[{"date_updated":"2023-10-04T12:10:31Z","ddc":["510"],"file_date_updated":"2023-10-04T12:09:18Z","department":[{"_id":"LaEr"}],"_id":"12792","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"publication_status":"published","file":[{"success":1,"checksum":"72057940f76654050ca84a221f21786c","file_id":"14397","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_CommMathPhysics_Cipolloni.pdf","date_created":"2023-10-04T12:09:18Z","creator":"dernst","file_size":859967,"date_updated":"2023-10-04T12:09:18Z"}],"language":[{"iso":"eng"}],"volume":401,"ec_funded":1,"abstract":[{"lang":"eng","text":"In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys 387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner–Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics."}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 401","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. On the spectral form factor for random matrices. Communications in Mathematical Physics. 401, 1665–1700.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “On the Spectral Form Factor for Random Matrices.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04692-y.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). On the spectral form factor for random matrices. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04692-y","ama":"Cipolloni G, Erdös L, Schröder DJ. On the spectral form factor for random matrices. Communications in Mathematical Physics. 2023;401:1665-1700. doi:10.1007/s00220-023-04692-y","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 401 (2023) 1665–1700.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “On the spectral form factor for random matrices,” Communications in Mathematical Physics, vol. 401. Springer Nature, pp. 1665–1700, 2023.","mla":"Cipolloni, Giorgio, et al. “On the Spectral Form Factor for Random Matrices.” Communications in Mathematical Physics, vol. 401, Springer Nature, 2023, pp. 1665–700, doi:10.1007/s00220-023-04692-y."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000957343500001"]},"title":"On the spectral form factor for random matrices","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Communications in Mathematical Physics","page":"1665-1700","date_published":"2023-07-01T00:00:00Z","doi":"10.1007/s00220-023-04692-y","date_created":"2023-04-02T22:01:11Z","acknowledgement":"We are grateful to the authors of [25] for sharing with us their insights and preliminary numerical results. We are especially thankful to Stephen Shenker for very valuable advice over several email communications. Helpful comments on the manuscript from Peter Forrester and from the anonymous referees are also acknowledged.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nLászló Erdős: Partially supported by ERC Advanced Grant \"RMTBeyond\" No. 101020331. Dominik Schröder: Supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"author":[{"full_name":"Corbet, René","last_name":"Corbet","first_name":"René"},{"first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"},{"full_name":"Lesnick, Michael","last_name":"Lesnick","first_name":"Michael"},{"orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2103.07823"],"isi":["000936496800001"]},"title":"Computing the multicover bifiltration","citation":{"mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” Discrete and Computational Geometry, vol. 70, Springer Nature, 2023, pp. 376–405, doi:10.1007/s00454-022-00476-8.","apa":"Corbet, R., Kerber, M., Lesnick, M., & Osang, G. F. (2023). Computing the multicover bifiltration. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00476-8","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. Discrete and Computational Geometry. 2023;70:376-405. doi:10.1007/s00454-022-00476-8","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, Discrete and Computational Geometry 70 (2023) 376–405.","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” Discrete and Computational Geometry, vol. 70. Springer Nature, pp. 376–405, 2023.","chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00476-8.","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2023. Computing the multicover bifiltration. Discrete and Computational Geometry. 70, 376–405."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"376-405","date_published":"2023-09-01T00:00:00Z","doi":"10.1007/s00454-022-00476-8","date_created":"2023-03-05T23:01:06Z","has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"Discrete and Computational Geometry","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank the anonymous reviewers for many helpful comments and suggestions, which led to substantial improvements of the paper. The first two authors were supported by the Austrian Science Fund (FWF) grant number P 29984-N35 and W1230. The first author was partly supported by an Austrian Marshall Plan Scholarship, and by the Brummer & Partners MathDataLab. A conference version of this paper was presented at the 37th International Symposium on Computational Geometry (SoCG 2021). Open access funding provided by the Royal Institute of Technology.","department":[{"_id":"HeEd"}],"file_date_updated":"2023-03-07T14:40:14Z","date_updated":"2023-10-04T12:03:40Z","ddc":["000"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"12709","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9605"}]},"volume":70,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"publication_status":"published","file":[{"file_size":1359323,"date_updated":"2023-03-07T14:40:14Z","creator":"cchlebak","file_name":"2023_DisCompGeo_Corbet.pdf","date_created":"2023-03-07T14:40:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"71ce7e59f7ee4620acc704fecca620c2","file_id":"12715"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 70","abstract":[{"text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness.","lang":"eng"}],"oa_version":"Published Version"},{"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"citation":{"mla":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” Journal of Applied and Computational Topology, vol. 7, Springer Nature, 2023, pp. 619–41, doi:10.1007/s41468-023-00116-x.","short":"J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology 7 (2023) 619–641.","ieee":"J. D. Boissonnat and M. Wintraecken, “The reach of subsets of manifolds,” Journal of Applied and Computational Topology, vol. 7. Springer Nature, pp. 619–641, 2023.","apa":"Boissonnat, J. D., & Wintraecken, M. (2023). The reach of subsets of manifolds. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-023-00116-x","ama":"Boissonnat JD, Wintraecken M. The reach of subsets of manifolds. Journal of Applied and Computational Topology. 2023;7:619-641. doi:10.1007/s41468-023-00116-x","chicago":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” Journal of Applied and Computational Topology. Springer Nature, 2023. https://doi.org/10.1007/s41468-023-00116-x.","ista":"Boissonnat JD, Wintraecken M. 2023. The reach of subsets of manifolds. Journal of Applied and Computational Topology. 7, 619–641."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Boissonnat","full_name":"Boissonnat, Jean Daniel","first_name":"Jean Daniel"},{"last_name":"Wintraecken","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs"}],"article_processing_charge":"No","title":"The reach of subsets of manifolds","acknowledgement":"We thank Eddie Aamari, David Cohen-Steiner, Isa Costantini, Fred Chazal, Ramsay Dyer, André Lieutier, and Alef Sterk for discussion and Pierre Pansu for encouragement. We further acknowledge the anonymous reviewers whose comments helped improve the exposition.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). The first author is further supported by the French government, through the 3IA Côte d’Azur Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-19-P3IA-0002. The second author is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Austrian science fund (FWF) M-3073.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"year":"2023","day":"01","publication":"Journal of Applied and Computational Topology","page":"619-641","date_published":"2023-09-01T00:00:00Z","doi":"10.1007/s41468-023-00116-x","date_created":"2023-03-26T22:01:08Z","_id":"12763","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-10-04T12:07:18Z","department":[{"_id":"HeEd"}],"abstract":[{"text":"Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1"}],"month":"09","intvolume":" 7","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":7,"ec_funded":1},{"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CONCUR: Conference on Concurrency Theory","end_date":"2023-09-23","location":"Antwerp, Belgium","start_date":"2023-09-18"},"status":"public","_id":"13221","file_date_updated":"2023-07-14T12:03:48Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_updated":"2023-10-09T07:14:03Z","ddc":["000"],"alternative_title":["LIPIcs"],"month":"09","intvolume":" 279","abstract":[{"lang":"eng","text":"The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications."}],"oa_version":"Published Version","volume":279,"ec_funded":1,"publication_identifier":{"isbn":["9783959772990"],"eissn":["1868-8969"]},"publication_status":"published","file":[{"file_name":"CONCUR23.pdf","date_created":"2023-07-14T12:03:48Z","file_size":755529,"date_updated":"2023-07-14T12:03:48Z","creator":"esarac","success":1,"checksum":"d40e57a04448ea5c77d7e1cfb9590a81","file_id":"13224","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"article_number":"17","author":[{"last_name":"Boker","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"external_id":{"arxiv":["2307.06016"]},"article_processing_charge":"No","title":"Safety and liveness of quantitative automata","citation":{"mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” 34th International Conference on Concurrency Theory, vol. 279, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.17.","short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative automata,” in 34th International Conference on Concurrency Theory, Antwerp, Belgium, 2023, vol. 279.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative automata. In: 34th International Conference on Concurrency Theory. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.17","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Safety and liveness of quantitative automata. In 34th International Conference on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Automata.” In 34th International Conference on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17.","ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness of quantitative automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"We thank Christof Löding for pointing us to some results on PSpace-hardess of universality problems and the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22.","doi":"10.4230/LIPIcs.CONCUR.2023.17","date_published":"2023-09-01T00:00:00Z","date_created":"2023-07-14T10:00:15Z","has_accepted_license":"1","year":"2023","day":"01","publication":"34th International Conference on Concurrency Theory"},{"article_number":"104205","author":[{"id":"41e64307-6672-11ee-b9ad-cc7a0075a479","first_name":"Serafim","last_name":"Babkin","full_name":"Babkin, Serafim","orcid":"0009-0003-7382-8036"},{"last_name":"Karcher","full_name":"Karcher, Jonas F.","first_name":"Jonas F."},{"first_name":"Igor S.","last_name":"Burmistrov","full_name":"Burmistrov, Igor S."},{"last_name":"Mirlin","full_name":"Mirlin, Alexander D.","first_name":"Alexander D."}],"article_processing_charge":"No","external_id":{"arxiv":["2306.09455"]},"title":"Generalized surface multifractality in two-dimensional disordered systems","citation":{"ieee":"S. Babkin, J. F. Karcher, I. S. Burmistrov, and A. D. Mirlin, “Generalized surface multifractality in two-dimensional disordered systems,” Physical Review B, vol. 108, no. 10. American Physical Society, 2023.","short":"S. Babkin, J.F. Karcher, I.S. Burmistrov, A.D. Mirlin, Physical Review B 108 (2023).","ama":"Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. Generalized surface multifractality in two-dimensional disordered systems. Physical Review B. 2023;108(10). doi:10.1103/PhysRevB.108.104205","apa":"Babkin, S., Karcher, J. F., Burmistrov, I. S., & Mirlin, A. D. (2023). Generalized surface multifractality in two-dimensional disordered systems. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.104205","mla":"Babkin, Serafim, et al. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.” Physical Review B, vol. 108, no. 10, 104205, American Physical Society, 2023, doi:10.1103/PhysRevB.108.104205.","ista":"Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. 2023. Generalized surface multifractality in two-dimensional disordered systems. Physical Review B. 108(10), 104205.","chicago":"Babkin, Serafim, Jonas F. Karcher, Igor S. Burmistrov, and Alexander D. Mirlin. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.104205."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We thank Ilya Gruzberg for many illuminating discussions. S.S.B., J.F.K., and A.D.M. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) via the Grant\r\nNo. MI 658/14-1. I.S.B. acknowledges support from Russian Science Foundation (Grant No. 22-42-04416).","date_published":"2023-09-01T00:00:00Z","doi":"10.1103/PhysRevB.108.104205","date_created":"2023-10-08T22:01:17Z","year":"2023","day":"01","publication":"Physical Review B","type":"journal_article","article_type":"original","status":"public","_id":"14406","department":[{"_id":"MaSe"}],"date_updated":"2023-10-09T07:09:30Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.09455"}],"month":"09","intvolume":" 108","abstract":[{"text":"Recently, a concept of generalized multifractality, which characterizes fluctuations and correlations of critical eigenstates, was introduced and explored for all 10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model (\r\nNL\r\nσ\r\nM\r\n) field theory, we extend the theory of generalized multifractality to boundaries of systems at criticality. Our numerical simulations on two-dimensional systems of symmetry classes A, C, and AII fully confirm the analytical predictions of pure-scaling observables and Weyl symmetry relations between critical exponents of surface generalized multifractality. This demonstrates the validity of the \r\nNL\r\nσ\r\nM\r\n for the description of Anderson-localization critical phenomena, not only in the bulk but also on the boundary. The critical exponents strongly violate generalized parabolicity, in analogy with earlier results for the bulk, corroborating the conclusion that the considered Anderson-localization critical points are not described by conformal field theories. We further derive relations between generalized surface multifractal spectra and linear combinations of Lyapunov exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption of invariance with respect to a logarithmic conformal map. Our numerics demonstrate that these relations hold with an excellent accuracy. Taken together, our results indicate an intriguing situation: the conformal invariance is broken but holds partially at critical points of Anderson localization.","lang":"eng"}],"oa_version":"Preprint","issue":"10","volume":108,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","language":[{"iso":"eng"}]},{"_id":"14410","status":"public","conference":{"name":"RRPR: Reproducible Research in Pattern Recognition","location":"Montreal, Canada","end_date":"2022-08-21","start_date":"2022-08-21"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. Tomaszewska and C. Lampert, “On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift,” in International Workshop on Reproducible Research in Pattern Recognition, Montreal, Canada, 2023, vol. 14068, pp. 67–73.","short":"P. Tomaszewska, C. Lampert, in:, International Workshop on Reproducible Research in Pattern Recognition, Springer Nature, 2023, pp. 67–73.","ama":"Tomaszewska P, Lampert C. On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift. In: International Workshop on Reproducible Research in Pattern Recognition. Vol 14068. Springer Nature; 2023:67-73. doi:10.1007/978-3-031-40773-4_6","apa":"Tomaszewska, P., & Lampert, C. (2023). On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift. In International Workshop on Reproducible Research in Pattern Recognition (Vol. 14068, pp. 67–73). Montreal, Canada: Springer Nature. https://doi.org/10.1007/978-3-031-40773-4_6","mla":"Tomaszewska, Paulina, and Christoph Lampert. “On the Implementation of Baselines and Lightweight Conditional Model Extrapolation (LIMES) under Class-Prior Shift.” International Workshop on Reproducible Research in Pattern Recognition, vol. 14068, Springer Nature, 2023, pp. 67–73, doi:10.1007/978-3-031-40773-4_6.","ista":"Tomaszewska P, Lampert C. 2023. On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift. International Workshop on Reproducible Research in Pattern Recognition. RRPR: Reproducible Research in Pattern Recognition, LNCS, vol. 14068, 67–73.","chicago":"Tomaszewska, Paulina, and Christoph Lampert. “On the Implementation of Baselines and Lightweight Conditional Model Extrapolation (LIMES) under Class-Prior Shift.” In International Workshop on Reproducible Research in Pattern Recognition, 14068:67–73. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-40773-4_6."},"date_updated":"2023-10-09T06:48:02Z","department":[{"_id":"ChLa"}],"title":"On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift","article_processing_charge":"No","author":[{"full_name":"Tomaszewska, Paulina","last_name":"Tomaszewska","first_name":"Paulina"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"oa_version":"None","abstract":[{"lang":"eng","text":"This paper focuses on the implementation details of the baseline methods and a recent lightweight conditional model extrapolation algorithm LIMES [5] for streaming data under class-prior shift. LIMES achieves superior performance over the baseline methods, especially concerning the minimum-across-day accuracy, which is important for the users of the system. In this work, the key measures to facilitate reproducibility and enhance the credibility of the results are described."}],"intvolume":" 14068","month":"08","alternative_title":["LNCS"],"scopus_import":"1","publisher":"Springer Nature","quality_controlled":"1","publication":"International Workshop on Reproducible Research in Pattern Recognition","language":[{"iso":"eng"}],"day":"20","publication_status":"published","year":"2023","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031407727"],"issn":["0302-9743"]},"date_created":"2023-10-08T22:01:18Z","volume":14068,"date_published":"2023-08-20T00:00:00Z","doi":"10.1007/978-3-031-40773-4_6","page":"67-73"},{"citation":{"ista":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2023. Hypernode automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 21.","chicago":"Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da Costa. “Hypernode Automata.” In 34th International Conference on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.21.","ieee":"E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Hypernode automata,” in 34th International Conference on Concurrency Theory, Antwerp, Belgium, 2023, vol. 279.","short":"E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","apa":"Bartocci, E., Henzinger, T. A., Nickovic, D., & Oliveira da Costa, A. (2023). Hypernode automata. In 34th International Conference on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.21","ama":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode automata. In: 34th International Conference on Concurrency Theory. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.21","mla":"Bartocci, Ezio, et al. “Hypernode Automata.” 34th International Conference on Concurrency Theory, vol. 279, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.21."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2305.02836"]},"article_processing_charge":"Yes","author":[{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"last_name":"Oliveira da Costa","full_name":"Oliveira da Costa, Ana","orcid":"0000-0002-8741-5799","first_name":"Ana","id":"f347ec37-6676-11ee-b395-a888cb7b4fb4"}],"title":"Hypernode automata","article_number":"21","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"year":"2023","has_accepted_license":"1","publication":"34th International Conference on Concurrency Theory","day":"01","date_created":"2023-10-08T22:01:16Z","doi":"10.4230/LIPIcs.CONCUR.2023.21","date_published":"2023-09-01T00:00:00Z","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF) SFB project\r\nSpyCoDe F8502, by the FWF projects ZK-35 and W1255-N23, and by the ERC Advanced Grant\r\nVAMOS 101020093.","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2023-10-09T07:43:44Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2023-10-09T07:42:45Z","_id":"14405","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CONCUR: Conference on Concurrency Theory","location":"Antwerp, Belgium","end_date":"2023-09-22","start_date":"2023-09-19"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"issn":["18688969"],"isbn":["9783959772990"]},"language":[{"iso":"eng"}],"file":[{"checksum":"215765e40454d806174ac0a223e8d6fa","file_id":"14413","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-10-09T07:42:45Z","file_name":"2023_LIPcs_Bartocci.pdf","creator":"dernst","date_updated":"2023-10-09T07:42:45Z","file_size":795790}],"ec_funded":1,"volume":279,"abstract":[{"text":"We introduce hypernode automata as a new specification formalism for hyperproperties of concurrent systems. They are finite automata with nodes labeled with hypernode logic formulas and transitions labeled with actions. A hypernode logic formula specifies relations between sequences of variable values in different system executions. Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces by constraining the values and the order of value changes of each variable without correlating the timing of the changes. Different execution traces are synchronized solely through the transitions of hypernode automata. Hypernode automata naturally combine asynchronicity at the node level with synchronicity at the transition level. We show that the model-checking problem for hypernode automata is decidable over action-labeled Kripke structures, whose actions induce transitions of the specification automata. For this reason, hypernode automaton is a suitable formalism for specifying and verifying asynchronous hyperproperties, such as declassifying observational determinism in multi-threaded programs.