17","title":"Determinacy in discrete-bidding infinite-duration games","publication_status":"published","file_date_updated":"2022-01-26T08:04:50Z","oa_version":"Published Version","article_processing_charge":"No","doi":"10.23638/LMCS-17(1:10)2021","scopus_import":"1","article_type":"original","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship).\r\n","publication_identifier":{"eissn":["1860-5974"]},"_id":"10674","date_created":"2022-01-25T16:32:13Z","file":[{"content_type":"application/pdf","creator":"alisjak","file_id":"10690","checksum":"b35586a50ed1ca8f44767de116d18d81","file_name":"2021_LMCS_AGHAJOHAR.pdf","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2022-01-26T08:04:50Z","date_created":"2022-01-26T08:04:50Z","file_size":819878}],"year":"2021","citation":{"ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” Logical Methods in Computer Science, vol. 17, no. 1. International Federation for Computational Logic, p. 10:1-10:23, 2021.","ista":"Aghajohari M, Avni G, Henzinger TA. 2021. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 17(1), 10:1-10:23.","ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 2021;17(1):10:1-10:23. doi:10.23638/LMCS-17(1:10)2021","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science. International Federation for Computational Logic, 2021. https://doi.org/10.23638/LMCS-17(1:10)2021.","apa":"Aghajohari, M., Avni, G., & Henzinger, T. A. (2021). Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. International Federation for Computational Logic. https://doi.org/10.23638/LMCS-17(1:10)2021","short":"M. Aghajohari, G. Avni, T.A. Henzinger, Logical Methods in Computer Science 17 (2021) 10:1-10:23.","mla":"Aghajohari, Milad, et al. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science, vol. 17, no. 1, International Federation for Computational Logic, 2021, p. 10:1-10:23, doi:10.23638/LMCS-17(1:10)2021."},"abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets.","lang":"eng"}]},{"intvolume":" 2","publication":"Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design","date_updated":"2022-01-26T08:20:41Z","department":[{"_id":"ToHe"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"}],"oa":1,"volume":2,"abstract":[{"lang":"eng","text":"Civl is a static verifier for concurrent programs designed around the conceptual framework of layered refinement,\r\nwhich views the task of verifying a program as a sequence of program simplification steps each justified by its own invariant. Civl verifies a layered concurrent program that compactly expresses all the programs in this sequence and the supporting invariants. This paper presents the design and implementation of the Civl verifier."}],"year":"2021","citation":{"short":"B. Kragl, S. Qadeer, in:, P. Ruzica, M.W. Whalen (Eds.), Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2021, pp. 143–152.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “The Civl Verifier.” In Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design, edited by Piskac Ruzica and Michael W. Whalen, 2:143–152. TU Wien Academic Press, 2021. https://doi.org/10.34727/2021/isbn.978-3-85448-046-4_23.","apa":"Kragl, B., & Qadeer, S. (2021). The Civl verifier. In P. Ruzica & M. W. Whalen (Eds.), Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design (Vol. 2, pp. 143–152). Virtual: TU Wien Academic Press. https://doi.org/10.34727/2021/isbn.978-3-85448-046-4_23","mla":"Kragl, Bernhard, and Shaz Qadeer. “The Civl Verifier.” Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design, edited by Piskac Ruzica and Michael W. Whalen, vol. 2, TU Wien Academic Press, 2021, pp. 143–152, doi:10.34727/2021/isbn.978-3-85448-046-4_23.","ama":"Kragl B, Qadeer S. The Civl verifier. In: Ruzica P, Whalen MW, eds. Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design. Vol 2. TU Wien Academic Press; 2021:143–152. doi:10.34727/2021/isbn.978-3-85448-046-4_23","ieee":"B. Kragl and S. Qadeer, “The Civl verifier,” in Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design, Virtual, 2021, vol. 2, pp. 143–152.","ista":"Kragl B, Qadeer S. 2021. The Civl verifier. Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, Conference Series, vol. 2, 143–152."},"_id":"10688","date_created":"2022-01-26T08:01:30Z","file":[{"checksum":"35438ac9f9750340b7f8ae4ae3220d9f","content_type":"application/pdf","file_id":"10689","creator":"cchlebak","file_size":390555,"relation":"main_file","date_created":"2022-01-26T08:04:29Z","date_updated":"2022-01-26T08:04:29Z","access_level":"open_access","success":1,"file_name":"2021_FCAD2021_Kragl.pdf"}],"editor":[{"first_name":"Piskac","last_name":"Ruzica","full_name":"Ruzica, Piskac"},{"first_name":"Michael W.","last_name":"Whalen","full_name":"Whalen, Michael W."}],"conference":{"start_date":"2021-10-20","location":"Virtual","name":"FMCAD: Formal Methods in Computer-Aided Design","end_date":"2021-10-22"},"publication_identifier":{"isbn":["978-3-85448-046-4"]},"acknowledgement":"This research was performed while Bernhard Kragl was at IST Austria, supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","doi":"10.34727/2021/isbn.978-3-85448-046-4_23","file_date_updated":"2022-01-26T08:04:29Z","article_processing_charge":"No","oa_version":"Published Version","title":"The Civl verifier","publication_status":"published","alternative_title":["Conference Series"],"language":[{"iso":"eng"}],"ddc":["000"],"status":"public","month":"10","publisher":"TU Wien Academic Press","date_published":"2021-10-01T00:00:00Z","type":"conference","project":[{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"01","page":"143–152","quality_controlled":"1"},{"publication_identifier":{"isbn":["978-1-61197-646-5"]},"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), ERC CoG 863818 (FoRM-SMArt), and by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","doi":"10.1137/1.9781611976465.38","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.06636"}],"scopus_import":"1","article_processing_charge":"No","oa_version":"Preprint","title":"Infinite-duration all-pay bidding games","publication_status":"published","abstract":[{"lang":"eng","text":"In a two-player zero-sum graph game the players move a token throughout a graph to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In bidding games, however, the players have budgets, and in each turn, we hold an “auction” (bidding) to determine which player moves the token: both players simultaneously submit bids and the higher bidder moves the token. The bidding mechanisms differ in their payment schemes. Bidding games were largely studied with variants of first-price bidding in which only the higher bidder pays his bid. We focus on all-pay bidding, where both players pay their bids. Finite-duration all-pay bidding games were studied and shown to be technically more challenging than their first-price counterparts. We study for the first time, infinite-duration all-pay bidding games. Our most interesting results are for mean-payoff objectives: we portray a complete picture for games played on strongly-connected graphs. We study both pure (deterministic) and mixed (probabilistic) strategies and completely characterize the optimal and almost-sure (with probability 1) payoffs the players can respectively guarantee. We show that mean-payoff games under all-pay bidding exhibit the intriguing mathematical properties of their first-price counterparts; namely, an equivalence with random-turn games in which in each turn, the player who moves is selected according to a (biased) coin toss. The equivalences for all-pay bidding are more intricate and unexpected than for first-price bidding."}],"year":"2021","citation":{"mla":"Avni, Guy, et al. “Infinite-Duration All-Pay Bidding Games.” Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms, edited by Dániel Marx, Society for Industrial and Applied Mathematics, 2021, pp. 617–36, doi:10.1137/1.9781611976465.38.","apa":"Avni, G., Jecker, I. R., & Zikelic, D. (2021). Infinite-duration all-pay bidding games. In D. Marx (Ed.), Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms (pp. 617–636). Virtual: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611976465.38","chicago":"Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Infinite-Duration All-Pay Bidding Games.” In Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms, edited by Dániel Marx, 617–36. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/1.9781611976465.38.","short":"G. Avni, I.R. Jecker, D. Zikelic, in:, D. Marx (Ed.), Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2021, pp. 617–636.","ama":"Avni G, Jecker IR, Zikelic D. Infinite-duration all-pay bidding games. In: Marx D, ed. Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2021:617-636. doi:10.1137/1.9781611976465.38","ista":"Avni G, Jecker IR, Zikelic D. 2021. Infinite-duration all-pay bidding games. Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 617–636.","ieee":"G. Avni, I. R. Jecker, and D. Zikelic, “Infinite-duration all-pay bidding games,” in Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms, Virtual, 2021, pp. 617–636."},"_id":"10694","date_created":"2022-01-27T12:11:23Z","editor":[{"full_name":"Marx, Dániel","first_name":"Dániel","last_name":"Marx"}],"conference":{"start_date":"2021-01-10","end_date":"2021-01-13","location":"Virtual","name":"SODA: Symposium on Discrete Algorithms"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni"},{"id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R","first_name":"Ismael R","last_name":"Jecker"},{"first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"oa":1,"arxiv":1,"publication":"Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms","ec_funded":1,"date_updated":"2025-07-14T09:10:12Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"day":"01","page":"617-636","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"publisher":"Society for Industrial and Applied Mathematics","external_id":{"arxiv":["2005.06636"]},"date_published":"2021-01-01T00:00:00Z","type":"conference","language":[{"iso":"eng"}],"status":"public","month":"01"},{"volume":157,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Autissier","first_name":"Pascal","full_name":"Autissier, Pascal"},{"id":"6A459894-5FDD-11E9-AF35-BB24E6697425","full_name":"Bonolis, Dante","first_name":"Dante","last_name":"Bonolis"},{"full_name":"Lamzouri, Youness","first_name":"Youness","last_name":"Lamzouri"}],"date_updated":"2023-08-17T06:59:16Z","publication":"Compositio Mathematica","department":[{"_id":"TiBr"}],"intvolume":" 157","arxiv":1,"oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","title":"The distribution of the maximum of partial sums of Kloosterman sums and other trace functions","publication_identifier":{"issn":["0010-437X"],"eissn":["1570-5846"]},"acknowledgement":"We would like to thank the anonymous referees for carefully reading the paper and for their remarks and suggestions.","article_type":"original","doi":"10.1112/s0010437x21007351","main_file_link":[{"url":"https://arxiv.org/abs/1909.03266","open_access":"1"}],"date_created":"2022-02-01T08:10:43Z","_id":"10711","abstract":[{"text":"In this paper, we investigate the distribution of the maximum of partial sums of families of m -periodic complex-valued functions satisfying certain conditions. We obtain precise uniform estimates for the distribution function of this maximum in a near-optimal range. Our results apply to partial sums of Kloosterman sums and other families of ℓ -adic trace functions, and are as strong as those obtained by Bober, Goldmakher, Granville and Koukoulopoulos for character sums. In particular, we improve on the recent work of the third author for Birch sums. However, unlike character sums, we are able to construct families of m -periodic complex-valued functions which satisfy our conditions, but for which the Pólya–Vinogradov inequality is sharp.","lang":"eng"}],"citation":{"ama":"Autissier P, Bonolis D, Lamzouri Y. The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. 2021;157(7):1610-1651. doi:10.1112/s0010437x21007351","ieee":"P. Autissier, D. Bonolis, and Y. Lamzouri, “The distribution of the maximum of partial sums of Kloosterman sums and other trace functions,” Compositio Mathematica, vol. 157, no. 7. Cambridge University Press, pp. 1610–1651, 2021.","ista":"Autissier P, Bonolis D, Lamzouri Y. 2021. The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. 157(7), 1610–1651.","short":"P. Autissier, D. Bonolis, Y. Lamzouri, Compositio Mathematica 157 (2021) 1610–1651.","apa":"Autissier, P., Bonolis, D., & Lamzouri, Y. (2021). The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/s0010437x21007351","chicago":"Autissier, Pascal, Dante Bonolis, and Youness Lamzouri. “The Distribution of the Maximum of Partial Sums of Kloosterman Sums and Other Trace Functions.” Compositio Mathematica. Cambridge University Press, 2021. https://doi.org/10.1112/s0010437x21007351.","mla":"Autissier, Pascal, et al. “The Distribution of the Maximum of Partial Sums of Kloosterman Sums and Other Trace Functions.” Compositio Mathematica, vol. 157, no. 7, Cambridge University Press, 2021, pp. 1610–51, doi:10.1112/s0010437x21007351."