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 279","month":"09"},{"month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.12060"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","scopus_import":"1","acknowledgement":"The authors are grateful to Joscha Henheik for his help with the formulas in Appendix B.","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We prove that the mesoscopic linear statistics ∑if(na(σi−z0)) of the eigenvalues {σi}i of large n×n non-Hermitian random matrices with complex centred i.i.d. entries are asymptotically Gaussian for any H20-functions f around any point z0 in the bulk of the spectrum on any mesoscopic scale 0Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-023-01229-1.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Mesoscopic central limit theorem for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01229-1","ama":"Cipolloni G, Erdös L, Schröder DJ. Mesoscopic central limit theorem for non-Hermitian random matrices. Probability Theory and Related Fields. 2023. doi:10.1007/s00440-023-01229-1","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2023).","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Mesoscopic central limit theorem for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2023.","mla":"Cipolloni, Giorgio, et al. “Mesoscopic Central Limit Theorem for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2023, doi:10.1007/s00440-023-01229-1."},"date_updated":"2023-10-09T07:19:01Z"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"issue":"6665","volume":381,"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"A light-triggered fabrication method extends the functionality of printable nanomaterials"}],"intvolume":" 381","month":"09","scopus_import":"1","date_updated":"2023-10-09T07:32:58Z","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"_id":"14404","status":"public","type":"journal_article","article_type":"letter_note","publication":"Science","day":"29","year":"2023","date_created":"2023-10-08T22:01:16Z","date_published":"2023-09-29T00:00:00Z","doi":"10.1126/science.adk3070","page":"1413-1414","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","publisher":"AAAS","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414.","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science. AAAS, 2023. https://doi.org/10.1126/science.adk3070.","short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” Science, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","apa":"Balazs, D., & Ibáñez, M. (2023). Widening the use of 3D printing. Science. AAAS. https://doi.org/10.1126/science.adk3070","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. Science. 2023;381(6665):1413-1414. doi:10.1126/science.adk3070","mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:10.1126/science.adk3070."},"title":"Widening the use of 3D printing","external_id":{"pmid":["37769110"]},"article_processing_charge":"No","author":[{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez"}],"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}]},{"ddc":["000"],"date_updated":"2023-10-09T09:22:37Z","file_date_updated":"2023-10-09T09:19:11Z","department":[{"_id":"KrCh"}],"_id":"14417","status":"public","type":"conference","conference":{"end_date":"2023-09-01","location":"Bordeaux, France","start_date":"2023-08-28","name":"MFCS: Symposium on Mathematical Foundations of Computer Science"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"402281b17ed669bbf149d0fdf68ac201","file_id":"14418","file_size":826843,"date_updated":"2023-10-09T09:19:11Z","creator":"dernst","file_name":"2023_LIPIcsMFCS_Baier.pdf","date_created":"2023-10-09T09:19:11Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959772921"],"eissn":["1868-8969"]},"publication_status":"published","volume":272,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Entropic risk (ERisk) is an established risk measure in finance, quantifying risk by an exponential re-weighting of rewards. We study ERisk for the first time in the context of turn-based stochastic games with the total reward objective. This gives rise to an objective function that demands the control of systems in a risk-averse manner. We show that the resulting games are determined and, in particular, admit optimal memoryless deterministic strategies. This contrasts risk measures that previously have been considered in the special case of Markov decision processes and that require randomization and/or memory. We provide several results on the decidability and the computational complexity of the threshold problem, i.e. whether the optimal value of ERisk exceeds a given threshold. In the most general case, the problem is decidable subject to Shanuel’s conjecture. If all inputs are rational, the resulting threshold problem can be solved using algebraic numbers, leading to decidability via a polynomial-time reduction to the existential theory of the reals. Further restrictions on the encoding of the input allow the solution of the threshold problem in NP∩coNP. Finally, an approximation algorithm for the optimal value of ERisk is provided.","lang":"eng"}],"month":"08","intvolume":" 272","alternative_title":["LIPIcs"],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk for turn-based stochastic games,” in 48th International Symposium on Mathematical Foundations of Computer Science, Bordeaux, France, 2023, vol. 272.","short":"C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, in:, 48th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","apa":"Baier, C., Chatterjee, K., Meggendorfer, T., & Piribauer, J. (2023). Entropic risk for turn-based stochastic games. In 48th International Symposium on Mathematical Foundations of Computer Science (Vol. 272). Bordeaux, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2023.15","ama":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based stochastic games. In: 48th International Symposium on Mathematical Foundations of Computer Science. Vol 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.MFCS.2023.15","mla":"Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” 48th International Symposium on Mathematical Foundations of Computer Science, vol. 272, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.MFCS.2023.15.","ista":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2023. Entropic risk for turn-based stochastic games. 48th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 272, 15.","chicago":"Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” In 48th International Symposium on Mathematical Foundations of Computer Science, Vol. 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.MFCS.2023.15."},"title":"Entropic risk for turn-based stochastic games","author":[{"last_name":"Baier","full_name":"Baier, Christel","first_name":"Christel"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer"},{"full_name":"Piribauer, Jakob","last_name":"Piribauer","first_name":"Jakob"}],"external_id":{"arxiv":["2307.06611"]},"article_processing_charge":"Yes","article_number":"15","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"day":"21","publication":"48th International Symposium on Mathematical Foundations of Computer Science","has_accepted_license":"1","year":"2023","doi":"10.4230/LIPIcs.MFCS.2023.15","date_published":"2023-08-21T00:00:00Z","date_created":"2023-10-09T09:21:05Z","acknowledgement":"This work was partly funded by the ERC CoG 863818 (ForM-SMArt), the DFG Grant\r\n389792660 as part of TRR 248 (Foundations of Perspicuous Software Systems), the Cluster of\r\nExcellence EXC 2050/1 (CeTI, project ID 390696704, as part of Germany’s Excellence Strategy), and the DFG projects BA-1679/11-1 and BA-1679/12-1.","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"ec_funded":1,"issue":"2","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9441"}]},"volume":52,"oa_version":"Submitted Version","abstract":[{"text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e., submanifolds of Rd defined as the zero set of some multivariate multivalued smooth function f:Rd→Rd−n, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M=f−1(0) is to consider its piecewise linear (PL) approximation M^\r\n based on a triangulation T of the ambient space Rd. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ=1/D (and unavoidably exponential in n). Since it is known that for δ=Ω(d2.5), M^ is O(D2)-close and isotopic to M\r\n, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M^ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. ","lang":"eng"}],"intvolume":" 52","month":"04","main_file_link":[{"url":"https://hal-emse.ccsd.cnrs.fr/3IA-COTEDAZUR/hal-04083489v1","open_access":"1"}],"scopus_import":"1","date_updated":"2023-10-10T07:34:35Z","department":[{"_id":"HeEd"}],"_id":"12960","status":"public","article_type":"original","type":"journal_article","publication":"SIAM Journal on Computing","day":"30","year":"2023","isi":1,"date_created":"2023-05-14T22:01:00Z","date_published":"2023-04-30T00:00:00Z","doi":"10.1137/21M1412918","page":"452-486","acknowledgement":"The authors have received funding from the European Research Council under the European Union's ERC grant greement 339025 GUDHI (Algorithmic Foundations of Geometric Un-derstanding in Higher Dimensions). The first author was supported by the French government,through the 3IA C\\^ote d'Azur Investments in the Future project managed by the National ResearchAgency (ANR) with the reference ANR-19-P3IA-0002. The third author was supported by the Eu-ropean Union's Horizon 2020 research and innovation programme under the Marie Sk\\lodowska-Curiegrant agreement 754411 and the FWF (Austrian Science Fund) grant M 3073.","oa":1,"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Boissonnat JD, Kachanovich S, Wintraecken M. 2023. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 52(2), 452–486.","chicago":"Boissonnat, Jean Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/21M1412918.","ieee":"J. D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations,” SIAM Journal on Computing, vol. 52, no. 2. Society for Industrial and Applied Mathematics, pp. 452–486, 2023.","short":"J.D. Boissonnat, S. Kachanovich, M. Wintraecken, SIAM Journal on Computing 52 (2023) 452–486.","ama":"Boissonnat JD, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 2023;52(2):452-486. doi:10.1137/21M1412918","apa":"Boissonnat, J. D., Kachanovich, S., & Wintraecken, M. (2023). Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1412918","mla":"Boissonnat, Jean Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” SIAM Journal on Computing, vol. 52, no. 2, Society for Industrial and Applied Mathematics, 2023, pp. 452–86, doi:10.1137/21M1412918."},"title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations","external_id":{"isi":["001013183000012"]},"article_processing_charge":"No","author":[{"last_name":"Boissonnat","full_name":"Boissonnat, Jean Daniel","first_name":"Jean Daniel"},{"last_name":"Kachanovich","full_name":"Kachanovich, Siargey","first_name":"Siargey"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses","grant_number":"M03073"}]},{"_id":"13134","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-10-10T07:37:16Z","department":[{"_id":"HeEd"}],"oa_version":"None","abstract":[{"text":"We propose a characterization of discrete analytical spheres, planes and lines in the body-centered cubic (BCC) grid, both in the Cartesian and in the recently proposed alternative compact coordinate system, in which each integer triplet addresses some voxel in the grid. We define spheres and planes through double Diophantine inequalities and investigate their relevant topological features, such as functionality or the interrelation between the thickness of the objects and their connectivity and separation properties. We define lines as the intersection of planes. The number of the planes (up to six) is equal to the number of the pairs of faces of a BCC voxel that are parallel to the line.","lang":"eng"}],"intvolume":" 142","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0031-3203"]},"issue":"10","volume":142,"article_number":"109693","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Discretization in Geometry and Dynamics","grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. 2023. Discrete analytical objects in the body-centered cubic grid. Pattern Recognition. 142(10), 109693.","chicago":"Čomić, Lidija, Gaëlle Largeteau-Skapin, Rita Zrour, Ranita Biswas, and Eric Andres. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” Pattern Recognition. Elsevier, 2023. https://doi.org/10.1016/j.patcog.2023.109693.","short":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, E. Andres, Pattern Recognition 142 (2023).","ieee":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, and E. Andres, “Discrete analytical objects in the body-centered cubic grid,” Pattern Recognition, vol. 142, no. 10. Elsevier, 2023.","ama":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. Discrete analytical objects in the body-centered cubic grid. Pattern Recognition. 2023;142(10). doi:10.1016/j.patcog.2023.109693","apa":"Čomić, L., Largeteau-Skapin, G., Zrour, R., Biswas, R., & Andres, E. (2023). Discrete analytical objects in the body-centered cubic grid. Pattern Recognition. Elsevier. https://doi.org/10.1016/j.patcog.2023.109693","mla":"Čomić, Lidija, et al. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” Pattern Recognition, vol. 142, no. 10, 109693, Elsevier, 2023, doi:10.1016/j.patcog.2023.109693."},"title":"Discrete analytical objects in the body-centered cubic grid","article_processing_charge":"No","external_id":{"isi":["001013526000001"]},"author":[{"first_name":"Lidija","last_name":"Čomić","full_name":"Čomić, Lidija"},{"full_name":"Largeteau-Skapin, Gaëlle","last_name":"Largeteau-Skapin","first_name":"Gaëlle"},{"full_name":"Zrour, Rita","last_name":"Zrour","first_name":"Rita"},{"last_name":"Biswas","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Andres, Eric","last_name":"Andres","first_name":"Eric"}],"acknowledgement":"The first author has been partially supported by the Ministry of Science, Technological Development and Innovation of the Republic of Serbia through the project no. 451-03-47/2023-01/200156. The fourth author is funded by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","quality_controlled":"1","publisher":"Elsevier","publication":"Pattern Recognition","day":"01","year":"2023","isi":1,"date_created":"2023-06-18T22:00:45Z","date_published":"2023-10-01T00:00:00Z","doi":"10.1016/j.patcog.2023.109693"},{"language":[{"iso":"eng"}],"file":[{"date_created":"2023-07-12T10:22:04Z","file_name":"2023_JACS_Bunting.pdf","creator":"cchlebak","date_updated":"2023-07-12T10:22:04Z","file_size":3155843,"checksum":"e07d5323f9c0e5cbd1ad6453f29440ab","file_id":"13219","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"volume":145,"issue":"27","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude."}],"intvolume":" 145","month":"06","ddc":["540"],"date_updated":"2023-10-11T08:45:10Z","department":[{"_id":"MaIb"},{"_id":"BiCh"}],"file_date_updated":"2023-07-12T10:22:04Z","_id":"13216","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"Journal of the American Chemical Society","day":"30","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-07-12T09:16:40Z","date_published":"2023-06-30T00:00:00Z","doi":"10.1021/jacs.3c04030","page":"14894-14902","acknowledgement":"B.C. acknowledges resources provided by the Cambridge Tier2 system operated by the University of Cambridge Research\r\nComputing Service funded by EPSRC Tier-2 capital grant EP/\r\nP020259/1.","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” Journal of the American Chemical Society, vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:10.1021/jacs.3c04030.","apa":"Bunting, R., Wodaczek, F., Torabi, T., & Cheng, B. (2023). Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c04030","ama":"Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 2023;145(27):14894-14902. doi:10.1021/jacs.3c04030","short":"R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902.","ieee":"R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane,” Journal of the American Chemical Society, vol. 145, no. 27. American Chemical Society, pp. 14894–14902, 2023.","chicago":"Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c04030.","ista":"Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 145(27), 14894–14902."},"title":"Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane","external_id":{"isi":["001020623900001"],"pmid":["37390457"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Bunting","orcid":"0000-0001-6928-074X","full_name":"Bunting, Rhys","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","first_name":"Rhys"},{"orcid":"0009-0000-1457-795X","full_name":"Wodaczek, Felix","last_name":"Wodaczek","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","first_name":"Felix"},{"last_name":"Torabi","full_name":"Torabi, Tina","first_name":"Tina"},{"last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"}]},{"status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14426","department":[{"_id":"EdHa"}],"file_date_updated":"2023-10-16T07:20:49Z","ddc":["570"],"date_updated":"2023-10-16T07:25:48Z","month":"10","intvolume":" 21","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions, comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion, is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC-to-hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type–specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver."}],"issue":"10","related_material":{"link":[{"url":"https://github.com/JulieKlepstad/LiverDevelopment","relation":"software"}]},"volume":21,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14431","checksum":"40a2b11b41d70a0e5939f8a52b66e389","file_size":6193110,"date_updated":"2023-10-16T07:20:49Z","creator":"dernst","file_name":"2023_PloSBiology_Unterweger.pdf","date_created":"2023-10-16T07:20:49Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1545-7885"]},"publication_status":"published","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"article_number":"e3002315","title":"Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics","author":[{"last_name":"Unterweger","full_name":"Unterweger, Iris A.","first_name":"Iris A."},{"first_name":"Julie","last_name":"Klepstad","full_name":"Klepstad, Julie"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"full_name":"Lundegaard, Pia R.","last_name":"Lundegaard","first_name":"Pia R."},{"full_name":"Trusina, Ala","last_name":"Trusina","first_name":"Ala"},{"last_name":"Ober","full_name":"Ober, Elke A.","first_name":"Elke A."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Unterweger, Iris A., et al. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology, vol. 21, no. 10, e3002315, Public Library of Science, 2023, doi:10.1371/journal.pbio.3002315.","ama":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 2023;21(10). doi:10.1371/journal.pbio.3002315","apa":"Unterweger, I. A., Klepstad, J., Hannezo, E. B., Lundegaard, P. R., Trusina, A., & Ober, E. A. (2023). Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002315","ieee":"I. A. Unterweger, J. Klepstad, E. B. Hannezo, P. R. Lundegaard, A. Trusina, and E. A. Ober, “Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics,” PLoS Biology, vol. 21, no. 10. Public Library of Science, 2023.","short":"I.A. Unterweger, J. Klepstad, E.B. Hannezo, P.R. Lundegaard, A. Trusina, E.A. Ober, PLoS Biology 21 (2023).","chicago":"Unterweger, Iris A., Julie Klepstad, Edouard B Hannezo, Pia R. Lundegaard, Ala Trusina, and Elke A. Ober. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002315.","ista":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. 2023. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 21(10), e3002315."},"quality_controlled":"1","publisher":"Public Library of Science","oa":1,"acknowledgement":"We thank the Ober group for discussion and comments on the manuscript. We are grateful to\r\nDr. F. Lemaigre for feedback on the manuscript and Dr. T. Piotrowski for invaluable support.\r\nWe thank the department of experimental medicine (AEM) in Copenhagen for expert fish\r\ncare. We gratefully acknowledge the DanStem Imaging Platform (University of Copenhagen)\r\nfor support and assistance in this work.\r\nThis work is supported by Novo Nordisk Foundation grant NNF17CC0027852 (EAO);\r\nNordisk Foundation grant NNF19OC0058327 (EAO); Novo Nordisk Foundation grant\r\nNNF17OC0031204 (PRL); https://novonordiskfonden.dk/en/; Danish National\r\nResearch Foundation grant DNRF116 (EAO and AT); https://dg.dk/en/; John and Birthe Meyer\r\nFoundation (PRL) and European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement No. 851288 (EH).","doi":"10.1371/journal.pbio.3002315","date_published":"2023-10-04T00:00:00Z","date_created":"2023-10-15T22:01:10Z","day":"04","publication":"PLoS Biology","has_accepted_license":"1","year":"2023"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"514-546","date_published":"2023-08-09T00:00:00Z","doi":"10.1007/978-3-031-38545-2_17","date_created":"2023-10-15T22:01:11Z","year":"2023","day":"09","publication":"43rd Annual International Cryptology Conference","author":[{"full_name":"Dodis, Yevgeniy","last_name":"Dodis","first_name":"Yevgeniy"},{"last_name":"Ferguson","full_name":"Ferguson, Niels","first_name":"Niels"},{"first_name":"Eli","full_name":"Goldin, Eli","last_name":"Goldin"},{"first_name":"Peter","last_name":"Hall","full_name":"Hall, Peter"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"article_processing_charge":"No","title":"Random oracle combiners: Breaking the concatenation barrier for collision-resistance","citation":{"apa":"Dodis, Y., Ferguson, N., Goldin, E., Hall, P., & Pietrzak, K. Z. (2023). Random oracle combiners: Breaking the concatenation barrier for collision-resistance. In 43rd Annual International Cryptology Conference (Vol. 14082, pp. 514–546). Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-38545-2_17","ama":"Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. Random oracle combiners: Breaking the concatenation barrier for collision-resistance. In: 43rd Annual International Cryptology Conference. Vol 14082. Springer Nature; 2023:514-546. doi:10.1007/978-3-031-38545-2_17","short":"Y. Dodis, N. Ferguson, E. Goldin, P. Hall, K.Z. Pietrzak, in:, 43rd Annual International Cryptology Conference, Springer Nature, 2023, pp. 514–546.","ieee":"Y. Dodis, N. Ferguson, E. Goldin, P. Hall, and K. Z. Pietrzak, “Random oracle combiners: Breaking the concatenation barrier for collision-resistance,” in 43rd Annual International Cryptology Conference, Santa Barbara, CA, United States, 2023, vol. 14082, pp. 514–546.","mla":"Dodis, Yevgeniy, et al. “Random Oracle Combiners: Breaking the Concatenation Barrier for Collision-Resistance.” 43rd Annual International Cryptology Conference, vol. 14082, Springer Nature, 2023, pp. 514–46, doi:10.1007/978-3-031-38545-2_17.","ista":"Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. 2023. Random oracle combiners: Breaking the concatenation barrier for collision-resistance. 43rd Annual International Cryptology Conference. CRYPTO: Advances in Cryptology, LNCS, vol. 14082, 514–546.","chicago":"Dodis, Yevgeniy, Niels Ferguson, Eli Goldin, Peter Hall, and Krzysztof Z Pietrzak. “Random Oracle Combiners: Breaking the Concatenation Barrier for Collision-Resistance.” In 43rd Annual International Cryptology Conference, 14082:514–46. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-38545-2_17."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://eprint.iacr.org/2023/1041","open_access":"1"}],"month":"08","intvolume":" 14082","abstract":[{"lang":"eng","text":"Suppose we have two hash functions h1 and h2, but we trust the security of only one of them. To mitigate this worry, we wish to build a hash combiner Ch1,h2 which is secure so long as one of the underlying hash functions is. This question has been well-studied in the regime of collision resistance. In this case, concatenating the two hash function outputs clearly works. Unfortunately, a long series of works (Boneh and Boyen, CRYPTO’06; Pietrzak, Eurocrypt’07; Pietrzak, CRYPTO’08) showed no (noticeably) shorter combiner for collision resistance is possible.\r\nIn this work, we revisit this pessimistic state of affairs, motivated by the observation that collision-resistance is insufficient for many interesting applications of cryptographic hash functions anyway. We argue the right formulation of the “hash combiner” is to build what we call random oracle (RO) combiners, utilizing stronger assumptions for stronger constructions.\r\nIndeed, we circumvent the previous lower bounds for collision resistance by constructing a simple length-preserving RO combiner C˜h1,h2Z1,Z2(M)=h1(M,Z1)⊕h2(M,Z2),where Z1,Z2\r\n are random salts of appropriate length. We show that this extra randomness is necessary for RO combiners, and indeed our construction is somewhat tight with this lower bound.\r\nOn the negative side, we show that one cannot generically apply the composition theorem to further replace “monolithic” hash functions h1 and h2 by some simpler indifferentiable construction (such as the Merkle-Damgård transformation) from smaller components, such as fixed-length compression functions. Finally, despite this issue, we directly prove collision resistance of the Merkle-Damgård variant of our combiner, where h1 and h2 are replaced by iterative Merkle-Damgård hashes applied to a fixed-length compression function. Thus, we can still subvert the concatenation barrier for collision-resistance combiners while utilizing practically small fixed-length components underneath."}],"oa_version":"Preprint","volume":14082,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031385445"],"eissn":["1611-3349"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"start_date":"2023-08-20","end_date":"2023-08-24","location":"Santa Barbara, CA, United States","name":"CRYPTO: Advances in Cryptology"},"status":"public","_id":"14428","department":[{"_id":"KrPi"}],"date_updated":"2023-10-16T08:02:11Z"},{"title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","editor":[{"first_name":"Cosima","full_name":"Baldari, Cosima","last_name":"Baldari"},{"first_name":"Michael","full_name":"Dustin, Michael","last_name":"Dustin"}],"author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"pmid":["37106180"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In The Immune Synapse, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3135-5_9.","ista":"Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology, vol. 2654, 137–147.","mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” The Immune Synapse, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:10.1007/978-1-0716-3135-5_9.","apa":"Leithner, A. F., Merrin, J., & Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari & M. Dustin (Eds.), The Immune Synapse (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-3135-5_9","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. The Immune Synapse. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:10.1007/978-1-0716-3135-5_9","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in The Immune Synapse, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147."},"project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"date_published":"2023-04-28T00:00:00Z","doi":"10.1007/978-1-0716-3135-5_9","date_created":"2023-05-22T08:41:48Z","page":"137-147","day":"28","publication":"The Immune Synapse","year":"2023","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"A.L. was funded by an Erwin Schrödinger postdoctoral fellowship of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary postdoctoral fellow. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication facility, and the Miba Machine Shop of ISTA for their excellent support.","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"date_updated":"2023-10-17T08:44:53Z","status":"public","type":"book_chapter","series_title":"MIMB","_id":"13052","volume":2654,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781071631355"],"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781071631348"]},"publication_status":"published","place":"New York, NY","month":"04","intvolume":" 2654","alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","oa_version":"None","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS.","lang":"eng"}]},{"project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"article_number":"3784","article_processing_charge":"No","external_id":{"arxiv":["2210.12443"],"isi":["001018100800002"],"pmid":["37355691"]},"author":[{"first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267"},{"first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu"},{"first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","last_name":"Hease"},{"first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","citation":{"short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” Nature Communications, vol. 14. Nature Research, 2023.","ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 2023;14. doi:10.1038/s41467-023-39493-3","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., & Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-023-39493-3","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications, vol. 14, 3784, Nature Research, 2023, doi:10.1038/s41467-023-39493-3.","ista":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784.","chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications. Nature Research, 2023. https://doi.org/10.1038/s41467-023-39493-3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Nature Research","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","date_created":"2023-07-09T22:01:11Z","date_published":"2023-06-24T00:00:00Z","doi":"10.1038/s41467-023-39493-3","year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"24","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13200","department":[{"_id":"JoFi"}],"file_date_updated":"2023-07-10T10:10:54Z","date_updated":"2023-10-17T11:46:12Z","ddc":["000"],"scopus_import":"1","intvolume":" 14","month":"06","abstract":[{"lang":"eng","text":"Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks."}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"volume":14,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"ec7ccd2c08f90d59cab302fd0d7776a4","file_id":"13206","file_size":1349134,"date_updated":"2023-07-10T10:10:54Z","creator":"alisjak","file_name":"2023_NatureComms_Qiu.pdf","date_created":"2023-07-10T10:10:54Z"}]},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties."}],"month":"07","intvolume":" 120","scopus_import":"1","file":[{"file_name":"2023_PNAS_Barbier.pdf","date_created":"2023-07-31T07:30:48Z","creator":"dernst","file_size":995933,"date_updated":"2023-07-31T07:30:48Z","success":1,"checksum":"1fc06228afdb3aa80cf8e7766bcf9dc5","file_id":"13323","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","related_material":{"link":[{"relation":"software","url":"https://github.com/fcamilli95/Structured-PCA-"}]},"volume":120,"issue":"30","_id":"13315","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-10-17T11:44:55Z","file_date_updated":"2023-07-31T07:30:48Z","department":[{"_id":"MaMo"}],"acknowledgement":"J.B. was funded by the European Union (ERC, CHORAL, project number 101039794). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank the reviewers for the insightful comments and, in particular, for suggesting the BAMP-inspired denoisers leading to AMP-AP.","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"day":"25","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","year":"2023","date_published":"2023-07-25T00:00:00Z","doi":"10.1073/pnas.2302028120","date_created":"2023-07-30T22:01:02Z","article_number":"e2302028120","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Barbier, J., Camilli, F., Mondelli, M., & Sáenz, M. (2023). Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2302028120","ama":"Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(30). doi:10.1073/pnas.2302028120","ieee":"J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in structured principal component analysis and how to reach them,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30. National Academy of Sciences, 2023.","short":"J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","mla":"Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30, e2302028120, National Academy of Sciences, 2023, doi:10.1073/pnas.2302028120.","ista":"Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 120(30), e2302028120.","chicago":"Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2302028120."},"title":"Fundamental limits in structured principal component analysis and how to reach them","author":[{"full_name":"Barbier, Jean","last_name":"Barbier","first_name":"Jean"},{"first_name":"Francesco","last_name":"Camilli","full_name":"Camilli, Francesco"},{"last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Manuel","full_name":"Sáenz, Manuel","last_name":"Sáenz"}],"external_id":{"pmid":["37463204"]},"article_processing_charge":"Yes (in subscription journal)"},{"project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e2300828120","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37523549"]},"author":[{"last_name":"Vardi","full_name":"Vardi, Ofek","first_name":"Ofek"},{"first_name":"Naama","full_name":"Maroudas-Sklare, Naama","last_name":"Maroudas-Sklare"},{"first_name":"Yuval","full_name":"Kolodny, Yuval","last_name":"Kolodny"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"},{"last_name":"Saragovi","full_name":"Saragovi, Amijai","first_name":"Amijai"},{"last_name":"Galili","full_name":"Galili, Nir","first_name":"Nir"},{"full_name":"Ferrera, Stav","last_name":"Ferrera","first_name":"Stav"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"full_name":"Yuran, Nir","last_name":"Yuran","first_name":"Nir"},{"last_name":"Affek","full_name":"Affek, Hagit P.","first_name":"Hagit P."},{"first_name":"Boaz","last_name":"Luz","full_name":"Luz, Boaz"},{"first_name":"Yonaton","last_name":"Goldsmith","full_name":"Goldsmith, Yonaton"},{"full_name":"Keren, Nir","last_name":"Keren","first_name":"Nir"},{"last_name":"Yochelis","full_name":"Yochelis, Shira","first_name":"Shira"},{"first_name":"Itay","last_name":"Halevy","full_name":"Halevy, Itay"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yossi","last_name":"Paltiel","full_name":"Paltiel, Yossi"}],"title":"Nuclear spin effects in biological processes","citation":{"chicago":"Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2300828120.","ista":"Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N, Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 120(32), e2300828120.","mla":"Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:10.1073/pnas.2300828120.","apa":"Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili, N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2300828120","ama":"Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(32). doi:10.1073/pnas.2300828120","short":"O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili, S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren, S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ieee":"O. Vardi et al., “Nuclear spin effects in biological processes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 32. National Academy of Sciences, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"N.M.-S. acknowledges the support of the Ministry of Energy, Israel, as part of the scholarship program for graduate students in the fields of energy. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation, Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support of the BSF-NSF 094 Grant No. 2022503.","date_created":"2023-08-13T22:01:12Z","date_published":"2023-07-31T00:00:00Z","doi":"10.1073/pnas.2300828120","year":"2023","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"31","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","_id":"14037","department":[{"_id":"MiLe"}],"file_date_updated":"2023-08-14T07:43:45Z","date_updated":"2023-10-17T11:45:25Z","ddc":["530"],"scopus_import":"1","intvolume":" 120","month":"07","abstract":[{"lang":"eng","text":"Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions."}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":120,"issue":"32","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"a5ed64788a5acef9b9a300a26fa5a177","file_id":"14047","file_size":1003092,"date_updated":"2023-08-14T07:43:45Z","creator":"dernst","file_name":"2023_PNAS_Vardi.pdf","date_created":"2023-08-14T07:43:45Z"}]},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"12683","department":[{"_id":"LaEr"}],"file_date_updated":"2023-02-27T09:43:27Z","date_updated":"2023-10-17T12:48:10Z","ddc":["510"],"scopus_import":"1","month":"02","intvolume":" 28","abstract":[{"lang":"eng","text":"We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices."}],"oa_version":"Published Version","volume":28,"ec_funded":1,"publication_identifier":{"eissn":["1083-589X"]},"publication_status":"published","file":[{"file_name":"2023_ElectCommProbability_Dubach.pdf","date_created":"2023-02-27T09:43:27Z","file_size":479105,"date_updated":"2023-02-27T09:43:27Z","creator":"dernst","success":1,"file_id":"12692","checksum":"a1c6f0a3e33688fd71309c86a9aad86e","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"author":[{"id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Guillaume","last_name":"Dubach","full_name":"Dubach, Guillaume","orcid":"0000-0001-6892-8137"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"}],"article_processing_charge":"No","external_id":{"arxiv":["2108.13694"],"isi":["000950650200005"]},"title":"Dynamics of a rank-one perturbation of a Hermitian matrix","citation":{"apa":"Dubach, G., & Erdös, L. (2023). Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-ECP516","ama":"Dubach G, Erdös L. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 2023;28:1-13. doi:10.1214/23-ECP516","short":"G. Dubach, L. Erdös, Electronic Communications in Probability 28 (2023) 1–13.","ieee":"G. Dubach and L. Erdös, “Dynamics of a rank-one perturbation of a Hermitian matrix,” Electronic Communications in Probability, vol. 28. Institute of Mathematical Statistics, pp. 1–13, 2023.","mla":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” Electronic Communications in Probability, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–13, doi:10.1214/23-ECP516.","ista":"Dubach G, Erdös L. 2023. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 28, 1–13.","chicago":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP516."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"acknowledgement":"G. Dubach gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. L. Erdős is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","page":"1-13","date_published":"2023-02-08T00:00:00Z","doi":"10.1214/23-ECP516","date_created":"2023-02-26T23:01:01Z","has_accepted_license":"1","isi":1,"year":"2023","day":"08","publication":"Electronic Communications in Probability"},{"article_type":"original","type":"journal_article","status":"public","_id":"12761","department":[{"_id":"LaEr"}],"date_updated":"2023-10-17T12:48:52Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.13218"}],"scopus_import":"1","intvolume":" 33","month":"02","abstract":[{"lang":"eng","text":"We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine\r\nthe fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent\r\nmultiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048)."}],"oa_version":"Preprint","ec_funded":1,"volume":33,"issue":"1","publication_status":"published","publication_identifier":{"issn":["1050-5164"]},"language":[{"iso":"eng"}],"project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}],"article_processing_charge":"No","external_id":{"isi":["000946432400015"],"arxiv":["2012.13218"]},"author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","last_name":"Cipolloni"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"title":"Functional central limit theorems for Wigner matrices","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Functional Central Limit Theorems for Wigner Matrices.” Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AAP1820.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 33(1), 447–489.","mla":"Cipolloni, Giorgio, et al. “Functional Central Limit Theorems for Wigner Matrices.” Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 447–89, doi:10.1214/22-AAP1820.","ama":"Cipolloni G, Erdös L, Schröder DJ. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 2023;33(1):447-489. doi:10.1214/22-AAP1820","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Functional central limit theorems for Wigner matrices. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AAP1820","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023) 447–489.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Functional central limit theorems for Wigner matrices,” Annals of Applied Probability, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 447–489, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","acknowledgement":"The second author is partially funded by the ERC Advanced Grant “RMTBEYOND” No. 101020331. The third author is supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","page":"447-489","date_created":"2023-03-26T22:01:08Z","doi":"10.1214/22-AAP1820","date_published":"2023-02-01T00:00:00Z","year":"2023","isi":1,"publication":"Annals of Applied Probability","day":"01"},{"external_id":{"arxiv":["2006.02356"],"isi":["000966611000003"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pierre Le","last_name":"Boudec","full_name":"Boudec, Pierre Le"},{"full_name":"Sawin, Will","last_name":"Sawin","first_name":"Will"}],"title":"The Hasse principle for random Fano hypersurfaces","citation":{"mla":"Browning, Timothy D., et al. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics, vol. 197, no. 3, Princeton University, 2023, pp. 1115–203, doi:10.4007/annals.2023.197.3.3.","short":"T.D. Browning, P.L. Boudec, W. Sawin, Annals of Mathematics 197 (2023) 1115–1203.","ieee":"T. D. Browning, P. L. Boudec, and W. Sawin, “The Hasse principle for random Fano hypersurfaces,” Annals of Mathematics, vol. 197, no. 3. Princeton University, pp. 1115–1203, 2023.","apa":"Browning, T. D., Boudec, P. L., & Sawin, W. (2023). The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. Princeton University. https://doi.org/10.4007/annals.2023.197.3.3","ama":"Browning TD, Boudec PL, Sawin W. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 2023;197(3):1115-1203. doi:10.4007/annals.2023.197.3.3","chicago":"Browning, Timothy D, Pierre Le Boudec, and Will Sawin. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics. Princeton University, 2023. https://doi.org/10.4007/annals.2023.197.3.3.","ista":"Browning TD, Boudec PL, Sawin W. 2023. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 197(3), 1115–1203."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1115-1203","date_created":"2020-10-19T14:28:50Z","date_published":"2023-05-01T00:00:00Z","doi":"10.4007/annals.2023.197.3.3","year":"2023","isi":1,"publication":"Annals of Mathematics","day":"01","oa":1,"quality_controlled":"1","publisher":"Princeton University","department":[{"_id":"TiBr"}],"date_updated":"2023-10-17T12:47:43Z","type":"journal_article","article_type":"original","status":"public","_id":"8682","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/when-is-necessary-sufficient/","description":"News on IST Homepage"}]},"volume":197,"issue":"3","publication_status":"published","publication_identifier":{"issn":["0003-486X"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2006.02356","open_access":"1"}],"intvolume":" 197","month":"05","abstract":[{"lang":"eng","text":"It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces."}],"oa_version":"Preprint"},{"year":"2023","has_accepted_license":"1","isi":1,"publication":"PLoS One","day":"27","page":"e0279838","date_created":"2023-03-05T23:01:05Z","doi":"10.1371/journal.pone.0279838","date_published":"2023-02-27T00:00:00Z","acknowledgement":"This research was supported by an Australian Government Research Training Program\r\n(RTP) Scholarship to JCM (https://www.dese.gov.au), and LB is supported by the Centre de\r\nrecherche sur le vieillissement Fellowship Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","citation":{"mla":"Mckerral, Jody C., et al. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” PLoS One, vol. 18, no. 2, Public Library of Science, 2023, p. e0279838, doi:10.1371/journal.pone.0279838.","short":"J.C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J.G. Mitchell, J.A. Filar, PLoS One 18 (2023) e0279838.","ieee":"J. C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J. G. Mitchell, and J. A. Filar, “Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations,” PLoS One, vol. 18, no. 2. Public Library of Science, p. e0279838, 2023.","ama":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 2023;18(2):e0279838. doi:10.1371/journal.pone.0279838","apa":"Mckerral, J. C., Kleshnina, M., Ejov, V., Bartle, L., Mitchell, J. G., & Filar, J. A. (2023). Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0279838","chicago":"Mckerral, Jody C., Maria Kleshnina, Vladimir Ejov, Louise Bartle, James G. Mitchell, and Jerzy A. Filar. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” PLoS One. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0279838.","ista":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. 2023. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 18(2), e0279838."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000996122900022"],"pmid":["36848357"]},"article_processing_charge":"No","author":[{"full_name":"Mckerral, Jody C.","last_name":"Mckerral","first_name":"Jody C."},{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"},{"first_name":"Vladimir","last_name":"Ejov","full_name":"Ejov, Vladimir"},{"full_name":"Bartle, Louise","last_name":"Bartle","first_name":"Louise"},{"full_name":"Mitchell, James G.","last_name":"Mitchell","first_name":"James G."},{"last_name":"Filar","full_name":"Filar, Jerzy A.","first_name":"Jerzy A."}],"title":"Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations","publication_status":"published","publication_identifier":{"eissn":["1932-6203"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12712","checksum":"798ed5739a4117b03173e5d56e0534c9","success":1,"date_updated":"2023-03-07T10:26:45Z","file_size":1257003,"creator":"cchlebak","date_created":"2023-03-07T10:26:45Z","file_name":"2023_PLOSOne_Mckerral.pdf"}],"issue":"2","volume":18,"abstract":[{"lang":"eng","text":"Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 18","month":"02","date_updated":"2023-10-17T12:53:30Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2023-03-07T10:26:45Z","_id":"12706","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"project":[{"name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","grant_number":"793482","_id":"2659CC84-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"author":[{"first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","last_name":"Eguchi","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","first_name":"Elodie","last_name":"Le Monnier","full_name":"Le Monnier, Elodie"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"article_processing_charge":"No","external_id":{"pmid":["37160366"],"isi":["001020132100005"]},"title":"Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons","citation":{"mla":"Eguchi, Kohgaku, et al. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience, vol. 43, no. 23, Society for Neuroscience, 2023, pp. 4197–216, doi:10.1523/JNEUROSCI.1514-22.2023.","ieee":"K. Eguchi, E. Le Monnier, and R. Shigemoto, “Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons,” The Journal of Neuroscience, vol. 43, no. 23. Society for Neuroscience, pp. 4197–4216, 2023.","short":"K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023) 4197–4216.","ama":"Eguchi K, Le Monnier E, Shigemoto R. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 2023;43(23):4197-4216. doi:10.1523/JNEUROSCI.1514-22.2023","apa":"Eguchi, K., Le Monnier, E., & Shigemoto, R. (2023). Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1514-22.2023","chicago":"Eguchi, Kohgaku, Elodie Le Monnier, and Ryuichi Shigemoto. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.1514-22.2023.","ista":"Eguchi K, Le Monnier E, Shigemoto R. 2023. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 43(23), 4197–4216."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Neuroscience","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by The Institute of Science and Technology (IST) Austria, the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 793482 (to K.E.) and by the European Research Council (ERC) Grant Agreement No. 694539 (to R.S.). We thank Nicoleta Condruz (IST Austria, Klosterneuburg, Austria) for technical assistance with sample preparation, the Electron Microscopy Facility of IST Austria (Klosterneuburg, Austria) for technical support with EM works, Natalia Baranova (University of Vienna, Vienna, Austria) and Martin Loose (IST Austria, Klosterneuburg, Austria) for advice on liposome preparation, and Yugo Fukazawa (University of Fukui, Fukui, Japan) for comments.","page":"4197-4216","date_published":"2023-06-07T00:00:00Z","doi":"10.1523/JNEUROSCI.1514-22.2023","date_created":"2023-07-09T22:01:12Z","isi":1,"has_accepted_license":"1","year":"2023","day":"07","publication":"The Journal of Neuroscience","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13202","department":[{"_id":"RySh"}],"file_date_updated":"2023-07-10T09:04:58Z","date_updated":"2023-10-18T07:12:47Z","ddc":["570"],"scopus_import":"1","month":"06","intvolume":" 43","abstract":[{"lang":"eng","text":"Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"oa_version":"Published Version","issue":"23","volume":43,"ec_funded":1,"publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"publication_status":"published","file":[{"date_created":"2023-07-10T09:04:58Z","file_name":"2023_JN_Eguchi.pdf","date_updated":"2023-07-10T09:04:58Z","file_size":7794425,"creator":"alisjak","checksum":"70b2141870e0bf1c94fd343e18fdbc32","file_id":"13205","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}]},{"day":"16","publication":"Annali della Scuola Normale Superiore di Pisa - Classe di Scienze","year":"2023","doi":"10.2422/2036-2145.202010_018","date_published":"2023-02-16T00:00:00Z","date_created":"2023-05-07T22:01:04Z","page":"173-204","publisher":"Scuola Normale Superiore - Edizioni della Normale","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della Normale, 2023, pp. 173–204, doi:10.2422/2036-2145.202010_018.","ama":"Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 2023;24(1):173-204. doi:10.2422/2036-2145.202010_018","apa":"Bonolis, D., & Browning, T. D. (2023). Uniform bounds for rational points on hyperelliptic fibrations. Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale. https://doi.org/10.2422/2036-2145.202010_018","short":"D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze 24 (2023) 173–204.","ieee":"D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic fibrations,” Annali della Scuola Normale Superiore di Pisa - Classe di Scienze, vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204, 2023.","chicago":"Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale, 2023. https://doi.org/10.2422/2036-2145.202010_018.","ista":"Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 24(1), 173–204."},"title":"Uniform bounds for rational points on hyperelliptic fibrations","author":[{"id":"6A459894-5FDD-11E9-AF35-BB24E6697425","first_name":"Dante","last_name":"Bonolis","full_name":"Bonolis, Dante"},{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"}],"external_id":{"arxiv":["2007.14182"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0391-173X"],"eissn":["2036-2145"]},"publication_status":"published","issue":"1","volume":24,"oa_version":"Preprint","abstract":[{"text":"We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface.\r\n","lang":"eng"}],"month":"02","intvolume":" 24","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2007.14182"}],"date_updated":"2023-10-18T06:54:30Z","department":[{"_id":"TiBr"}],"_id":"12916","status":"public","article_type":"original","type":"journal_article"},{"project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"citation":{"ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","apa":"Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422","mla":"Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","last_name":"Confavreux","full_name":"Confavreux, Basile J"}],"title":"Synapseek: Meta-learning synaptic plasticity rules","publisher":"Institute of Science and Technology Austria","year":"2023","has_accepted_license":"1","day":"12","page":"148","date_created":"2023-10-12T14:13:25Z","date_published":"2023-10-12T00:00:00Z","doi":"10.15479/at:ista:14422","_id":"14422","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","date_updated":"2023-10-18T09:20:56Z","supervisor":[{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"ddc":["610"],"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"file_date_updated":"2023-10-18T07:56:08Z","abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-10-12T14:54:52Z","file_size":30599717,"creator":"cchlebak","date_created":"2023-10-12T14:53:50Z","file_name":"Confavreux_Thesis_2A.pdf","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file","checksum":"7f636555eae7803323df287672fd13ed","file_id":"14424","embargo":"2024-10-12"},{"file_name":"Confavreux Thesis.zip","date_created":"2023-10-18T07:38:34Z","file_size":68406739,"date_updated":"2023-10-18T07:56:08Z","creator":"cchlebak","checksum":"725e85946db92290a4583a0de9779e1b","file_id":"14440","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"}],"ec_funded":1,"related_material":{"record":[{"id":"9633","status":"public","relation":"part_of_dissertation"}]}},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"30","year":"2023","has_accepted_license":"1","date_created":"2023-09-28T14:23:04Z","doi":"10.15479/at:ista:14374","date_published":"2023-09-30T00:00:00Z","page":"206","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14374.","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374","apa":"Roos, B. (2023). Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023.","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023.","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374.","ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria."},"title":"Boundary superconductivity in BCS theory","article_processing_charge":"No","author":[{"last_name":"Roos","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space."}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_size":2365702,"date_updated":"2023-10-06T11:35:56Z","creator":"broos","file_name":"phd-thesis-draft_pdfa_acrobat.pdf","date_created":"2023-10-06T11:35:56Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"14398","checksum":"ef039ffc3de2cb8dee5b14110938e9b6"},{"file_id":"14399","checksum":"81dcac33daeefaf0111db52f41bb1fd0","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2023-10-06T11:38:01Z","file_name":"Version5.zip","creator":"broos","date_updated":"2023-10-06T11:38:01Z","file_size":4691734}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"13207","relation":"part_of_dissertation"},{"status":"public","id":"10850","relation":"part_of_dissertation"}]},"_id":"14374","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","ddc":["515","539"],"date_updated":"2023-10-27T10:37:30Z","supervisor":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"file_date_updated":"2023-10-06T11:38:01Z"},{"_id":"13207","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2023-10-27T10:37:29Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"file_date_updated":"2023-07-11T08:19:15Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity."}],"month":"05","intvolume":" 12","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"13208","checksum":"5501da33be010b5c81440438287584d5","file_size":304619,"date_updated":"2023-07-11T08:19:15Z","creator":"alisjak","file_name":"2023_EMS_Hainzl.pdf","date_created":"2023-07-11T08:19:15Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1664-039X"],"eissn":["1664-0403"]},"publication_status":"published","volume":12,"related_material":{"record":[{"status":"public","id":"14374","relation":"dissertation_contains"}]},"issue":"4","ec_funded":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 12(4), 1507–1540.","chicago":"Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/439.","apa":"Hainzl, C., Roos, B., & Seiringer, R. (2023). Boundary superconductivity in the BCS model. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/439","ama":"Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 2023;12(4):1507–1540. doi:10.4171/JST/439","short":"C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540.","ieee":"C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS model,” Journal of Spectral Theory, vol. 12, no. 4. EMS Press, pp. 1507–1540, 2023.","mla":"Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:10.4171/JST/439."},"title":"Boundary superconductivity in the BCS model","author":[{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","last_name":"Roos"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"external_id":{"isi":["000997933500008"],"arxiv":["2201.08090"]},"article_processing_charge":"No","acknowledgement":"We thank Egor Babaev for encouraging us to study this problem, and Rupert Frank for many fruitful discussions. scussions. Funding. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (Barbara Roos and Robert Seiringer) is gratefully acknowledged.","quality_controlled":"1","publisher":"EMS Press","oa":1,"day":"18","publication":"Journal of Spectral Theory","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.4171/JST/439","date_published":"2023-05-18T00:00:00Z","date_created":"2023-07-10T16:35:45Z","page":"1507–1540"},{"_id":"14452","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-10-30T13:04:11Z","department":[{"_id":"NiBa"}],"file_date_updated":"2023-10-30T12:57:53Z","oa_version":"Published Version","abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√. We illustrate our results with some numerical examples.","lang":"eng"}],"month":"10","intvolume":" 225","scopus_import":"1","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14469","checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a","success":1,"creator":"dernst","date_updated":"2023-10-30T12:57:53Z","file_size":1439032,"date_created":"2023-10-30T12:57:53Z","file_name":"2023_Genetics_Barton.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"12949","relation":"research_data"}]},"volume":225,"issue":"2","ec_funded":1,"article_number":"iyad133","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal model with dominance. Genetics. Oxford Academic. https://doi.org/10.1093/genetics/iyad133","ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133","ieee":"N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023.","short":"N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics, vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:10.1093/genetics/iyad133.","ista":"Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133.","chicago":"Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal Model with Dominance.” Genetics. Oxford Academic, 2023. https://doi.org/10.1093/genetics/iyad133."},"title":"The infinitesimal model with dominance","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Etheridge","full_name":"Etheridge, Alison M.","first_name":"Alison M."},{"last_name":"Véber","full_name":"Véber, Amandine","first_name":"Amandine"}],"external_id":{"arxiv":["2211.03515"]},"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"NHB was supported in part by ERC Grants 250152 and 101055327. AV was partly supported by the chaire Modélisation Mathématique et Biodiversité of Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation X.","publisher":"Oxford Academic","quality_controlled":"1","oa":1,"day":"01","publication":"Genetics","has_accepted_license":"1","year":"2023","doi":"10.1093/genetics/iyad133","date_published":"2023-10-01T00:00:00Z","date_created":"2023-10-29T23:01:15Z"},{"oa":1,"publisher":"Institute of Science and Technology Austria","month":"05","abstract":[{"lang":"eng","text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed."}],"oa_version":"Published Version","date_created":"2023-05-13T09:49:09Z","contributor":[{"first_name":"Amandine","contributor_type":"researcher","last_name":"Veber"},{"first_name":"Alison","contributor_type":"researcher","last_name":"Etheridge"}],"date_published":"2023-05-13T00:00:00Z","doi":"10.15479/AT:ISTA:12949","related_material":{"record":[{"status":"public","id":"14452","relation":"used_in_publication"}]},"year":"2023","has_accepted_license":"1","file":[{"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","checksum":"b0ce7d4b1ee7e7265430ceed36fc3336","file_id":"12950","success":1,"date_updated":"2023-05-13T09:36:33Z","file_size":13662,"creator":"nbarton","date_created":"2023-05-13T09:36:33Z","file_name":"Neutral identities 16th Jan"},{"date_created":"2023-05-13T09:38:17Z","file_name":"p, zA, zD, N=30 neutral III","date_updated":"2023-05-13T09:38:17Z","file_size":181619928,"creator":"nbarton","file_id":"12951","checksum":"ad5035ad4f7d3b150a252c79884f6a83","success":1,"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file"},{"date_created":"2023-05-13T09:41:59Z","file_name":"p, zA, zD, N=30 neutral IV","creator":"nbarton","date_updated":"2023-05-13T09:41:59Z","file_size":605902074,"checksum":"62182a1de796256edd6f4223704312ef","file_id":"12952","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream"},{"creator":"nbarton","file_size":1018238746,"date_updated":"2023-05-13T09:46:52Z","file_name":"p, zA, zD, N=30 selected k=5","date_created":"2023-05-13T09:46:52Z","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","success":1,"file_id":"12953","checksum":"af775dda5c4f6859cb1e5a81ec40a667"},{"file_id":"12954","checksum":"af26f3394c387d3ada14b434cd68b1e5","success":1,"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","date_created":"2023-05-13T09:42:05Z","file_name":"Pairwise F N=30 neutral II","date_updated":"2023-05-13T09:42:05Z","file_size":3197160,"creator":"nbarton"},{"content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","success":1,"file_id":"12955","checksum":"d5da7dc0e7282dd48222e26d12e34220","file_size":55492,"date_updated":"2023-05-13T09:42:06Z","creator":"nbarton","file_name":"Pedigrees N=30 neutral II","date_created":"2023-05-13T09:42:06Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","file_id":"12956","checksum":"00f386d80677590e29f6235d49cba58d","success":1,"creator":"nbarton","date_updated":"2023-05-13T09:46:06Z","file_size":474003467,"date_created":"2023-05-13T09:46:06Z","file_name":"selected reps N=30 selected k=1,2 300 reps III"},{"file_id":"12957","checksum":"658cef3eaea6136a4d24da4f074191d7","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","date_created":"2023-05-13T09:46:08Z","file_name":"Algorithm for caclulating identities.nb","creator":"nbarton","date_updated":"2023-05-13T09:46:08Z","file_size":121209},{"file_size":1803898,"date_updated":"2023-05-13T09:46:08Z","creator":"nbarton","file_name":"Infinitesimal with dominance.nb","date_created":"2023-05-13T09:46:08Z","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","success":1,"file_id":"12958","checksum":"db9b6dddd7a596d974e25f5e78f5c45c"},{"access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"91f80a9fb58cae8eef2d8bf59fe30189","file_id":"12967","success":1,"creator":"nbarton","date_updated":"2023-05-16T04:09:08Z","file_size":990,"date_created":"2023-05-16T04:09:08Z","file_name":"ReadMe.txt"}],"day":"13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","keyword":["Quantitative genetics","infinitesimal model"],"project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"status":"public","_id":"12949","article_processing_charge":"No","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"file_date_updated":"2023-05-16T04:09:08Z","title":"The infinitesimal model with dominance","department":[{"_id":"NiBa"}],"date_updated":"2023-10-30T13:04:11Z","citation":{"ista":"Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949.","chicago":"Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.","ieee":"N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023.","short":"N.H. Barton, (2023).","apa":"Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949","ama":"Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949","mla":"Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949."},"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Preprint","abstract":[{"text":"Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model’s weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"07","intvolume":" 202","alternative_title":["PMLR"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.02390"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2640-3498"]},"publication_status":"published","volume":202,"ec_funded":1,"_id":"14461","status":"public","type":"conference","conference":{"start_date":"2023-07-23","end_date":"2023-07-29","location":"Honolulu, Hawaii, HI, United States","name":"ICML: International Conference on Machine Learning"},"date_updated":"2023-10-31T09:40:45Z","department":[{"_id":"DaAl"}],"acknowledgement":"The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), as well as experimental support from the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois Schloegl. AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT), the support of Fondation Hadamard with a PRMO grant, and the support of CNRS with a CoopIntEER IEA grant (project ALFRED).","quality_controlled":"1","publisher":"ML Research Press","oa":1,"day":"30","publication":"Proceedings of the 40th International Conference on Machine Learning","year":"2023","date_published":"2023-07-30T00:00:00Z","date_created":"2023-10-29T23:01:17Z","page":"24020-24044","project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Markov I, Vladu A, Guo Q, Alistarh D-A. Quantized distributed training of large models with convergence guarantees. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:24020-24044.","apa":"Markov, I., Vladu, A., Guo, Q., & Alistarh, D.-A. (2023). Quantized distributed training of large models with convergence guarantees. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 24020–24044). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"I. Markov, A. Vladu, Q. Guo, and D.-A. Alistarh, “Quantized distributed training of large models with convergence guarantees,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 24020–24044.","short":"I. Markov, A. Vladu, Q. Guo, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 24020–24044.","mla":"Markov, Ilia, et al. “Quantized Distributed Training of Large Models with Convergence Guarantees.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 24020–44.","ista":"Markov I, Vladu A, Guo Q, Alistarh D-A. 2023. Quantized distributed training of large models with convergence guarantees. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 24020–24044.","chicago":"Markov, Ilia, Adrian Vladu, Qi Guo, and Dan-Adrian Alistarh. “Quantized Distributed Training of Large Models with Convergence Guarantees.” In Proceedings of the 40th International Conference on Machine Learning, 202:24020–44. ML Research Press, 2023."},"title":"Quantized distributed training of large models with convergence guarantees","author":[{"first_name":"Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","last_name":"Markov","full_name":"Markov, Ilia"},{"full_name":"Vladu, Adrian","last_name":"Vladu","first_name":"Adrian"},{"last_name":"Guo","full_name":"Guo, Qi","first_name":"Qi"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"external_id":{"arxiv":["2302.02390"]},"article_processing_charge":"No"},{"status":"public","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29","location":"Honolulu, Hawaii, HI, United States","start_date":"2023-07-23"},"type":"conference","_id":"14462","department":[{"_id":"MoHe"}],"date_updated":"2023-10-31T09:54:05Z","intvolume":" 202","month":"07","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v202/fichtenberger23a/fichtenberger23a.pdf"}],"alternative_title":["PMLR"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study fine-grained error bounds for differentially private algorithms for counting under continual observation. Our main insight is that the matrix mechanism when using lower-triangular matrices can be used in the continual observation model. More specifically, we give an explicit factorization for the counting matrix Mcount and upper bound the error explicitly. We also give a fine-grained analysis, specifying the exact constant in the upper bound. Our analysis is based on upper and lower bounds of the completely bounded norm (cb-norm) of Mcount\r\n. Along the way, we improve the best-known bound of 28 years by Mathias (SIAM Journal on Matrix Analysis and Applications, 1993) on the cb-norm of Mcount for a large range of the dimension of Mcount. Furthermore, we are the first to give concrete error bounds for various problems under continual observation such as binary counting, maintaining a histogram, releasing an approximately cut-preserving synthetic graph, many graph-based statistics, and substring and episode counting. Finally, we note that our result can be used to get a fine-grained error bound for non-interactive local learning and the first lower bounds on the additive error for (ϵ,δ)-differentially-private counting under continual observation. Subsequent to this work, Henzinger et al. (SODA, 2023) showed that our factorization also achieves fine-grained mean-squared error."}],"ec_funded":1,"volume":202,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2640-3498"]},"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "}],"title":"Constant matters: Fine-grained error bound on differentially private continual observation","article_processing_charge":"No","author":[{"full_name":"Fichtenberger, Hendrik","last_name":"Fichtenberger","first_name":"Hendrik"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"first_name":"Jalaj","last_name":"Upadhyay","full_name":"Upadhyay, Jalaj"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fichtenberger H, Henzinger MH, Upadhyay J. 2023. Constant matters: Fine-grained error bound on differentially private continual observation. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 10072–10092.","chicago":"Fichtenberger, Hendrik, Monika H Henzinger, and Jalaj Upadhyay. “Constant Matters: Fine-Grained Error Bound on Differentially Private Continual Observation.” In Proceedings of the 40th International Conference on Machine Learning, 202:10072–92. ML Research Press, 2023.","short":"H. Fichtenberger, M.H. Henzinger, J. Upadhyay, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 10072–10092.","ieee":"H. Fichtenberger, M. H. Henzinger, and J. Upadhyay, “Constant matters: Fine-grained error bound on differentially private continual observation,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 10072–10092.","apa":"Fichtenberger, H., Henzinger, M. H., & Upadhyay, J. (2023). Constant matters: Fine-grained error bound on differentially private continual observation. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 10072–10092). Honolulu, Hawaii, HI, United States: ML Research Press.","ama":"Fichtenberger H, Henzinger MH, Upadhyay J. Constant matters: Fine-grained error bound on differentially private continual observation. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:10072-10092.","mla":"Fichtenberger, Hendrik, et al. “Constant Matters: Fine-Grained Error Bound on Differentially Private Continual Observation.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10072–92."},"oa":1,"quality_controlled":"1","publisher":"ML Research Press","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project Z 422-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. 2020–2024. JU’s research was funded by Decanal Research Grant. A part of this work was done when JU was visiting Indian Statistical Institute, Delhi. The authors would like to thank Rajat Bhatia, Aleksandar Nikolov, Shanta Laisharam, Vern Paulsen, Ryan Rogers, Abhradeep Thakurta, and Sarvagya Upadhyay for useful discussions.","date_created":"2023-10-29T23:01:17Z","date_published":"2023-07-30T00:00:00Z","page":"10072-10092","publication":"Proceedings of the 40th International Conference on Machine Learning","day":"30","year":"2023"},{"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Shevchenko, Aleksandr, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209.","short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:31151-31209.","chicago":"Shevchenko, Aleksandr, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In Proceedings of the 40th International Conference on Machine Learning, 202:31151–209. ML Research Press, 2023.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209."},"title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko"},{"last_name":"Kögler","full_name":"Kögler, Kevin","first_name":"Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b"},{"first_name":"Hamed","last_name":"Hassani","full_name":"Hassani, Hamed"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"article_processing_charge":"No","external_id":{"arxiv":["2212.13468"]},"acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","quality_controlled":"1","publisher":"ML Research Press","oa":1,"day":"30","publication":"Proceedings of the 40th International Conference on Machine Learning","year":"2023","date_published":"2023-07-30T00:00:00Z","date_created":"2023-10-29T23:01:17Z","page":"31151-31209","_id":"14459","status":"public","type":"conference","conference":{"location":"Honolulu, Hawaii, HI, United States","end_date":"2023-07-29","start_date":"2023-07-23","name":"ICML: International Conference on Machine Learning"},"date_updated":"2023-10-31T08:52:28Z","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"oa_version":"Preprint","abstract":[{"text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.","lang":"eng"}],"month":"07","intvolume":" 202","alternative_title":["PMLR"],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.13468","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2640-3498"]},"publication_status":"published","volume":202},{"_id":"14460","status":"public","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2023-07-23","location":"Honolulu, Hawaii, HI, United States","end_date":"2023-07-29"},"type":"conference","date_updated":"2023-10-31T09:33:51Z","department":[{"_id":"DaAl"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We provide an efficient implementation of the backpropagation algorithm, specialized to the case where the weights of the neural network being trained are sparse. Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and common layer types (e.g., convolutional or linear). We provide a fast vectorized implementation on commodity CPUs, and show that it can yield speedups in end-to-end runtime experiments, both in transfer learning using already-sparsified networks, and in training sparse networks from scratch. Thus, our results provide the first support for sparse training on commodity hardware."}],"intvolume":" 202","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.04852"}],"alternative_title":["PMLR"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2640-3498"]},"ec_funded":1,"volume":202,"project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Nikdan, Mahdi, et al. “SparseProp: Efficient Sparse Backpropagation for Faster Training of Neural Networks at the Edge.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 26215–27.","short":"M. Nikdan, T. Pegolotti, E.B. Iofinova, E. Kurtic, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 26215–26227.","ieee":"M. Nikdan, T. Pegolotti, E. B. Iofinova, E. Kurtic, and D.-A. Alistarh, “SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 26215–26227.","apa":"Nikdan, M., Pegolotti, T., Iofinova, E. B., Kurtic, E., & Alistarh, D.-A. (2023). SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 26215–26227). Honolulu, Hawaii, HI, United States: ML Research Press.","ama":"Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:26215-26227.","chicago":"Nikdan, Mahdi, Tommaso Pegolotti, Eugenia B Iofinova, Eldar Kurtic, and Dan-Adrian Alistarh. “SparseProp: Efficient Sparse Backpropagation for Faster Training of Neural Networks at the Edge.” In Proceedings of the 40th International Conference on Machine Learning, 202:26215–27. ML Research Press, 2023.","ista":"Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. 2023. SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 26215–26227."},"title":"SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge","external_id":{"arxiv":["2302.04852"]},"article_processing_charge":"No","author":[{"first_name":"Mahdi","id":"66374281-f394-11eb-9cf6-869147deecc0","full_name":"Nikdan, Mahdi","last_name":"Nikdan"},{"full_name":"Pegolotti, Tommaso","last_name":"Pegolotti","first_name":"Tommaso"},{"orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B","last_name":"Iofinova","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","first_name":"Eugenia B"},{"last_name":"Kurtic","full_name":"Kurtic, Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"acknowledgement":"We would like to thank Elias Frantar for his valuable assistance and support at the outset of this project, and the anonymous ICML and SNN reviewers for very constructive feedback. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. DA acknowledges generous ERC support, via Starting Grant 805223 ScaleML. ","oa":1,"publisher":"ML Research Press","quality_controlled":"1","publication":"Proceedings of the 40th International Conference on Machine Learning","day":"30","year":"2023","date_created":"2023-10-29T23:01:17Z","date_published":"2023-07-30T00:00:00Z","page":"26215-26227"},{"date_updated":"2023-10-31T11:43:12Z","department":[{"_id":"KrPi"}],"_id":"14457","status":"public","type":"conference","conference":{"location":"Quito, Ecuador","end_date":"2023-10-06","start_date":"2023-10-03","name":"LATINCRYPT: Conference on Cryptology and Information Security in Latin America"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031444685"],"issn":["0302-9743"]},"publication_status":"published","volume":14168,"oa_version":"Preprint","abstract":[{"text":"Threshold secret sharing allows a dealer to split a secret s into n shares, such that any t shares allow for reconstructing s, but no t-1 shares reveal any information about s. Leakage-resilient secret sharing requires that the secret remains hidden, even when an adversary additionally obtains a limited amount of leakage from every share. Benhamouda et al. (CRYPTO’18) proved that Shamir’s secret sharing scheme is one bit leakage-resilient for reconstruction threshold t≥0.85n and conjectured that the same holds for t = c.n for any constant 0≤c≤1. Nielsen and Simkin (EUROCRYPT’20) showed that this is the best one can hope for by proving that Shamir’s scheme is not secure against one-bit leakage when t0c.n/log(n).\r\nIn this work, we strengthen the lower bound of Nielsen and Simkin. We consider noisy leakage-resilience, where a random subset of leakages is replaced by uniformly random noise. We prove a lower bound for Shamir’s secret sharing, similar to that of Nielsen and Simkin, which holds even when a constant fraction of leakages is replaced by random noise. To this end, we first prove a lower bound on the share size of any noisy-leakage-resilient sharing scheme. We then use this lower bound to show that there exist universal constants c1, c2, such that for sufficiently large n it holds that Shamir’s secret sharing scheme is not noisy-leakage-resilient for t≤c1.n/log(n), even when a c2 fraction of leakages are replaced by random noise.\r\n\r\n\r\n\r\n","lang":"eng"}],"month":"10","intvolume":" 14168","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://eprint.iacr.org/2023/1017","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C. Hoffmann, M. Simkin, in:, 8th International Conference on Cryptology and Information Security in Latin America, Springer Nature, 2023, pp. 215–228.","ieee":"C. Hoffmann and M. Simkin, “Stronger lower bounds for leakage-resilient secret sharing,” in 8th International Conference on Cryptology and Information Security in Latin America, Quito, Ecuador, 2023, vol. 14168, pp. 215–228.","apa":"Hoffmann, C., & Simkin, M. (2023). Stronger lower bounds for leakage-resilient secret sharing. In 8th International Conference on Cryptology and Information Security in Latin America (Vol. 14168, pp. 215–228). Quito, Ecuador: Springer Nature. https://doi.org/10.1007/978-3-031-44469-2_11","ama":"Hoffmann C, Simkin M. Stronger lower bounds for leakage-resilient secret sharing. In: 8th International Conference on Cryptology and Information Security in Latin America. Vol 14168. Springer Nature; 2023:215-228. doi:10.1007/978-3-031-44469-2_11","mla":"Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient Secret Sharing.” 8th International Conference on Cryptology and Information Security in Latin America, vol. 14168, Springer Nature, 2023, pp. 215–28, doi:10.1007/978-3-031-44469-2_11.","ista":"Hoffmann C, Simkin M. 2023. Stronger lower bounds for leakage-resilient secret sharing. 8th International Conference on Cryptology and Information Security in Latin America. LATINCRYPT: Conference on Cryptology and Information Security in Latin America, LNCS, vol. 14168, 215–228.","chicago":"Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient Secret Sharing.” In 8th International Conference on Cryptology and Information Security in Latin America, 14168:215–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44469-2_11."},"title":"Stronger lower bounds for leakage-resilient secret sharing","author":[{"full_name":"Hoffmann, Charlotte","orcid":"0000-0003-2027-5549","last_name":"Hoffmann","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","first_name":"Charlotte"},{"first_name":"Mark","last_name":"Simkin","full_name":"Simkin, Mark"}],"article_processing_charge":"No","day":"01","publication":"8th International Conference on Cryptology and Information Security in Latin America","year":"2023","doi":"10.1007/978-3-031-44469-2_11","date_published":"2023-10-01T00:00:00Z","date_created":"2023-10-29T23:01:16Z","page":"215-228","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29","location":"Honolulu, Hawaii, HI, United States","start_date":"2023-07-23"},"status":"public","_id":"14458","department":[{"_id":"DaAl"}],"date_updated":"2023-10-31T09:59:42Z","scopus_import":"1","alternative_title":["PMLR"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.00774"}],"month":"07","intvolume":" 202","abstract":[{"lang":"eng","text":"We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Preprint","volume":202,"ec_funded":1,"publication_identifier":{"eissn":["2640-3498"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Frantar, Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.00774"]},"title":"SparseGPT: Massive language models can be accurately pruned in one-shot","citation":{"chicago":"Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models Can Be Accurately Pruned in One-Shot.” In Proceedings of the 40th International Conference on Machine Learning, 202:10323–37. ML Research Press, 2023.","ista":"Frantar E, Alistarh D-A. 2023. SparseGPT: Massive language models can be accurately pruned in one-shot. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 10323–10337.","mla":"Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models Can Be Accurately Pruned in One-Shot.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10323–37.","ama":"Frantar E, Alistarh D-A. SparseGPT: Massive language models can be accurately pruned in one-shot. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:10323-10337.","apa":"Frantar, E., & Alistarh, D.-A. (2023). SparseGPT: Massive language models can be accurately pruned in one-shot. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 10323–10337). Honolulu, Hawaii, HI, United States: ML Research Press.","short":"E. Frantar, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 10323–10337.","ieee":"E. Frantar and D.-A. Alistarh, “SparseGPT: Massive language models can be accurately pruned in one-shot,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 10323–10337."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ML Research Press","quality_controlled":"1","oa":1,"acknowledgement":"The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No. 805223 ScaleML), as well as experimental support from Eldar Kurtic, and from the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois Schloegl.","page":"10323-10337","date_published":"2023-07-30T00:00:00Z","date_created":"2023-10-29T23:01:16Z","year":"2023","day":"30","publication":"Proceedings of the 40th International Conference on Machine Learning"},{"department":[{"_id":"JuFi"}],"date_updated":"2023-10-31T10:58:28Z","status":"public","type":"journal_article","article_type":"original","_id":"14451","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1433-3058"],"issn":["0941-0643"]},"publication_status":"epub_ahead","month":"10","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00521-023-09033-7"}],"oa_version":"Published Version","abstract":[{"text":"We investigate the potential of Multi-Objective, Deep Reinforcement Learning for stock and cryptocurrency single-asset trading: in particular, we consider a Multi-Objective algorithm which generalizes the reward functions and discount factor (i.e., these components are not specified a priori, but incorporated in the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT, XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of the proposed Multi-Objective algorithm, and provide preliminary statistical evidence showing increased predictive stability over the corresponding Single-Objective strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge over the corresponding Single-Objective strategy when the reward mechanism is sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss the generalization properties with respect to the discount factor. The entirety of our code is provided in open-source format.","lang":"eng"}],"title":"Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading","author":[{"last_name":"Cornalba","full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149","id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico"},{"last_name":"Disselkamp","full_name":"Disselkamp, Constantin","first_name":"Constantin"},{"full_name":"Scassola, Davide","last_name":"Scassola","first_name":"Davide"},{"first_name":"Christopher","full_name":"Helf, Christopher","last_name":"Helf"}],"external_id":{"arxiv":["2203.04579"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cornalba, Federico, Constantin Disselkamp, Davide Scassola, and Christopher Helf. “Multi-Objective Reward Generalization: Improving Performance of Deep Reinforcement Learning for Applications in Single-Asset Trading.” Neural Computing and Applications. Springer Nature, 2023. https://doi.org/10.1007/s00521-023-09033-7.","ista":"Cornalba F, Disselkamp C, Scassola D, Helf C. 2023. Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications.","mla":"Cornalba, Federico, et al. “Multi-Objective Reward Generalization: Improving Performance of Deep Reinforcement Learning for Applications in Single-Asset Trading.” Neural Computing and Applications, Springer Nature, 2023, doi:10.1007/s00521-023-09033-7.","ama":"Cornalba F, Disselkamp C, Scassola D, Helf C. Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications. 2023. doi:10.1007/s00521-023-09033-7","apa":"Cornalba, F., Disselkamp, C., Scassola, D., & Helf, C. (2023). Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications. Springer Nature. https://doi.org/10.1007/s00521-023-09033-7","short":"F. Cornalba, C. Disselkamp, D. Scassola, C. Helf, Neural Computing and Applications (2023).","ieee":"F. Cornalba, C. Disselkamp, D. Scassola, and C. Helf, “Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading,” Neural Computing and Applications. Springer Nature, 2023."},"project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"date_published":"2023-10-05T00:00:00Z","doi":"10.1007/s00521-023-09033-7","date_created":"2023-10-22T22:01:16Z","day":"05","publication":"Neural Computing and Applications","year":"2023","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by Università degli Studi di Trieste within the CRUI-CARE Agreement. Funding was provided by Austrian Science Fund (Grant No. F65), Horizon 2020 (Grant No. 754411) and Österreichische Forschungsförderungsgesellschaft."},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"volume":46,"issue":"10","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"In the presence of an obstacle, active particles condensate into a surface “wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of “fast” and “slow” active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion “diversity,” defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter."}],"intvolume":" 46","month":"10","scopus_import":"1","date_updated":"2023-10-31T11:16:41Z","department":[{"_id":"AnSa"}],"_id":"14442","status":"public","article_type":"original","type":"journal_article","publication":"The European Physical Journal E","day":"01","year":"2023","date_created":"2023-10-22T22:01:13Z","doi":"10.1140/epje/s10189-023-00354-y","date_published":"2023-10-01T00:00:00Z","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and Millennium Science Initiative Program NCN19_170D of ANID, Chile. P.d.C. was supported by Scholarships Nos. 2021/10139-2 and 2022/13872-5 and ICTP-SAIFR Grant No. 2021/14335-0, all granted by São Paulo Research Foundation (FAPESP), Brazil.","quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00354-y.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Mixtures of self-propelled particles interacting with asymmetric obstacles. The European Physical Journal E. 46(10), 95.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” The European Physical Journal E, vol. 46, no. 10, 95, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00354-y.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, The European Physical Journal E 46 (2023).","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Mixtures of self-propelled particles interacting with asymmetric obstacles,” The European Physical Journal E, vol. 46, no. 10. Springer Nature, 2023.","ama":"Rojas Vega MN, De Castro P, Soto R. Mixtures of self-propelled particles interacting with asymmetric obstacles. The European Physical Journal E. 2023;46(10). doi:10.1140/epje/s10189-023-00354-y","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Mixtures of self-propelled particles interacting with asymmetric obstacles. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00354-y"},"title":"Mixtures of self-propelled particles interacting with asymmetric obstacles","article_processing_charge":"No","external_id":{"pmid":["37819444"]},"author":[{"id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","first_name":"Mauricio Nicolas","last_name":"Rojas Vega","full_name":"Rojas Vega, Mauricio Nicolas"},{"full_name":"De Castro, Pablo","last_name":"De Castro","first_name":"Pablo"},{"first_name":"Rodrigo","full_name":"Soto, Rodrigo","last_name":"Soto"}],"article_number":"95"},{"abstract":[{"text":"We prove several results about substructures in Latin squares. First, we explain how to adapt our recent work on high-girth Steiner triple systems to the setting of Latin squares, resolving a conjecture of Linial that there exist Latin squares with arbitrarily high girth. As a consequence, we see that the number of order- n Latin squares with no intercalate (i.e., no 2×2 Latin subsquare) is at least (e−9/4n−o(n))n2. Equivalently, P[N=0]≥e−n2/4−o(n2)=e−(1+o(1))EN\r\n , where N is the number of intercalates in a uniformly random order- n Latin square. \r\nIn fact, extending recent work of Kwan, Sah, and Sawhney, we resolve the general large-deviation problem for intercalates in random Latin squares, up to constant factors in the exponent: for any constant 0<δ≤1 we have P[N≤(1−δ)EN]=exp(−Θ(n2)) and for any constant δ>0 we have P[N≥(1+δ)EN]=exp(−Θ(n4/3logn)). \r\nFinally, as an application of some new general tools for studying substructures in random Latin squares, we show that in almost all order- n Latin squares, the number of cuboctahedra (i.e., the number of pairs of possibly degenerate 2×2 submatrices with the same arrangement of symbols) is of order n4, which is the minimum possible. As observed by Gowers and Long, this number can be interpreted as measuring ``how associative'' the quasigroup associated with the Latin square is.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2202.05088","open_access":"1"}],"month":"09","intvolume":" 256","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":256,"issue":"2","_id":"14444","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-10-31T11:27:30Z","department":[{"_id":"MaKw"}],"acknowledgement":"Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302. Sah was supported by the PD Soros Fellowship. Simkin was supported by the Center of Mathematical Sciences and Applications at Harvard University.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"year":"2023","day":"01","publication":"Israel Journal of Mathematics","page":"363-416","doi":"10.1007/s11856-023-2513-9","date_published":"2023-09-01T00:00:00Z","date_created":"2023-10-22T22:01:14Z","citation":{"mla":"Kwan, Matthew Alan, et al. “Substructures in Latin Squares.” Israel Journal of Mathematics, vol. 256, no. 2, Springer Nature, 2023, pp. 363–416, doi:10.1007/s11856-023-2513-9.","ieee":"M. A. Kwan, A. Sah, M. Sawhney, and M. Simkin, “Substructures in Latin squares,” Israel Journal of Mathematics, vol. 256, no. 2. Springer Nature, pp. 363–416, 2023.","short":"M.A. Kwan, A. Sah, M. Sawhney, M. Simkin, Israel Journal of Mathematics 256 (2023) 363–416.","apa":"Kwan, M. A., Sah, A., Sawhney, M., & Simkin, M. (2023). Substructures in Latin squares. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-023-2513-9","ama":"Kwan MA, Sah A, Sawhney M, Simkin M. Substructures in Latin squares. Israel Journal of Mathematics. 2023;256(2):363-416. doi:10.1007/s11856-023-2513-9","chicago":"Kwan, Matthew Alan, Ashwin Sah, Mehtaab Sawhney, and Michael Simkin. “Substructures in Latin Squares.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-023-2513-9.","ista":"Kwan MA, Sah A, Sawhney M, Simkin M. 2023. Substructures in Latin squares. Israel Journal of Mathematics. 256(2), 363–416."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567"},{"full_name":"Sah, Ashwin","last_name":"Sah","first_name":"Ashwin"},{"first_name":"Mehtaab","last_name":"Sawhney","full_name":"Sawhney, Mehtaab"},{"first_name":"Michael","last_name":"Simkin","full_name":"Simkin, Michael"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2202.05088"]},"title":"Substructures in Latin squares"},{"author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"first_name":"Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","full_name":"Kueffner, Konstantin","orcid":"0000-0001-8974-2542","last_name":"Kueffner"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik"}],"external_id":{"arxiv":["2308.00341"]},"article_processing_charge":"No","title":"Monitoring algorithmic fairness under partial observations","citation":{"apa":"Henzinger, T. A., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness under partial observations. In 23rd International Conference on Runtime Verification (Vol. 14245, pp. 291–311). Thessaloniki, Greece: Springer Nature. https://doi.org/10.1007/978-3-031-44267-4_15","ama":"Henzinger TA, Kueffner K, Mallik K. Monitoring algorithmic fairness under partial observations. In: 23rd International Conference on Runtime Verification. Vol 14245. Springer Nature; 2023:291-311. doi:10.1007/978-3-031-44267-4_15","short":"T.A. Henzinger, K. Kueffner, K. Mallik, in:, 23rd International Conference on Runtime Verification, Springer Nature, 2023, pp. 291–311.","ieee":"T. A. Henzinger, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness under partial observations,” in 23rd International Conference on Runtime Verification, Thessaloniki, Greece, 2023, vol. 14245, pp. 291–311.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness under Partial Observations.” 23rd International Conference on Runtime Verification, vol. 14245, Springer Nature, 2023, pp. 291–311, doi:10.1007/978-3-031-44267-4_15.","ista":"Henzinger TA, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness under partial observations. 23rd International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 14245, 291–311.","chicago":"Henzinger, Thomas A, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness under Partial Observations.” In 23rd International Conference on Runtime Verification, 14245:291–311. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_15."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"page":"291-311","date_published":"2023-10-01T00:00:00Z","doi":"10.1007/978-3-031-44267-4_15","date_created":"2023-10-29T23:01:15Z","year":"2023","day":"01","publication":"23rd International Conference on Runtime Verification","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.","department":[{"_id":"ToHe"}],"date_updated":"2023-10-31T11:48:20Z","type":"conference","conference":{"location":"Thessaloniki, Greece","end_date":"2023-10-06","start_date":"2023-10-03","name":"RV: Conference on Runtime Verification"},"status":"public","_id":"14454","volume":14245,"ec_funded":1,"publication_identifier":{"isbn":["9783031442667"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2308.00341"}],"month":"10","intvolume":" 14245","abstract":[{"text":"As AI and machine-learned software are used increasingly for making decisions that affect humans, it is imperative that they remain fair and unbiased in their decisions. To complement design-time bias mitigation measures, runtime verification techniques have been introduced recently to monitor the algorithmic fairness of deployed systems. Previous monitoring techniques assume full observability of the states of the (unknown) monitored system. Moreover, they can monitor only fairness properties that are specified as arithmetic expressions over the probabilities of different events. In this work, we extend fairness monitoring to systems modeled as partially observed Markov chains (POMC), and to specifications containing arithmetic expressions over the expected values of numerical functions on event sequences. The only assumptions we make are that the underlying POMC is aperiodic and starts in the stationary distribution, with a bound on its mixing time being known. These assumptions enable us to estimate a given property for the entire distribution of possible executions of the monitored POMC, by observing only a single execution. Our monitors observe a long run of the system and, after each new observation, output updated PAC-estimates of how fair or biased the system is. The monitors are computationally lightweight and, using a prototype implementation, we demonstrate their effectiveness on several real-world examples.","lang":"eng"}],"oa_version":"Preprint"},{"author":[{"first_name":"Jozef","last_name":"Jakubík","full_name":"Jakubík, Jozef"},{"last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martina","full_name":"Chvosteková, Martina","last_name":"Chvosteková"},{"first_name":"Anna","full_name":"Krakovská, Anna","last_name":"Krakovská"}],"article_processing_charge":"Yes","title":"Against the flow of time with multi-output models","citation":{"chicago":"Jakubík, Jozef, Mary Phuong, Martina Chvosteková, and Anna Krakovská. “Against the Flow of Time with Multi-Output Models.” Measurement Science Review. Sciendo, 2023. https://doi.org/10.2478/msr-2023-0023.","ista":"Jakubík J, Phuong M, Chvosteková M, Krakovská A. 2023. Against the flow of time with multi-output models. Measurement Science Review. 23(4), 175–183.","mla":"Jakubík, Jozef, et al. “Against the Flow of Time with Multi-Output Models.” Measurement Science Review, vol. 23, no. 4, Sciendo, 2023, pp. 175–83, doi:10.2478/msr-2023-0023.","apa":"Jakubík, J., Phuong, M., Chvosteková, M., & Krakovská, A. (2023). Against the flow of time with multi-output models. Measurement Science Review. Sciendo. https://doi.org/10.2478/msr-2023-0023","ama":"Jakubík J, Phuong M, Chvosteková M, Krakovská A. Against the flow of time with multi-output models. Measurement Science Review. 2023;23(4):175-183. doi:10.2478/msr-2023-0023","ieee":"J. Jakubík, M. Phuong, M. Chvosteková, and A. Krakovská, “Against the flow of time with multi-output models,” Measurement Science Review, vol. 23, no. 4. Sciendo, pp. 175–183, 2023.","short":"J. Jakubík, M. Phuong, M. Chvosteková, A. Krakovská, Measurement Science Review 23 (2023) 175–183."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Sciendo","quality_controlled":"1","oa":1,"acknowledgement":"The work was supported by the Scientific Grant Agency of the Ministry of Education of the Slovak Republic and the Slovak Academy of Sciences, projects APVV-21-0216, VEGA2-0096-21 and VEGA 2-0023-22.","page":"175-183","date_published":"2023-08-01T00:00:00Z","doi":"10.2478/msr-2023-0023","date_created":"2023-10-22T22:01:15Z","has_accepted_license":"1","year":"2023","day":"01","publication":"Measurement Science Review","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"14446","department":[{"_id":"ChLa"}],"file_date_updated":"2023-10-31T12:07:23Z","date_updated":"2023-10-31T12:12:47Z","ddc":["510"],"scopus_import":"1","month":"08","intvolume":" 23","abstract":[{"text":"Recent work has paid close attention to the first principle of Granger causality, according to which cause precedes effect. In this context, the question may arise whether the detected direction of causality also reverses after the time reversal of unidirectionally coupled data. Recently, it has been shown that for unidirectionally causally connected autoregressive (AR) processes X → Y, after time reversal of data, the opposite causal direction Y → X is indeed detected, although typically as part of the bidirectional X↔ Y link. As we argue here, the answer is different when the measured data are not from AR processes but from linked deterministic systems. When the goal is the usual forward data analysis, cross-mapping-like approaches correctly detect X → Y, while Granger causality-like approaches, which should not be used for deterministic time series, detect causal independence X → Y. The results of backward causal analysis depend on the predictability of the reversed data. Unlike AR processes, observables from deterministic dynamical systems, even complex nonlinear ones, can be predicted well forward, while backward predictions can be difficult (notably when the time reversal of a function leads to one-to-many relations). To address this problem, we propose an approach based on models that provide multiple candidate predictions for the target, combined with a loss function that consideres only the best candidate. The resulting good forward and backward predictability supports the view that unidirectionally causally linked deterministic dynamical systems X → Y can be expected to detect the same link both before and after time reversal.","lang":"eng"}],"oa_version":"Published Version","volume":23,"issue":"4","publication_identifier":{"eissn":["1335-8871"]},"publication_status":"published","file":[{"success":1,"checksum":"b069cc10fa6a7c96b2bc9f728165f9e6","file_id":"14476","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_MeasurementScienceRev_Jakubik.pdf","date_created":"2023-10-31T12:07:23Z","creator":"dernst","file_size":2639783,"date_updated":"2023-10-31T12:07:23Z"}],"language":[{"iso":"eng"}]},{"volume":80,"issue":"10","publication_identifier":{"eissn":["2168-6238"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 80","abstract":[{"lang":"eng","text":"Importance Climate change, pollution, urbanization, socioeconomic inequality, and psychosocial effects of the COVID-19 pandemic have caused massive changes in environmental conditions that affect brain health during the life span, both on a population level as well as on the level of the individual. How these environmental factors influence the brain, behavior, and mental illness is not well known.\r\nObservations A research strategy enabling population neuroscience to contribute to identify brain mechanisms underlying environment-related mental illness by leveraging innovative enrichment tools for data federation, geospatial observation, climate and pollution measures, digital health, and novel data integration techniques is described. This strategy can inform innovative treatments that target causal cognitive and molecular mechanisms of mental illness related to the environment. An example is presented of the environMENTAL Project that is leveraging federated cohort data of over 1.5 million European citizens and patients enriched with deep phenotyping data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms related to environmental adversity underlying symptoms of depression, anxiety, stress, and substance misuse.\r\nConclusions and Relevance This research will lead to the development of objective biomarkers and evidence-based interventions that will significantly improve outcomes of environment-related mental illness."}],"pmid":1,"oa_version":"None","department":[{"_id":"GaNo"}],"date_updated":"2023-10-31T12:17:20Z","type":"journal_article","article_type":"review","status":"public","_id":"14443","page":"1066-1074","doi":"10.1001/jamapsychiatry.2023.2996","date_published":"2023-10-01T00:00:00Z","date_created":"2023-10-22T22:01:14Z","year":"2023","day":"01","publication":"JAMA Psychiatry","quality_controlled":"1","publisher":"American Medical Association","author":[{"full_name":"Schumann, Gunter","last_name":"Schumann","first_name":"Gunter"},{"first_name":"Ole A.","full_name":"Andreassen, Ole A.","last_name":"Andreassen"},{"full_name":"Banaschewski, Tobias","last_name":"Banaschewski","first_name":"Tobias"},{"full_name":"Calhoun, Vince D.","last_name":"Calhoun","first_name":"Vince D."},{"first_name":"Nicholas","full_name":"Clinton, Nicholas","last_name":"Clinton"},{"last_name":"Desrivieres","full_name":"Desrivieres, Sylvane","first_name":"Sylvane"},{"full_name":"Brandlistuen, Ragnhild Eek","last_name":"Brandlistuen","first_name":"Ragnhild Eek"},{"full_name":"Feng, Jianfeng","last_name":"Feng","first_name":"Jianfeng"},{"last_name":"Hese","full_name":"Hese, Soeren","first_name":"Soeren"},{"full_name":"Hitchen, Esther","last_name":"Hitchen","first_name":"Esther"},{"last_name":"Hoffmann","full_name":"Hoffmann, Per","first_name":"Per"},{"last_name":"Jia","full_name":"Jia, Tianye","first_name":"Tianye"},{"first_name":"Viktor","last_name":"Jirsa","full_name":"Jirsa, Viktor"},{"first_name":"Andre F.","full_name":"Marquand, Andre F.","last_name":"Marquand"},{"last_name":"Nees","full_name":"Nees, Frauke","first_name":"Frauke"},{"first_name":"Markus M.","last_name":"Nöthen","full_name":"Nöthen, Markus M."},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"first_name":"Elli","last_name":"Polemiti","full_name":"Polemiti, Elli"},{"first_name":"Markus","last_name":"Ralser","full_name":"Ralser, Markus"},{"full_name":"Rapp, Michael","last_name":"Rapp","first_name":"Michael"},{"last_name":"Schepanski","full_name":"Schepanski, Kerstin","first_name":"Kerstin"},{"full_name":"Schikowski, Tamara","last_name":"Schikowski","first_name":"Tamara"},{"full_name":"Slater, Mel","last_name":"Slater","first_name":"Mel"},{"full_name":"Sommer, Peter","last_name":"Sommer","first_name":"Peter"},{"first_name":"Bernd Carsten","last_name":"Stahl","full_name":"Stahl, Bernd Carsten"},{"full_name":"Thompson, Paul M.","last_name":"Thompson","first_name":"Paul M."},{"first_name":"Sven","last_name":"Twardziok","full_name":"Twardziok, Sven"},{"last_name":"Van Der Meer","full_name":"Van Der Meer, Dennis","first_name":"Dennis"},{"first_name":"Henrik","last_name":"Walter","full_name":"Walter, Henrik"},{"first_name":"Lars","last_name":"Westlye","full_name":"Westlye, Lars"}],"external_id":{"pmid":["37610741"]},"article_processing_charge":"No","title":"Addressing global environmental challenges to mental health using population neuroscience: A review","citation":{"ieee":"G. Schumann et al., “Addressing global environmental challenges to mental health using population neuroscience: A review,” JAMA Psychiatry, vol. 80, no. 10. American Medical Association, pp. 1066–1074, 2023.","short":"G. Schumann, O.A. Andreassen, T. Banaschewski, V.D. Calhoun, N. Clinton, S. Desrivieres, R.E. Brandlistuen, J. Feng, S. Hese, E. Hitchen, P. Hoffmann, T. Jia, V. Jirsa, A.F. Marquand, F. Nees, M.M. Nöthen, G. Novarino, E. Polemiti, M. Ralser, M. Rapp, K. Schepanski, T. Schikowski, M. Slater, P. Sommer, B.C. Stahl, P.M. Thompson, S. Twardziok, D. Van Der Meer, H. Walter, L. Westlye, JAMA Psychiatry 80 (2023) 1066–1074.","apa":"Schumann, G., Andreassen, O. A., Banaschewski, T., Calhoun, V. D., Clinton, N., Desrivieres, S., … Westlye, L. (2023). Addressing global environmental challenges to mental health using population neuroscience: A review. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2023.2996","ama":"Schumann G, Andreassen OA, Banaschewski T, et al. Addressing global environmental challenges to mental health using population neuroscience: A review. JAMA Psychiatry. 2023;80(10):1066-1074. doi:10.1001/jamapsychiatry.2023.2996","mla":"Schumann, Gunter, et al. “Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review.” JAMA Psychiatry, vol. 80, no. 10, American Medical Association, 2023, pp. 1066–74, doi:10.1001/jamapsychiatry.2023.2996.","ista":"Schumann G, Andreassen OA, Banaschewski T, Calhoun VD, Clinton N, Desrivieres S, Brandlistuen RE, Feng J, Hese S, Hitchen E, Hoffmann P, Jia T, Jirsa V, Marquand AF, Nees F, Nöthen MM, Novarino G, Polemiti E, Ralser M, Rapp M, Schepanski K, Schikowski T, Slater M, Sommer P, Stahl BC, Thompson PM, Twardziok S, Van Der Meer D, Walter H, Westlye L. 2023. Addressing global environmental challenges to mental health using population neuroscience: A review. JAMA Psychiatry. 80(10), 1066–1074.","chicago":"Schumann, Gunter, Ole A. Andreassen, Tobias Banaschewski, Vince D. Calhoun, Nicholas Clinton, Sylvane Desrivieres, Ragnhild Eek Brandlistuen, et al. “Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review.” JAMA Psychiatry. American Medical Association, 2023. https://doi.org/10.1001/jamapsychiatry.2023.2996."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Open access funding provided by Institute of Science and Technology (IST Austria).","page":"287-337","date_created":"2023-10-22T22:01:13Z","date_published":"2023-11-01T00:00:00Z","doi":"10.1007/s00220-023-04841-3","year":"2023","has_accepted_license":"1","publication":"Communications in Mathematical Physics","day":"01","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2207.03156"]},"author":[{"full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928","last_name":"Brooks","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","first_name":"Morris"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"title":"The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy","citation":{"ista":"Brooks M, Seiringer R. 2023. The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. 404, 287–337.","chicago":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part I - The Quantum Correction to the Classical Energy.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04841-3.","ama":"Brooks M, Seiringer R. The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. 