},"year":"2021","type":"journal_article","external_id":{"isi":["000667289300001"],"arxiv":["1909.03266"]},"date_published":"2021-06-28T00:00:00Z","publisher":"Cambridge University Press","status":"public","isi":1,"month":"06","keyword":["Algebra and Number Theory"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"28","page":"1610-1651","issue":"7"},{"publication_identifier":{"issn":["2157-5045"],"eissn":["1948-206X"]},"acknowledgement":"N. L. and R. S. gratefully acknowledge financial support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement No 694227). B. S. acknowledges support from the Swiss National Science Foundation (grant 200020_172623) and from the NCCR SwissMAP. N. L. would like to thank\r\nAndreas Deuchert and David Mitrouskas for interesting discussions. B. S. and R. S. would\r\nlike to thank Rupert Frank for stimulating discussions about the time-evolution of a polaron.\r\n","article_type":"original","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1904.12532","open_access":"1"}],"doi":"10.2140/APDE.2021.14.2079","article_processing_charge":"No","oa_version":"Preprint","publication_status":"published","title":" The Landau–Pekar equations: Adiabatic theorem and accuracy","abstract":[{"lang":"eng","text":"We prove an adiabatic theorem for the Landau–Pekar equations. This allows us to derive new results on the accuracy of their use as effective equations for the time evolution generated by the Fröhlich Hamiltonian with large coupling constant α. In particular, we show that the time evolution of Pekar product states with coherent phonon field and the electron being trapped by the phonons is well approximated by the Landau–Pekar equations until times short compared to α2."}],"citation":{"ieee":"N. K. Leopold, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “ The Landau–Pekar equations: Adiabatic theorem and accuracy,” Analysis and PDE, vol. 14, no. 7. Mathematical Sciences Publishers, pp. 2079–2100, 2021.","ista":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. 2021. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 14(7), 2079–2100.","ama":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 2021;14(7):2079-2100. doi:10.2140/APDE.2021.14.2079","short":"N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE 14 (2021) 2079–2100.","chicago":"Leopold, Nikolai K, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/APDE.2021.14.2079.","apa":"Leopold, N. K., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. Mathematical Sciences Publishers. https://doi.org/10.2140/APDE.2021.14.2079","mla":"Leopold, Nikolai K., et al. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE, vol. 14, no. 7, Mathematical Sciences Publishers, 2021, pp. 2079–100, doi:10.2140/APDE.2021.14.2079."},"year":"2021","date_created":"2022-02-06T23:01:33Z","_id":"10738","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Leopold","first_name":"Nikolai K","full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822"},{"full_name":"Rademacher, Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","orcid":"0000-0001-5059-4466","last_name":"Rademacher","first_name":"Simone Anna Elvira"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"volume":14,"oa":1,"intvolume":" 14","arxiv":1,"ec_funded":1,"date_updated":"2023-10-17T11:26:45Z","publication":"Analysis and PDE","department":[{"_id":"RoSe"}],"day":"10","page":"2079-2100","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"issue":"7","publisher":"Mathematical Sciences Publishers","type":"journal_article","date_published":"2021-11-10T00:00:00Z","external_id":{"isi":["000733976600004"],"arxiv":["1904.12532"]},"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"11"},{"arxiv":1,"language":[{"iso":"eng"}],"ec_funded":1,"date_updated":"2023-09-07T13:44:16Z","status":"public","publication":"arXiv","department":[{"_id":"MiLe"}],"month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","last_name":"Rzadkowski"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"last_name":"Mentink","first_name":"Johan H.","full_name":"Mentink, Johan H."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]},"oa":1,"type":"preprint","date_published":"2021-05-31T00:00:00Z","external_id":{"arxiv":["2105.15193"]},"abstract":[{"lang":"eng","text":"Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a new variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of non-additive systems very well. In particular, we observe substantial improvement over the standard coherent state estimates in the most challenging intermediate coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications."}],"citation":{"ista":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for non-additive systems. arXiv, 10.48550/arXiv.2105.15193.","ieee":"W. Rzadkowski, M. Lemeshko, and J. H. Mentink, “Artificial neural network states for non-additive systems,” arXiv. .","ama":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for non-additive systems. arXiv. doi:10.48550/arXiv.2105.15193","short":"W. Rzadkowski, M. Lemeshko, J.H. Mentink, ArXiv (n.d.).","apa":"Rzadkowski, W., Lemeshko, M., & Mentink, J. H. (n.d.). Artificial neural network states for non-additive systems. arXiv. https://doi.org/10.48550/arXiv.2105.15193","chicago":"Rzadkowski, Wojciech, Mikhail Lemeshko, and Johan H. Mentink. “Artificial Neural Network States for Non-Additive Systems.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2105.15193.","mla":"Rzadkowski, Wojciech, et al. “Artificial Neural Network States for Non-Additive Systems.” ArXiv, doi:10.48550/arXiv.2105.15193."},"year":"2021","project":[{"call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"date_created":"2022-02-17T11:18:57Z","_id":"10762","day":"31","acknowledgement":"We acknowledge fruitful discussions with Giacomo Bighin, Giammarco Fabiani, Areg Ghazaryan, Christoph\r\nLampert, and Artem Volosniev at various stages of this work. W.R. is a recipient of a DOC Fellowship of the\r\nAustrian Academy of Sciences and has received funding from the EU Horizon 2020 programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). This work is part of the Shell-NWO/FOM-initiative “Computational sciences for energy research” of Shell and Chemical Sciences, Earth and Life Sciences, Physical Sciences, FOM and STW.","page":"2105.15193","doi":"10.48550/arXiv.2105.15193","main_file_link":[{"url":"https://arxiv.org/abs/2105.15193","open_access":"1"}],"oa_version":"Preprint","article_processing_charge":"No","title":"Artificial neural network states for non-additive systems","publication_status":"submitted"},{"department":[{"_id":"ChLa"}],"month":"06","date_updated":"2023-09-07T13:42:08Z","status":"public","publication":"arXiv","arxiv":1,"language":[{"iso":"eng"}],"type":"preprint","external_id":{"arxiv":["2102.05996"]},"date_published":"2021-06-07T00:00:00Z","related_material":{"record":[{"id":"10799","status":"public","relation":"dissertation_contains"}]},"oa":1,"author":[{"first_name":"Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Lampert","first_name":"Christoph"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-02-28T14:13:59Z","_id":"10803","citation":{"mla":"Konstantinov, Nikola H., and Christoph Lampert. “Fairness through Regularization for Learning to Rank.” ArXiv, 2102.05996, doi:10.48550/arXiv.2102.05996.","apa":"Konstantinov, N. H., & Lampert, C. (n.d.). Fairness through regularization for learning to rank. arXiv. https://doi.org/10.48550/arXiv.2102.05996","short":"N.H. Konstantinov, C. Lampert, ArXiv (n.d.).","chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Fairness through Regularization for Learning to Rank.