2023;404:287-337. doi:10.1007/s00220-023-04841-3","apa":"Brooks, M., & Seiringer, R. (2023). The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04841-3","ieee":"M. Brooks and R. Seiringer, “The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy,” Communications in Mathematical Physics, vol. 404. Springer Nature, pp. 287–337, 2023.","short":"M. Brooks, R. Seiringer, Communications in Mathematical Physics 404 (2023) 287–337.","mla":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part I - The Quantum Correction to the Classical Energy.” Communications in Mathematical Physics, vol. 404, Springer Nature, 2023, pp. 287–337, doi:10.1007/s00220-023-04841-3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 404","month":"11","abstract":[{"lang":"eng","text":"We study the Fröhlich polaron model in R3, and establish the subleading term in the strong coupling asymptotics of its ground state energy, corresponding to the quantum corrections to the classical energy determined by the Pekar approximation."}],"oa_version":"Published Version","ec_funded":1,"volume":404,"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14477","checksum":"1ae49b39247cb6b40ff75997381581b8","success":1,"creator":"dernst","date_updated":"2023-10-31T12:21:39Z","file_size":832375,"date_created":"2023-10-31T12:21:39Z","file_name":"2023_CommMathPhysics_Brooks.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"14441","file_date_updated":"2023-10-31T12:21:39Z","department":[{"_id":"RoSe"}],"date_updated":"2023-10-31T12:22:51Z","ddc":["510"]},{"year":"2023","day":"22","publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","page":"11980-11989","date_published":"2023-08-22T00:00:00Z","doi":"10.1109/CVPR52729.2023.01153","date_created":"2023-10-22T22:01:16Z","quality_controlled":"1","publisher":"IEEE","oa":1,"citation":{"mla":"Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial in-Face Frank-Wolfe Directions.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, vol. 2023, IEEE, 2023, pp. 11980–89, doi:10.1109/CVPR52729.2023.01153.","ieee":"V. Kolmogorov, “Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Vancouver, Canada, 2023, vol. 2023, pp. 11980–11989.","short":"V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 11980–11989.","ama":"Kolmogorov V. Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Vol 2023. IEEE; 2023:11980-11989. doi:10.1109/CVPR52729.2023.01153","apa":"Kolmogorov, V. (2023). Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Vol. 2023, pp. 11980–11989). Vancouver, Canada: IEEE. https://doi.org/10.1109/CVPR52729.2023.01153","chicago":"Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial in-Face Frank-Wolfe Directions.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2023:11980–89. IEEE, 2023. https://doi.org/10.1109/CVPR52729.2023.01153.","ista":"Kolmogorov V. 2023. Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2023, 11980–11989."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2010.09567"]},"title":"Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions","publication_identifier":{"isbn":["9798350301298"],"issn":["1063-6919"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":2023,"abstract":[{"lang":"eng","text":"We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in [16], [35]. As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subroutine based on in-face Frank-Wolfe directions, introduced in [4] in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2010.09567","open_access":"1"}],"month":"08","intvolume":" 2023","date_updated":"2023-10-31T12:01:24Z","department":[{"_id":"VlKo"}],"_id":"14448","type":"conference","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Vancouver, Canada","end_date":"2023-06-24","start_date":"2023-06-17"},"status":"public"},{"article_number":"112132","project":[{"call_identifier":"H2020","_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.","ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no. 3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.","short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).","ieee":"D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” Cell Reports, vol. 42, no. 3. Elsevier, 2023.","apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 2023;42(3). doi:10.1016/j.celrep.2023.112132"},"title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","author":[{"first_name":"David B.","full_name":"Lyons, David B.","last_name":"Lyons"},{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"last_name":"Choi","full_name":"Choi, Jaemyung","first_name":"Jaemyung"},{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","first_name":"Elizabeth","last_name":"Hollwey","full_name":"Hollwey, Elizabeth"},{"full_name":"Colicchio, Jack","last_name":"Colicchio","first_name":"Jack"},{"last_name":"Anderson","full_name":"Anderson, Ian","first_name":"Ian"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"},{"full_name":"Howard, Martin","last_name":"Howard","first_name":"Martin"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"article_processing_charge":"Yes","external_id":{"isi":["000944921600001"]},"acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L.","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"28","publication":"Cell Reports","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-03-28T00:00:00Z","doi":"10.1016/j.celrep.2023.112132","date_created":"2023-02-23T09:17:44Z","_id":"12672","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"date_updated":"2023-11-02T12:23:45Z","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"file_date_updated":"2023-05-11T10:41:42Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation."}],"month":"03","intvolume":" 42","scopus_import":"1","file":[{"date_created":"2023-05-11T10:41:42Z","file_name":"2023_CellReports_Lyons.pdf","creator":"kschuh","date_updated":"2023-05-11T10:41:42Z","file_size":8401261,"file_id":"12941","checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2211-1247"]},"publication_status":"published","volume":42,"issue":"3","ec_funded":1},{"department":[{"_id":"RoSe"}],"file_date_updated":"2023-07-03T10:36:25Z","date_updated":"2023-11-02T12:30:50Z","ddc":["500"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13178","ec_funded":1,"volume":11,"publication_status":"published","publication_identifier":{"eissn":["2050-5094"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-07-03T10:36:25Z","file_name":"2023_ForumofMathematics.Sigma_Mitrouskas.pdf","creator":"alisjak","date_updated":"2023-07-03T10:36:25Z","file_size":943192,"file_id":"13186","checksum":"f672eb7dd015c472c9a04f1b9bf9df7d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 11","month":"06","abstract":[{"text":"We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar.","lang":"eng"}],"oa_version":"Published Version","external_id":{"isi":["001005008800001"],"arxiv":["2203.02454"]},"article_processing_charge":"Yes","author":[{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas"},{"last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"title":"Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron","citation":{"ista":"Mitrouskas DJ, Mysliwy K, Seiringer R. 2023. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. 11, 1–52.","chicago":"Mitrouskas, David Johannes, Krzysztof Mysliwy, and Robert Seiringer. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” Forum of Mathematics. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.45.","short":"D.J. Mitrouskas, K. Mysliwy, R. Seiringer, Forum of Mathematics 11 (2023) 1–52.","ieee":"D. J. Mitrouskas, K. Mysliwy, and R. Seiringer, “Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron,” Forum of Mathematics, vol. 11. Cambridge University Press, pp. 1–52, 2023.","apa":"Mitrouskas, D. J., Mysliwy, K., & Seiringer, R. (2023). Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. Cambridge University Press. https://doi.org/10.1017/fms.2023.45","ama":"Mitrouskas DJ, Mysliwy K, Seiringer R. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. 2023;11:1-52. doi:10.1017/fms.2023.45","mla":"Mitrouskas, David Johannes, et al. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” Forum of Mathematics, vol. 11, Cambridge University Press, 2023, pp. 1–52, doi:10.1017/fms.2023.45."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"1-52","date_created":"2023-07-02T22:00:43Z","doi":"10.1017/fms.2023.45","date_published":"2023-06-13T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Forum of Mathematics","day":"13","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","acknowledgement":"This research was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.)."},{"date_updated":"2023-11-06T09:56:24Z","ddc":["570"],"file_date_updated":"2023-11-06T09:47:50Z","department":[{"_id":"AnKi"}],"_id":"14484","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"review","status":"public","publication_status":"published","publication_identifier":{"eissn":["1530-8995"],"issn":["1081-0706"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_AnnualReviews_Kicheva.pdf","date_created":"2023-11-06T09:47:50Z","creator":"dernst","file_size":434819,"date_updated":"2023-11-06T09:47:50Z","success":1,"checksum":"461726014cf5907010afbd418d3c13ec","file_id":"14491","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"volume":39,"abstract":[{"lang":"eng","text":"Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 39","month":"10","citation":{"ieee":"A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,” Annual Review of Cell and Developmental Biology, vol. 39. Annual Reviews, pp. 91–121, 2023.","short":"A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39 (2023) 91–121.","apa":"Kicheva, A., & Briscoe, J. (2023). Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-020823-011522","ama":"Kicheva A, Briscoe J. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 2023;39:91-121. doi:10.1146/annurev-cellbio-020823-011522","mla":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology, vol. 39, Annual Reviews, 2023, pp. 91–121, doi:10.1146/annurev-cellbio-020823-011522.","ista":"Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 39, 91–121.","chicago":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2023. https://doi.org/10.1146/annurev-cellbio-020823-011522."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37418774"]},"author":[{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"}],"title":"Control of tissue development by morphogens","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F07802","name":"Morphogen control of growth and pattern in the spinal cord"}],"year":"2023","has_accepted_license":"1","publication":"Annual Review of Cell and Developmental Biology","day":"16","page":"91-121","date_created":"2023-11-05T23:00:53Z","date_published":"2023-10-16T00:00:00Z","doi":"10.1146/annurev-cellbio-020823-011522","acknowledgement":"We are grateful to Zena Hadjivasiliou for comments on this article. A.K. is supported by grants from the European Research Council under the European Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe (101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051), and by a grant from the European Research Council under the EU Horizon 2020 research and innovation program (742138).","oa":1,"publisher":"Annual Reviews","quality_controlled":"1"},{"date_published":"2023-10-31T00:00:00Z","doi":"10.1007/s11263-023-01899-3","date_created":"2023-11-05T23:00:54Z","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"publication_status":"epub_ahead","year":"2023","day":"31","language":[{"iso":"eng"}],"publication":"International Journal of Computer Vision","quality_controlled":"1","publisher":"Springer Nature","scopus_import":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s11263-023-01899-3"}],"month":"10","abstract":[{"text":"Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handling both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with individual latent spaces for identity and illumination. The prior model is learned in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis, even when applied to unseen subjects under uncontrolled illumination. This work is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide extensive evaluation and ablative studies of our model and also provide an application, where any face can be relighted using textual input.","lang":"eng"}],"oa_version":"Published Version","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.","author":[{"full_name":"Rao, Pramod","last_name":"Rao","first_name":"Pramod"},{"full_name":"Mallikarjun, B. R.","last_name":"Mallikarjun","first_name":"B. R."},{"full_name":"Fox, Gereon","last_name":"Fox","first_name":"Gereon"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"full_name":"Zhan, Fangneng","last_name":"Zhan","first_name":"Fangneng"},{"first_name":"Ayush","full_name":"Tewari, Ayush","last_name":"Tewari"},{"first_name":"Christian","full_name":"Theobalt, Christian","last_name":"Theobalt"},{"last_name":"Elgharib","full_name":"Elgharib, Mohamed","first_name":"Mohamed"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"BeBi"}],"title":"A deeper analysis of volumetric relightiable faces","citation":{"short":"P. Rao, B.R. Mallikarjun, G. Fox, T. Weyrich, B. Bickel, H. Pfister, W. Matusik, F. Zhan, A. Tewari, C. Theobalt, M. Elgharib, International Journal of Computer Vision (2023).","ieee":"P. Rao et al., “A deeper analysis of volumetric relightiable faces,” International Journal of Computer Vision. Springer Nature, 2023.","apa":"Rao, P., Mallikarjun, B. R., Fox, G., Weyrich, T., Bickel, B., Pfister, H., … Elgharib, M. (2023). A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-023-01899-3","ama":"Rao P, Mallikarjun BR, Fox G, et al. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. 2023. doi:10.1007/s11263-023-01899-3","mla":"Rao, Pramod, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International Journal of Computer Vision, Springer Nature, 2023, doi:10.1007/s11263-023-01899-3.","ista":"Rao P, Mallikarjun BR, Fox G, Weyrich T, Bickel B, Pfister H, Matusik W, Zhan F, Tewari A, Theobalt C, Elgharib M. 2023. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision.","chicago":"Rao, Pramod, B. R. Mallikarjun, Gereon Fox, Tim Weyrich, Bernd Bickel, Hanspeter Pfister, Wojciech Matusik, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International Journal of Computer Vision. Springer Nature, 2023. https://doi.org/10.1007/s11263-023-01899-3."},"date_updated":"2023-11-06T08:52:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_type":"original","status":"public","_id":"14488"},{"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"14487","department":[{"_id":"FrPe"}],"file_date_updated":"2023-11-07T08:10:44Z","date_updated":"2023-11-07T08:12:34Z","ddc":["550"],"scopus_import":"1","month":"10","intvolume":" 59","abstract":[{"lang":"eng","text":"High Mountain Asia (HMA) is among the most vulnerable water towers globally and yet future projections of water availability in and from its high-mountain catchments remain uncertain, as their hydrologic response to ongoing environmental changes is complex. Mechanistic modeling approaches incorporating cryospheric, hydrological, and vegetation processes in high spatial, temporal, and physical detail have never been applied for high-elevation catchments of HMA. We use a land surface model at high spatial and temporal resolution (100 m and hourly) to simulate the coupled dynamics of energy, water, and vegetation for the 350 km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological year against a large set of observations to gain insight into the partitioning of the water balance at the subseasonal scale and across elevation bands. During the simulated hydrological year, we find that evapotranspiration is a key component of the total water balance, as it causes about the equivalent of 20% of all the available precipitation or 154% of the water production from glacier melt in the basin to return directly to the atmosphere. The depletion of the cryospheric water budget is dominated by snow melt, but at high elevations is primarily dictated by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%) at the catchment scale, accounting for the equivalent of 11% of snowfall, 17% of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should consider sublimation and other evaporative fluxes explicitly, as otherwise water balance estimates can be ill-quantified."}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"14494","relation":"research_data"}]},"issue":"10","volume":59,"publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"7ba9c87228dc09029b16bc800a0ef1a1","file_id":"14495","file_size":5554901,"date_updated":"2023-11-07T08:10:44Z","creator":"dernst","file_name":"2023_WaterResourcesResearch_Buri.pdf","date_created":"2023-11-07T08:10:44Z"}],"language":[{"iso":"eng"}],"article_number":"e2022WR033841","author":[{"last_name":"Buri","full_name":"Buri, Pascal","first_name":"Pascal"},{"last_name":"Fatichi","full_name":"Fatichi, Simone","first_name":"Simone"},{"last_name":"Shaw","full_name":"Shaw, Thomas","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e"},{"last_name":"Miles","full_name":"Miles, Evan S.","first_name":"Evan S."},{"id":"22a2674a-61ce-11ee-94b5-d18813baf16f","first_name":"Michael","last_name":"Mccarthy","full_name":"Mccarthy, Michael"},{"first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","last_name":"Fyffe","full_name":"Fyffe, Catriona Louise"},{"first_name":"Stefan","last_name":"Fugger","full_name":"Fugger, Stefan"},{"first_name":"Shaoting","last_name":"Ren","full_name":"Ren, Shaoting"},{"full_name":"Kneib, Marin","last_name":"Kneib","first_name":"Marin"},{"last_name":"Jouberton","full_name":"Jouberton, Achille","first_name":"Achille"},{"full_name":"Steiner, Jakob","last_name":"Steiner","first_name":"Jakob"},{"last_name":"Fujita","full_name":"Fujita, Koji","first_name":"Koji"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087","last_name":"Pellicciotti"}],"article_processing_charge":"Yes (via OA deal)","title":"Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment","citation":{"chicago":"Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan S. Miles, Michael McCarthy, Catriona Louise Fyffe, Stefan Fugger, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High-Elevation Catchment.” Water Resources Research. Wiley, 2023. https://doi.org/10.1029/2022WR033841.","ista":"Buri P, Fatichi S, Shaw T, Miles ES, McCarthy M, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. 59(10), e2022WR033841.","mla":"Buri, Pascal, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High-Elevation Catchment.” Water Resources Research, vol. 59, no. 10, e2022WR033841, Wiley, 2023, doi:10.1029/2022WR033841.","ama":"Buri P, Fatichi S, Shaw T, et al. Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. 2023;59(10). doi:10.1029/2022WR033841","apa":"Buri, P., Fatichi, S., Shaw, T., Miles, E. S., McCarthy, M., Fyffe, C. L., … Pellicciotti, F. (2023). Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. Wiley. https://doi.org/10.1029/2022WR033841","ieee":"P. Buri et al., “Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment,” Water Resources Research, vol. 59, no. 10. Wiley, 2023.","short":"P. Buri, S. Fatichi, T. Shaw, E.S. Miles, M. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, Water Resources Research 59 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"This project has received funding from the JSPS-SNSF (Japan Society for the Promotion of Science and Swiss National Science Foundation) Bilateral Programmes project (HOPE, High-ele-vation precipitation in High Mountain Asia; Grant 183633), and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (RAVEN, Rapid mass losses of debris-covered glaciers in High Mountain Asia; Grant 772751). We want to thank in particular T. Gurung, S. Joshi, J. Shea, W. Immerzeel, and others involved, as well as ICIMOD, for their efforts over the past years in observing the meteorology of the Langtang catchment, collecting and organizing the data and making them publicly available. We also thank the National Geographic Society (Grant NGS-61784R-19) and the Mount Everest Foundation (reference 19-24) for providing fieldwork funding for C. L. Fyffe. We thank T. Kramer for help with the WSL Hyperion cluster. We are grate-ful for comments by three anonymous reviewers and the Associate Editor, who greatly helped to improve the manuscript further. Open access funding provided by ETH-Bereich Forschungsanstalten.","doi":"10.1029/2022WR033841","date_published":"2023-10-25T00:00:00Z","date_created":"2023-11-05T23:00:53Z","has_accepted_license":"1","year":"2023","day":"25","publication":"Water Resources Research"},{"doi":"10.1103/PhysRevResearch.5.043016","date_published":"2023-10-05T00:00:00Z","date_created":"2023-11-05T23:00:53Z","day":"05","publication":"Physical Review Research","has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We thank Zh. Alpichshev, A. Volosniev, and A. V. Zampetaki for fruitful discussions and comments. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","title":"Rotor lattice model of ferroelectric large polarons","author":[{"first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","full_name":"Koutentakis, Georgios","last_name":"Koutentakis"},{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2301.09875"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Koutentakis, A. Ghazaryan, M. Lemeshko, Physical Review Research 5 (2023).","ieee":"G. Koutentakis, A. Ghazaryan, and M. Lemeshko, “Rotor lattice model of ferroelectric large polarons,” Physical Review Research, vol. 5, no. 4. American Physical Society, 2023.","ama":"Koutentakis G, Ghazaryan A, Lemeshko M. Rotor lattice model of ferroelectric large polarons. Physical Review Research. 2023;5(4). doi:10.1103/PhysRevResearch.5.043016","apa":"Koutentakis, G., Ghazaryan, A., & Lemeshko, M. (2023). Rotor lattice model of ferroelectric large polarons. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043016","mla":"Koutentakis, Georgios, et al. “Rotor Lattice Model of Ferroelectric Large Polarons.” Physical Review Research, vol. 5, no. 4, 043016, American Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043016.","ista":"Koutentakis G, Ghazaryan A, Lemeshko M. 2023. Rotor lattice model of ferroelectric large polarons. Physical Review Research. 5(4), 043016.","chicago":"Koutentakis, Georgios, Areg Ghazaryan, and Mikhail Lemeshko. “Rotor Lattice Model of Ferroelectric Large Polarons.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043016."