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2102.05996.","ama":"Konstantinov NH, Lampert C. Fairness through regularization for learning to rank. arXiv. doi:10.48550/arXiv.2102.05996","ieee":"N. H. Konstantinov and C. Lampert, “Fairness through regularization for learning to rank,” arXiv. .","ista":"Konstantinov NH, Lampert C. Fairness through regularization for learning to rank. arXiv, 2102.05996."},"year":"2021","article_number":"2102.05996","abstract":[{"text":"Given the abundance of applications of ranking in recent years, addressing fairness concerns around automated ranking systems becomes necessary for increasing the trust among end-users. Previous work on fair ranking has mostly focused on application-specific fairness notions, often tailored to online advertising, and it rarely considers learning as part of the process. In this work, we show how to transfer numerous fairness notions from binary classification to a learning to rank setting. Our formalism allows us to design methods for incorporating fairness objectives with provable generalization guarantees. An extensive experimental evaluation shows that our method can improve ranking fairness substantially with no or only little loss of model quality.","lang":"eng"}],"publication_status":"submitted","title":"Fairness through regularization for learning to rank","article_processing_charge":"No","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2102.05996","open_access":"1"}],"doi":"10.48550/arXiv.2102.05996","day":"07"},{"issue":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","page":"1898-1903","day":"22","month":"11","status":"public","language":[{"iso":"eng"}],"ddc":["540"],"keyword":["general medicine"],"date_published":"2021-11-22T00:00:00Z","type":"journal_article","publisher":"American Chemical Society","_id":"10806","file":[{"date_created":"2022-03-02T15:33:18Z","file_size":1257973,"date_updated":"2022-03-02T15:33:18Z","relation":"main_file","file_name":"2021_JACSAu_Calcabrini.pdf","access_level":"open_access","success":1,"checksum":"1c66a35369e911312a359111420318a9","file_id":"10807","creator":"cchlebak","content_type":"application/pdf"}],"date_created":"2022-03-02T15:24:16Z","year":"2021","citation":{"mla":"Calcabrini, Mariano, et al. “Ligand Conversion in Nanocrystal Synthesis: The Oxidation of Alkylamines to Fatty Acids by Nitrate.” JACS Au, vol. 1, no. 11, American Chemical Society, 2021, pp. 1898–903, doi:10.1021/jacsau.1c00349.","short":"M. Calcabrini, D. Van den Eynden, S. Sanchez Ribot, R. Pokratath, J. Llorca, J. De Roo, M. Ibáñez, JACS Au 1 (2021) 1898–1903.","apa":"Calcabrini, M., Van den Eynden, D., Sanchez Ribot, S., Pokratath, R., Llorca, J., De Roo, J., & Ibáñez, M. (2021). Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate. JACS Au. American Chemical Society. https://doi.org/10.1021/jacsau.1c00349","chicago":"Calcabrini, Mariano, Dietger Van den Eynden, Sergi Sanchez Ribot, Rohan Pokratath, Jordi Llorca, Jonathan De Roo, and Maria Ibáñez. “Ligand Conversion in Nanocrystal Synthesis: The Oxidation of Alkylamines to Fatty Acids by Nitrate.” JACS Au. American Chemical Society, 2021. https://doi.org/10.1021/jacsau.1c00349.","ista":"Calcabrini M, Van den Eynden D, Sanchez Ribot S, Pokratath R, Llorca J, De Roo J, Ibáñez M. 2021. Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate. JACS Au. 1(11), 1898–1903.","ieee":"M. Calcabrini et al., “Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate,” JACS Au, vol. 1, no. 11. American Chemical Society, pp. 1898–1903, 2021.","ama":"Calcabrini M, Van den Eynden D, Sanchez Ribot S, et al. Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate. JACS Au. 2021;1(11):1898-1903. doi:10.1021/jacsau.1c00349"},"abstract":[{"lang":"eng","text":"Ligands are a fundamental part of nanocrystals. They control and direct nanocrystal syntheses and provide colloidal stability. Bound ligands also affect the nanocrystals’ chemical reactivity and electronic structure. Surface chemistry is thus crucial to understand nanocrystal properties and functionality. Here, we investigate the synthesis of metal oxide nanocrystals (CeO2-x, ZnO, and NiO) from metal nitrate precursors, in the presence of oleylamine ligands. Surprisingly, the nanocrystals are capped exclusively with a fatty acid instead of oleylamine. Analysis of the reaction mixtures with nuclear magnetic resonance spectroscopy revealed several reaction byproducts and intermediates that are common to the decomposition of Ce, Zn, Ni, and Zr nitrate precursors. Our evidence supports the oxidation of alkylamine and formation of a carboxylic acid, thus unraveling this counterintuitive surface chemistry."}],"publication_status":"published","title":"Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate","file_date_updated":"2022-03-02T15:33:18Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","doi":"10.1021/jacsau.1c00349","article_type":"original","acknowledgement":"This work was financially supported by IST Austria and the Werner Siemens Foundation. M.C. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. The work was also financially supported by University of Basel, SNSF NCCR Molecular Systems Engineering (project number: 182895) and SNSF R’equip (project number: 189622). J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program and MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128 projects.","publication_identifier":{"eissn":["2691-3704"],"issn":["2691-3704"]},"department":[{"_id":"MaIb"}],"publication":"JACS Au","date_updated":"2023-05-05T08:45:36Z","ec_funded":1,"intvolume":" 1","related_material":{"record":[{"id":"12885","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://doi.org/10.26434/chemrxiv-2021-cn2fr","relation":"earlier_version"}]},"oa":1,"volume":1,"author":[{"full_name":"Calcabrini, Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","first_name":"Mariano"},{"first_name":"Dietger","last_name":"Van den Eynden","full_name":"Van den Eynden, Dietger"},{"id":"ddae5a59-f6e0-11ea-865d-d9dc61e77a2a","full_name":"Sanchez Ribot, Sergi","first_name":"Sergi","last_name":"Sanchez Ribot"},{"full_name":"Pokratath, Rohan","first_name":"Rohan","last_name":"Pokratath"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"full_name":"De Roo, Jonathan","last_name":"De Roo","first_name":"Jonathan"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"department":[{"_id":"MaIb"}],"date_updated":"2023-08-17T07:00:35Z","publication":"Science","intvolume":" 371","volume":371,"author":[{"last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-03-03T09:51:48Z","_id":"10809","citation":{"mla":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science, vol. 371, no. 6530, American Association for the Advancement of Science, 2021, pp. 678–79, doi:10.1126/science.abg0886.","apa":"Liu, Y., & Ibáñez, M. (2021). Tidying up the mess. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abg0886","short":"Y. Liu, M. Ibáñez, Science 371 (2021) 678–679.","chicago":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abg0886.","ama":"Liu Y, Ibáñez M. Tidying up the mess. Science. 2021;371(6530):678-679. doi:10.1126/science.abg0886","ista":"Liu Y, Ibáñez M. 2021. Tidying up the mess. Science. 371(6530), 678–679.","ieee":"Y. Liu and M. Ibáñez, “Tidying up the mess,” Science, vol. 371, no. 6530. American Association for the Advancement of Science, pp. 678–679, 2021."},"year":"2021","abstract":[{"text":"Thermoelectric materials are engines that convert heat into an electrical current. Intuitively, the efficiency of this process depends on how many electrons (charge carriers) can move and how easily they do so, how much energy those moving electrons transport, and how easily the temperature gradient is maintained. In terms of material properties, an excellent thermoelectric material requires a high electrical conductivity σ, a high Seebeck coefficient S (a measure of the induced thermoelectric voltage as a function of temperature gradient), and a low thermal conductivity κ. The challenge is that these three properties are strongly interrelated in a conflicting manner (1). On page 722 of this issue, Roychowdhury et al. (2) have found a way to partially break these ties in silver antimony telluride (AgSbTe2) with the addition of cadmium (Cd) cations, which increase the ordering in this inherently disordered thermoelectric material.","lang":"eng"}],"title":"Tidying up the mess","publication_status":"published","oa_version":"None","article_processing_charge":"No","scopus_import":"1","doi":"10.1126/science.abg0886","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_type":"letter_note","isi":1,"month":"02","status":"public","language":[{"iso":"eng"}],"keyword":["multidisciplinary"],"type":"journal_article","external_id":{"isi":["000617551600027"],"pmid":["33574201"]},"date_published":"2021-02-12T00:00:00Z","pmid":1,"publisher":"American Association for the Advancement of Science","issue":"6530","quality_controlled":"1","page":"678-679","day":"12"},{"page":"830-842","day":"16","quality_controlled":"1","issue":"12","project":[{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","publisher":"Springer Nature","type":"journal_article","date_published":"2021-12-16T00:00:00Z","ddc":["610"],"language":[{"iso":"eng"}],"keyword":["general medicine"],"month":"12","status":"public","scopus_import":"1","doi":"10.1038/s43588-021-00157-1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/647800"}],"acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","publication_identifier":{"issn":["2662-8457"]},"article_type":"original","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","publication_status":"published","article_processing_charge":"No","oa_version":"Submitted Version","file_date_updated":"2022-06-18T22:30:03Z","citation":{"ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1."},"year":"2021","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"file":[{"checksum":"9fec5b667909ef52be96d502e4f8c2ae","creator":"patrickd","file_id":"11430","content_type":"application/pdf","embargo":"2022-06-17","relation":"main_file","date_updated":"2022-06-18T22:30:03Z","file_size":1699466,"date_created":"2022-06-02T12:51:07Z","file_name":"Guzmanetal2021.pdf","access_level":"open_access"},{"creator":"patrickd","file_id":"11431","content_type":"application/pdf","title":"Supplementary Material","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","file_name":"Guzmanetal2021Suppl.pdf","access_level":"open_access","embargo":"2022-06-17","file_size":3005651,"relation":"supplementary_material","date_created":"2022-06-02T12:53:47Z","date_updated":"2022-06-18T22:30:03Z"}],"date_created":"2022-03-04T08:32:36Z","_id":"10816","author":[{"first_name":"José","last_name":"Guzmán","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl"},{"first_name":"Claudia ","last_name":"Espinoza Martinez","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia "},{"first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Xiaomin"},{"first_name":"Benjamin","last_name":"Suter","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"SSU"}],"volume":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/spot-the-difference/","relation":"press_release"}],"record":[{"id":"10110","relation":"software","status":"public"}]},"oa":1,"intvolume":" 1","department":[{"_id":"PeJo"}],"ec_funded":1,"date_updated":"2023-08-10T22:30:10Z","publication":"Nature Computational Science"},{"oa":1,"volume":27,"author":[{"last_name":"Feng","first_name":"Xudong","full_name":"Feng, Xudong"},{"full_name":"Liu, Jiafeng","last_name":"Liu","first_name":"Jiafeng"},{"full_name":"Wang, Huamin","last_name":"Wang","first_name":"Huamin"},{"full_name":"Yang, Yin","last_name":"Yang","first_name":"Yin"},{"full_name":"Bao, Hujun","first_name":"Hujun","last_name":"Bao"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Weiwei","last_name":"Xu","full_name":"Xu, Weiwei"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BeBi"}],"publication":"IEEE Transactions on Visualization and Computer Graphics","ec_funded":1,"date_updated":"2023-08-08T13:45:46Z","intvolume":" 27","publication_status":"published","title":"Computational design of skinned Quad-Robots","file_date_updated":"2021-05-25T15:08:49Z","article_processing_charge":"No","oa_version":"Published Version","doi":"10.1109/TVCG.2019.2957218","scopus_import":"1","publication_identifier":{"eissn":["10772626"],"issn":["19410506"]},"acknowledgement":"The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).","_id":"9408","date_created":"2021-05-23T22:01:42Z","file":[{"file_name":"2021_TVCG_Feng.pdf","access_level":"open_access","success":1,"relation":"main_file","file_size":6183002,"date_created":"2021-05-25T15:08:49Z","date_updated":"2021-05-25T15:08:49Z","file_id":"9427","creator":"kschuh","content_type":"application/pdf","checksum":"a78e6ac94e33ade4ffaea66943d5f7dc"}],"year":"2021","article_number":"2881-2895","citation":{"ieee":"X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021.","ista":"Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895.","ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218.","short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218."},"abstract":[{"lang":"eng","text":"We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype."}],"date_published":"2021-06-01T00:00:00Z","external_id":{"isi":["000649620700009"],"pmid":["31804937"]},"type":"journal_article","publisher":"IEEE","pmid":1,"month":"06","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["000"],"quality_controlled":"1","day":"01","issue":"6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020"}]},{"publisher":"Royal Society of London","pmid":1,"external_id":{"isi":["000651501400001"],"pmid":[" 33975485"]},"date_published":"2021-05-12T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"month":"05","isi":1,"status":"public","day":"12","quality_controlled":"1","issue":"5","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"}],"author":[{"first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","first_name":"Hildegard","last_name":"Uecker"},{"full_name":"Neve, Paul","first_name":"Paul","last_name":"Neve"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":17,"intvolume":" 17","department":[{"_id":"NiBa"}],"publication":"Biology letters","ec_funded":1,"date_updated":"2025-05-28T11:42:50Z","doi":"10.1098/rsbl.2020.0913","scopus_import":"1","acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","publication_identifier":{"eissn":["1744957X"]},"publication_status":"published","title":"Adaptation at different points along antibiotic concentration gradients","file_date_updated":"2021-05-25T14:09:03Z","article_processing_charge":"No","oa_version":"Published Version","year":"2021","article_number":"20200913","citation":{"mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913."},"abstract":[{"text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.","lang":"eng"}],"_id":"9410","date_created":"2021-05-23T22:01:43Z","file":[{"file_id":"9425","creator":"kschuh","content_type":"application/pdf","checksum":"9c13c1f5af7609c97c741f11d293188a","file_name":"2021_BiologyLetters_Lagator.pdf","access_level":"open_access","success":1,"relation":"main_file","file_size":726759,"date_updated":"2021-05-25T14:09:03Z","date_created":"2021-05-25T14:09:03Z"}]},{"intvolume":" 44","date_updated":"2023-08-08T13:36:28Z","publication":"European Physical Journal E","department":[{"_id":"ScWa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Sukhov, Alexander","last_name":"Sukhov","first_name":"Alexander"},{"full_name":"Hubert, Maxime","last_name":"Hubert","first_name":"Maxime"},{"orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","first_name":"Galien M","last_name":"Grosjean"},{"full_name":"Trosman, Oleg","first_name":"Oleg","last_name":"Trosman"},{"first_name":"Sebastian","last_name":"Ziegler","full_name":"Ziegler, Sebastian"},{"last_name":"Collard","first_name":"Ylona","full_name":"Collard, Ylona"},{"full_name":"Vandewalle, Nicolas","first_name":"Nicolas","last_name":"Vandewalle"},{"last_name":"Smith","first_name":"Ana Sunčana","full_name":"Smith, Ana Sunčana"},{"last_name":"Harting","first_name":"Jens","full_name":"Harting, Jens"}],"volume":44,"oa":1,"abstract":[{"text":"The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations.","lang":"eng"}],"citation":{"ieee":"A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021.","ista":"Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 44(4), 59.","ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2","short":"A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard, N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).","chicago":"Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2."},"year":"2021","article_number":"59","file":[{"creator":"kschuh","file_id":"9422","content_type":"application/pdf","checksum":"0ef342d011afbe3c5cb058fda9a3f395","success":1,"access_level":"open_access","file_name":"2021_EPJE_Sukhov.pdf","file_size":2507870,"relation":"main_file","date_updated":"2021-05-25T11:32:14Z","date_created":"2021-05-25T11:32:14Z"}],"date_created":"2021-05-23T22:01:44Z","_id":"9411","publication_identifier":{"issn":["12928941"],"eissn":["1292895X"]},"acknowledgement":"This work was financially supported by the DFG Priority Programme SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA 4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing time.","scopus_import":"1","doi":"10.1140/epje/s10189-021-00065-2","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-05-25T11:32:14Z","title":"Regimes of motion of magnetocapillary swimmers","publication_status":"published","ddc":["530"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"04","publisher":"Springer","type":"journal_article","date_published":"2021-04-24T00:00:00Z","external_id":{"isi":["000643251300001"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"issue":"4","day":"24","quality_controlled":"1"},{"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"day":"23","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["510"],"month":"03","isi":1,"status":"public","publisher":"Institute of Mathematical Statistics","date_published":"2021-03-23T00:00:00Z","external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"type":"journal_article","article_number":"24","year":"2021","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP591","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” Electronic Journal of Probability, vol. 26. Institute of Mathematical Statistics, 2021.","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021)."},"abstract":[{"text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness.","lang":"eng"}],"_id":"9412","date_created":"2021-05-23T22:01:44Z","file":[{"creator":"kschuh","file_id":"9423","content_type":"application/pdf","checksum":"864ab003ad4cffea783f65aa8c2ba69f","file_name":"2021_EJP_Cipolloni.pdf","success":1,"access_level":"open_access","file_size":865148,"date_updated":"2021-05-25T13:24:19Z","date_created":"2021-05-25T13:24:19Z","relation":"main_file"}],"doi":"10.1214/21-EJP591","scopus_import":"1","publication_identifier":{"eissn":["10836489"]},"title":"Fluctuation around the circular law for random matrices with real entries","publication_status":"published","file_date_updated":"2021-05-25T13:24:19Z","article_processing_charge":"No","oa_version":"Published Version","arxiv":1,"intvolume":" 26","department":[{"_id":"LaEr"}],"publication":"Electronic Journal of Probability","ec_funded":1,"date_updated":"2023-08-08T13:39:19Z","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","last_name":"Cipolloni"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":26},{"date_created":"2021-05-23T22:01:45Z","_id":"9414","citation":{"ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723","ista":"Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879.","ieee":"K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.","short":"K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723","mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723."},"year":"2021","abstract":[{"lang":"eng","text":"Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density."}],"title":"Spatial variation of microtubule depolymerization in large asters","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"doi":"10.1091/MBC.E20-11-0723","acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"article_type":"original","department":[{"_id":"MaLo"}],"date_updated":"2023-08-08T13:36:02Z","ec_funded":1,"publication":"Molecular Biology of the Cell","intvolume":" 32","volume":32,"oa":1,"author":[{"full_name":"Ishihara, Keisuke","first_name":"Keisuke","last_name":"Ishihara"},{"last_name":"Decker","first_name":"Franziska","full_name":"Decker, Franziska"},{"full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","first_name":"Paulo R"},{"first_name":"James F.","last_name":"Pelletier","full_name":"Pelletier, James F."},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"full_name":"Brugués, Jan","first_name":"Jan","last_name":"Brugués"},{"full_name":"Mitchison, Timothy J.","last_name":"Mitchison","first_name":"Timothy J."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","project":[{"call_identifier":"H2020","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","short":"CC BY-NC-SA (3.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)"},"quality_controlled":"1","page":"869-879","day":"19","isi":1,"month":"04","status":"public","language":[{"iso":"eng"}],"type":"journal_article","external_id":{"isi":["000641574700005"]},"date_published":"2021-04-19T00:00:00Z","publisher":"American Society for Cell Biology"},{"file_date_updated":"2021-05-24T11:15:57Z","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","title":"The inductive bias of ReLU networks on orthogonally separable data","day":"01","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=krz7T0xU9Z_"}],"scopus_import":"1","_id":"9416","has_accepted_license":"1","file":[{"checksum":"f34ff17017527db5ba6927f817bdd125","file_id":"9417","creator":"bphuong","content_type":"application/pdf","relation":"main_file","date_updated":"2021-05-24T11:15:57Z","file_size":502356,"date_created":"2021-05-24T11:15:57Z","file_name":"iclr2021_conference.pdf","access_level":"open_access"}],"date_created":"2021-05-24T11:16:46Z","conference":{"end_date":"2021-05-07","name":" ICLR: International Conference on Learning Representations","location":"Virtual","start_date":"2021-05-03"},"abstract":[{"text":"We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks.","lang":"eng"}],"year":"2021","citation":{"mla":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” 9th International Conference on Learning Representations, 2021.","chicago":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” In 9th International Conference on Learning Representations, 2021.","apa":"Phuong, M., & Lampert, C. (2021). The inductive bias of ReLU networks on orthogonally separable data. In 9th International Conference on Learning Representations. Virtual.","short":"M. Phuong, C. Lampert, in:, 9th International Conference on Learning Representations, 2021.","ama":"Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable data. In: 9th International Conference on Learning Representations. ; 2021.","ista":"Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally separable data. 9th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally separable data,” in 9th International Conference on Learning Representations, Virtual, 2021."},"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9418"}]},"date_published":"2021-05-01T00:00:00Z","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","last_name":"Bui Thi Mai"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"status":"public","publication":"9th International Conference on Learning Representations","date_updated":"2023-09-07T13:29:50Z","month":"05","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"language":[{"iso":"eng"}],"ddc":["000"]},{"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"date_updated":"2023-09-08T11:11:12Z","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"related_material":{"record":[{"id":"7435","status":"deleted","relation":"part_of_dissertation"},{"id":"7481","status":"public","relation":"part_of_dissertation"},{"id":"9416","status":"public","relation":"part_of_dissertation"},{"id":"7479","status":"public","relation":"part_of_dissertation"}]},"oa":1,"author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","last_name":"Bui Thi Mai"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9418","file":[{"file_name":"mph-thesis-v519-pdfimages.pdf","access_level":"open_access","success":1,"date_updated":"2021-05-24T11:22:29Z","date_created":"2021-05-24T11:22:29Z","file_size":2673905,"relation":"main_file","content_type":"application/pdf","file_id":"9419","creator":"bphuong","checksum":"4f0abe64114cfed264f9d36e8d1197e3"},{"creator":"bphuong","file_id":"9420","content_type":"application/zip","checksum":"f5699e876bc770a9b0df8345a77720a2","access_level":"closed","file_name":"thesis.zip","date_created":"2021-05-24T11:56:02Z","relation":"source_file","date_updated":"2021-05-24T11:56:02Z","file_size":92995100}],"date_created":"2021-05-24T13:06:23Z","year":"2021","citation":{"chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021."},"supervisor":[{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"}],"abstract":[{"text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models.","lang":"eng"}],"publication_status":"published","title":"Underspecification in deep learning","file_date_updated":"2021-05-24T11:56:02Z","article_processing_charge":"No","oa_version":"Published Version","doi":"10.15479/AT:ISTA:9418","publication_identifier":{"issn":["2663-337X"]},"month":"05","status":"public","language":[{"iso":"eng"}],"ddc":["000"],"alternative_title":["ISTA Thesis"],"date_published":"2021-05-30T00:00:00Z","type":"dissertation","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","page":"125","day":"30"},{"issue":"6","has_accepted_license":"1","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"}],"quality_controlled":"1","page":"675–685","day":"01","month":"06","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["539"],"date_published":"2021-06-01T00:00:00Z","external_id":{"isi":["000655563800002"],"arxiv":["2011.09486"]},"type":"journal_article","publisher":"Nature Research","_id":"9428","date_created":"2021-05-28T09:03:50Z","file":[{"content_type":"application/pdf","file_id":"10026","creator":"patrickd","checksum":"316ed42ea1b42b0f1a3025bb476266fc","file_name":"RevisedQMBSreview.pdf","access_level":"open_access","embargo":"2021-12-01","file_size":10028836,"date_created":"2021-09-20T09:27:43Z","relation":"main_file","date_updated":"2021-12-02T23:30:03Z"}],"year":"2021","citation":{"mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2.","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685."},"abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"publication_status":"published","title":"Quantum many-body scars and weak breaking of ergodicity","file_date_updated":"2021-12-02T23:30:03Z","oa_version":"Preprint","article_processing_charge":"No","doi":"10.1038/s41567-021-01230-2","article_type":"review","publication_identifier":{"eissn":["1745-2481"]},"acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","department":[{"_id":"MaSe"}],"publication":"Nature Physics","ec_funded":1,"date_updated":"2023-10-18T08:20:59Z","arxiv":1,"intvolume":" 17","oa":1,"volume":17,"author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"24","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508"},{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy"},{"grant_number":"I03600","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","issue":"1","publisher":"Springer Nature","external_id":{"isi":["000658769900010"]},"date_published":"2021-05-24T00:00:00Z","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["572"],"status":"public","month":"05","isi":1,"article_type":"original","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-021-23123-x","file_date_updated":"2021-05-28T12:39:43Z","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"article_number":"3058","year":"2021","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021."},"_id":"9429","file":[{"relation":"main_file","date_created":"2021-05-28T12:39:43Z","date_updated":"2021-05-28T12:39:43Z","file_size":9358599,"file_name":"2021_NatureCommunications_Morandell.pdf","access_level":"open_access","success":1,"checksum":"337e0f7959c35ec959984cacdcb472ba","content_type":"application/pdf","creator":"kschuh","file_id":"9430"}],"date_created":"2021-05-28T11:49:46Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin","first_name":"Jasmin","last_name":"Morandell"},{"last_name":"Schwarz","first_name":"Lena A","full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","first_name":"Bernadette"},{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","first_name":"Armel"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","first_name":"Caroline","last_name":"Kreuzinger"},{"orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","first_name":"Christoph","last_name":"Dotter"},{"full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","first_name":"Lisa"},{"full_name":"Dobler, Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","last_name":"Dobler","first_name":"Zoe"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM"},{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"oa":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}],"record":[{"relation":"earlier_version","status":"public","id":"7800"},{"status":"public","relation":"dissertation_contains","id":"12401"}]},"volume":12,"acknowledged_ssus":[{"_id":"PreCl"}],"intvolume":" 12","publication":"Nature Communications","date_updated":"2024-09-10T12:04:26Z","ec_funded":1,"department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}]},{"oa":1,"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/"}]},"volume":12,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"last_name":"Nikulin","first_name":"Nadia","full_name":"Nikulin, Nadia"},{"last_name":"Feathers","first_name":"Jon-Philip R.","full_name":"Feathers, Jon-Philip R."},{"full_name":"Klanschnig, Marco","last_name":"Klanschnig","first_name":"Marco"},{"last_name":"Thader","first_name":"Andreas","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Marc C.","last_name":"Johnson","first_name":"Marc C."},{"full_name":"Vogt, Volker M.","first_name":"Volker M.","last_name":"Vogt"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"},{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."}],"publication":"Nature Communications","date_updated":"2023-08-08T13:53:53Z","department":[{"_id":"FlSc"}],"intvolume":" 12","file_date_updated":"2021-06-09T15:21:14Z","article_processing_charge":"No","oa_version":"Published Version","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","publication_status":"published","article_type":"original","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-021-23506-0","scopus_import":"1","_id":"9431","file":[{"success":1,"access_level":"open_access","file_name":"2021_NatureCommunications_Obr.pdf","file_size":6166295,"date_created":"2021-06-09T15:21:14Z","date_updated":"2021-06-09T15:21:14Z","relation":"main_file","creator":"kschuh","file_id":"9538","content_type":"application/pdf","checksum":"53ccc53d09a9111143839dbe7784e663"}],"date_created":"2021-05-28T14:25:50Z","abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"year":"2021","article_number":"3226","citation":{"mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0"},"date_published":"2021-05-28T00:00:00Z","external_id":{"isi":["000659145000011"]},"type":"journal_article","publisher":"Nature Research","status":"public","month":"05","isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"language":[{"iso":"eng"}],"ddc":["570"],"quality_controlled":"1","day":"28","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445"}],"issue":"1"}]