},"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"article_number":"043016","issue":"4","volume":5,"ec_funded":1,"file":[{"creator":"dernst","file_size":1127522,"date_updated":"2023-11-07T07:52:46Z","file_name":"2023_PhysReviewResearch_Koutentakis.pdf","date_created":"2023-11-07T07:52:46Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"cb8de8fed6e09df1a18bd5a5aec5c55c","file_id":"14493"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","month":"10","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present a minimal model of ferroelectric large polarons, which are suggested as one of the mechanisms responsible for the unique charge transport properties of hybrid perovskites. We demonstrate that short-ranged charge–rotor interactions lead to long-range ferroelectric ordering of rotors, which strongly affects the carrier mobility. In the nonperturbative regime, where our theory cannot be reduced to any of the earlier models, we reveal that the polaron is characterized by large coherence length and a roughly tenfold increase of the effective mass as compared to the bare mass. These results are in good agreement with other theoretical predictions for ferroelectric polarons. Our model establishes a general phenomenological framework for ferroelectric polarons providing the starting point for future studies of their role in the transport properties of hybrid organic-inorganic perovskites.","lang":"eng"}],"department":[{"_id":"MiLe"}],"file_date_updated":"2023-11-07T07:52:46Z","ddc":["530"],"date_updated":"2023-11-07T07:53:39Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14486"},{"publication_identifier":{"issn":["1369-5266"]},"publication_status":"published","file":[{"creator":"amally","file_size":737872,"date_updated":"2023-11-02T17:03:20Z","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","date_created":"2023-11-02T17:03:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","file_id":"14482"}],"language":[{"iso":"eng"}],"volume":75,"issue":"10","abstract":[{"text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","month":"10","intvolume":" 75","date_updated":"2023-11-07T08:17:13Z","ddc":["580"],"file_date_updated":"2023-11-02T17:03:20Z","department":[{"_id":"JiFr"}],"_id":"14313","type":"journal_article","article_type":"review","status":"public","has_accepted_license":"1","year":"2023","day":"01","publication":"Current Opinion in Plant Biology","doi":"10.1016/j.pbi.2023.102443","date_published":"2023-10-01T00:00:00Z","date_created":"2023-09-10T22:01:11Z","acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology.","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.","apa":"Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443","ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.","mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023, doi:10.1016/j.pbi.2023.102443."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["37666097"]},"article_processing_charge":"No","title":"Rapid auxin signaling: Unknowns old and new","article_number":"102443"},{"_id":"14494","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","date_updated":"2023-11-07T08:12:35Z","citation":{"chicago":"Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan Miles, Michael McCarthy, Catriona Louise Fyffe, Stefan Fugger, et al. “Model Output Data to ‘Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8402426.","ista":"Buri P, Fatichi S, Shaw T, Miles E, McCarthy M, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment’, Zenodo, 10.5281/ZENODO.8402426.","mla":"Buri, Pascal, et al. Model Output Data to “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.” Zenodo, 2023, doi:10.5281/ZENODO.8402426.","ieee":"P. Buri et al., “Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.’” Zenodo, 2023.","short":"P. Buri, S. Fatichi, T. Shaw, E. Miles, M. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, (2023).","apa":"Buri, P., Fatichi, S., Shaw, T., Miles, E., McCarthy, M., Fyffe, C. L., … Pellicciotti, F. (2023). Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” Zenodo. https://doi.org/10.5281/ZENODO.8402426","ama":"Buri P, Fatichi S, Shaw T, et al. Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” 2023. doi:10.5281/ZENODO.8402426"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"author":[{"last_name":"Buri","full_name":"Buri, Pascal","first_name":"Pascal"},{"first_name":"Simone","full_name":"Fatichi, Simone","last_name":"Fatichi"},{"last_name":"Shaw","full_name":"Shaw, Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas"},{"full_name":"Miles, Evan ","last_name":"Miles","first_name":"Evan "},{"first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","full_name":"McCarthy, Michael","last_name":"McCarthy"},{"first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","last_name":"Fyffe","full_name":"Fyffe, Catriona Louise"},{"first_name":"Stefan","full_name":"Fugger, Stefan","last_name":"Fugger"},{"full_name":"Ren, Shaoting","last_name":"Ren","first_name":"Shaoting"},{"full_name":"Kneib, Marin","last_name":"Kneib","first_name":"Marin"},{"last_name":"Jouberton","full_name":"Jouberton, Achille","first_name":"Achille"},{"first_name":"Jakob","full_name":"Steiner, Jakob","last_name":"Steiner"},{"last_name":"Fujita","full_name":"Fujita, Koji","first_name":"Koji"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087"}],"article_processing_charge":"No","title":"Model output data to \"Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment\"","department":[{"_id":"FrPe"}],"abstract":[{"text":"We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023).\r\n\r\nBuri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841","lang":"eng"}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://10.5281/ZENODO.8402426"}],"oa":1,"month":"10","has_accepted_license":"1","year":"2023","day":"03","doi":"10.5281/ZENODO.8402426","date_published":"2023-10-03T00:00:00Z","related_material":{"record":[{"id":"14487","status":"public","relation":"used_in_publication"}]},"date_created":"2023-11-07T08:01:39Z"},{"date_created":"2023-11-07T09:02:48Z","doi":"10.1017/fmp.2023.17","date_published":"2023-08-24T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Forum of Mathematics, Pi","day":"24","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","acknowledgement":"Kwan was supported for part of this work by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-2141064. Sah was supported by the PD Soros Fellowship. Sauermann was supported by NSF Award DMS-2100157, and for part of this work by a Sloan Research Fellowship.","article_processing_charge":"Yes","external_id":{"arxiv":["2208.02874"]},"author":[{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567"},{"first_name":"Ashwin","full_name":"Sah, Ashwin","last_name":"Sah"},{"full_name":"Sauermann, Lisa","last_name":"Sauermann","first_name":"Lisa"},{"first_name":"Mehtaab","last_name":"Sawhney","full_name":"Sawhney, Mehtaab"}],"title":"Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture","citation":{"mla":"Kwan, Matthew Alan, et al. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi, vol. 11, e21, Cambridge University Press, 2023, doi:10.1017/fmp.2023.17.","short":"M.A. Kwan, A. Sah, L. Sauermann, M. Sawhney, Forum of Mathematics, Pi 11 (2023).","ieee":"M. A. Kwan, A. Sah, L. Sauermann, and M. Sawhney, “Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture,” Forum of Mathematics, Pi, vol. 11. Cambridge University Press, 2023.","apa":"Kwan, M. A., Sah, A., Sauermann, L., & Sawhney, M. (2023). Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. Cambridge University Press. https://doi.org/10.1017/fmp.2023.17","ama":"Kwan MA, Sah A, Sauermann L, Sawhney M. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 2023;11. doi:10.1017/fmp.2023.17","chicago":"Kwan, Matthew Alan, Ashwin Sah, Lisa Sauermann, and Mehtaab Sawhney. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi. Cambridge University Press, 2023. https://doi.org/10.1017/fmp.2023.17.","ista":"Kwan MA, Sah A, Sauermann L, Sawhney M. 2023. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 11, e21."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"bd95085b-d553-11ed-ba76-e55d3349be45","grant_number":"101076777","name":"Randomness and structure in combinatorics"}],"article_number":"e21","volume":11,"publication_status":"published","publication_identifier":{"issn":["2050-5086"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-11-07T09:16:23Z","file_size":1218719,"date_created":"2023-11-07T09:16:23Z","file_name":"2023_ForumMathematics_Kwan.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"54b824098d59073cc87a308d458b0a3e","file_id":"14500","success":1}],"scopus_import":"1","intvolume":" 11","month":"08","abstract":[{"text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper, we study edge statistics in Ramsey graphs, in particular obtaining very precise control of the distribution of the number of edges in a random vertex subset of a C-Ramsey graph. This brings together two ongoing lines of research: the study of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability for low-degree polynomials of independent random variables.\r\n\r\nThe proof proceeds via an ‘additive structure’ dichotomy on the degree sequence and involves a wide range of different tools from Fourier analysis, random matrix theory, the theory of Boolean functions, probabilistic combinatorics and low-rank approximation. In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright theorem on small-ball probability for polynomials of Gaussians, which we believe is of independent interest. One of the consequences of our result is the resolution of an old conjecture of Erdős and McKay, for which Erdős reiterated in several of his open problem collections and for which he offered one of his notorious monetary prizes.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"MaKw"}],"file_date_updated":"2023-11-07T09:16:23Z","date_updated":"2023-11-07T09:18:57Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Discrete Mathematics and Combinatorics","Geometry and Topology","Mathematical Physics","Statistics and Probability","Algebra and Number Theory","Analysis"],"status":"public","_id":"14499"},{"department":[{"_id":"MiLe"}],"date_updated":"2023-11-13T08:01:57Z","status":"public","type":"journal_article","article_type":"original","_id":"14513","volume":1042,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0370-1573"]},"publication_status":"published","month":"11","intvolume":" 1042","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2202.11071","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Cold atomic gases have become a paradigmatic system for exploring fundamental physics, which at the same time allows for applications in quantum technologies. The accelerating developments in the field have led to a highly advanced set of engineering techniques that, for example, can tune interactions, shape the external geometry, select among a large set of atomic species with different properties, or control the number of atoms. In particular, it is possible to operate in lower dimensions and drive atomic systems into the strongly correlated regime. In this review, we discuss recent advances in few-body cold atom systems confined in low dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in one dimension and provide an introduction to the static properties before we review the state-of-the-art research into quantum dynamical processes stimulated by the presence of correlations. Besides discussing the fundamental physical phenomena arising in these systems, we also provide an overview of the calculational and numerical tools and methods that are commonly used, thus delivering a balanced and comprehensive overview of the field. We conclude by giving an outlook on possible future directions that are interesting to explore in these correlated systems.","lang":"eng"}],"title":"Few-body Bose gases in low dimensions - A laboratory for quantum dynamics","author":[{"first_name":"S. I.","last_name":"Mistakidis","full_name":"Mistakidis, S. I."},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barfknecht","full_name":"Barfknecht, R. E.","first_name":"R. E."},{"full_name":"Fogarty, T.","last_name":"Fogarty","first_name":"T."},{"last_name":"Busch","full_name":"Busch, Th","first_name":"Th"},{"first_name":"A.","last_name":"Foerster","full_name":"Foerster, A."},{"full_name":"Schmelcher, P.","last_name":"Schmelcher","first_name":"P."},{"first_name":"N. T.","full_name":"Zinner, N. T.","last_name":"Zinner"}],"external_id":{"arxiv":["2202.11071"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mistakidis, S. I., Artem Volosniev, R. E. Barfknecht, T. Fogarty, Th Busch, A. Foerster, P. Schmelcher, and N. T. Zinner. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” Physics Reports. Elsevier, 2023. https://doi.org/10.1016/j.physrep.2023.10.004.","ista":"Mistakidis SI, Volosniev A, Barfknecht RE, Fogarty T, Busch T, Foerster A, Schmelcher P, Zinner NT. 2023. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. 1042, 1–108.","mla":"Mistakidis, S. I., et al. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” Physics Reports, vol. 1042, Elsevier, 2023, pp. 1–108, doi:10.1016/j.physrep.2023.10.004.","ama":"Mistakidis SI, Volosniev A, Barfknecht RE, et al. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. 2023;1042:1-108. doi:10.1016/j.physrep.2023.10.004","apa":"Mistakidis, S. I., Volosniev, A., Barfknecht, R. E., Fogarty, T., Busch, T., Foerster, A., … Zinner, N. T. (2023). Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. Elsevier. https://doi.org/10.1016/j.physrep.2023.10.004","short":"S.I. Mistakidis, A. Volosniev, R.E. Barfknecht, T. Fogarty, T. Busch, A. Foerster, P. Schmelcher, N.T. Zinner, Physics Reports 1042 (2023) 1–108.","ieee":"S. I. Mistakidis et al., “Few-body Bose gases in low dimensions - A laboratory for quantum dynamics,” Physics Reports, vol. 1042. Elsevier, pp. 1–108, 2023."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1016/j.physrep.2023.10.004","date_published":"2023-11-29T00:00:00Z","date_created":"2023-11-12T23:00:54Z","page":"1-108","day":"29","publication":"Physics Reports","year":"2023","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This review could not have been written without the many fruitful discussions and great collaborations with colleagues throughout the years, there are too many to mention. Here we acknowledge conversations regarding the context of the review with Joachim Brand, Fabian Brauneis, Adolfo del Campo, Alberto Cappellaro, Panagiotis Giannakeas, Tommaso Macrí, Oleksandr Marchukov, Lukas Rammelmüller and Manuel Valiente. S. I. M. acknowledges support from the NSF through a grant for ITAMP at Harvard University. T.F. acknowledges support from JSPS KAKENHI Grant Number JP23K03290 and T.F. and Th.B. acknowledge support from the Okinawa Institute for Science and Technology Graduate University, and JST Grant Number JPMJPF2221. A.F. and R. E. B. acknowledge support from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) - Edital Universal 406563/2021-7. A. G. V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. P. S. is supported by the Cluster of Excellence ‘Advanced Imaging of Matter’ of the Deutsche Forschungsgemeinschaft (DFG) - EXC2056 - project ID 390715994. N. T. Z. is partially supported by the Independent Research Fund Denmark ."},{"day":"26","file":[{"file_name":"README.md","date_created":"2023-04-26T12:30:06Z","creator":"alaurits","file_size":4567,"date_updated":"2023-04-26T12:30:06Z","success":1,"checksum":"85ede12d38bb8d944022a8cba4d719f5","file_id":"12870","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream"},{"file_name":"simulations_era=10_flux_varied_europe.zip","date_created":"2023-04-26T12:27:34Z","creator":"alaurits","file_size":732586731,"date_updated":"2023-04-26T12:27:34Z","success":1,"file_id":"12871","checksum":"25bf79452ae895f9c8a20571a096b4c3","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"},{"relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"checksum":"bca48d80ece73eb169aee7211a4a751a","file_id":"12872","creator":"alaurits","file_size":1743893150,"date_updated":"2023-04-26T12:29:53Z","file_name":"simulations_era=10_flux_varied_torus.zip","date_created":"2023-04-26T12:29:53Z"},{"file_name":"simulations_era=10_R_varied_torus.zip","date_created":"2023-04-26T12:29:19Z","creator":"alaurits","file_size":878391851,"date_updated":"2023-04-26T12:29:19Z","success":1,"checksum":"e77a655db15486a387a36362fbf0b665","file_id":"12873","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"},{"file_name":"simulations_era=100.zip","date_created":"2023-04-26T12:30:05Z","creator":"alaurits","file_size":201652478,"date_updated":"2023-04-26T12:30:05Z","success":1,"checksum":"8556406513adc4aa2e0417f46680f627","file_id":"12874","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"}],"year":"2023","has_accepted_license":"1","date_created":"2023-04-26T12:34:49Z","doi":"10.15479/AT:ISTA:12869","related_material":{"record":[{"relation":"used_in_publication","status":"for_moderation","id":"14505"},{"id":"12890","status":"public","relation":"used_in_publication"}]},"date_published":"2023-04-26T00:00:00Z","acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","oa_version":"Published Version","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. ","lang":"eng"}],"month":"04","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","short":"F.R. Klausen, A.B. Lauritsen, (2023)."},"date_updated":"2023-11-13T07:47:29Z","file_date_updated":"2023-04-26T12:30:06Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"title":"Research data for: A stochastic cellular automaton model of culture formation","article_processing_charge":"No","author":[{"first_name":"Frederik Ravn","last_name":"Klausen","full_name":"Klausen, Frederik Ravn"},{"last_name":"Lauritsen","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"_id":"12869","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data"},{"status":"public","article_type":"original","type":"journal_article","_id":"12890","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_updated":"2023-11-13T07:47:30Z","month":"11","intvolume":" 108","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.02153"}],"oa_version":"Preprint","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.","lang":"eng"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}],"record":[{"relation":"research_data","status":"public","id":"12869"}]},"issue":"5","volume":108,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"publication_status":"published","article_number":"054307","title":"Stochastic cellular automaton model of culture formation","author":[{"last_name":"Klausen","full_name":"Klausen, Frederik Ravn","first_name":"Frederik Ravn"},{"first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","last_name":"Lauritsen"}],"external_id":{"arxiv":["2305.02153"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.108.054307","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” Physical Review E, vol. 108, no. 5. American Physical Society, 2023.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","doi":"10.1103/PhysRevE.108.054307","date_published":"2023-11-08T00:00:00Z","date_created":"2023-05-04T08:35:01Z","day":"08","publication":"Physical Review E","year":"2023"},{"volume":282,"publication_identifier":{"isbn":["9783959773034"],"issn":["1868-8969"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14521","checksum":"c1f98831cb5149d6c030c41999e6e960","file_size":793495,"date_updated":"2023-11-13T08:44:34Z","creator":"dernst","file_name":"2023_LIPIcs_Beaver.pdf","date_created":"2023-11-13T08:44:34Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LIPIcs"],"main_file_link":[{"url":"https://eprint.iacr.org/2021/1643","open_access":"1"}],"month":"10","intvolume":" 282","abstract":[{"text":"We revisit decentralized random beacons with a focus on practical distributed applications. Decentralized random beacons (Beaver and So, Eurocrypt'93) provide the functionality for n parties to generate an unpredictable sequence of bits in a way that cannot be biased, which is useful for any decentralized protocol requiring trusted randomness. Existing beacon constructions are highly inefficient in practical settings where protocol parties need to rejoin after crashes or disconnections, and more significantly where smart contracts may rely on arbitrary index points in high-volume streams. For this, we introduce a new notion of history-generating decentralized random beacons (HGDRBs). Roughly, the history-generation property of HGDRBs allows for previous beacon outputs to be efficiently generated knowing only the current value and the public key. At application layers, history-generation supports registering a sparser set of on-chain values if desired, so that apps like lotteries can utilize on-chain values without incurring high-frequency costs, enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose chains. Unlike rollups, HG is tailored specifically to recovering and verifying pseudorandom bit sequences and thus enjoys unique optimizations investigated in this work. We introduce STROBE: an efficient HGDRB construction which generalizes the original squaring-based RSA approach of Beaver and So. STROBE enjoys several useful properties that make it suited for practical applications that use beacons: 1) history-generating: it can regenerate and verify high-throughput beacon streams, supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying: NIZK-free, with state and validation employing a single ring element; 3) eco-friendly: stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient: the last beacon suffices to derive all past outputs, thus O(1) storage requirements for nodes serving the whole history.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"ElKo"}],"file_date_updated":"2023-11-13T08:44:34Z","date_updated":"2023-11-13T08:52:01Z","ddc":["000"],"type":"conference","conference":{"name":"AFT: Conference on Advances in Financial Technologies","start_date":"2023-10-23","end_date":"2023-10-25","location":"Princeton, NJ, United States"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14516","date_published":"2023-10-01T00:00:00Z","doi":"10.4230/LIPIcs.AFT.2023.7","date_created":"2023-11-12T23:00:55Z","has_accepted_license":"1","year":"2023","day":"01","publication":"5th Conference on Advances in Financial Technologies","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"Work done when all the authors were at Novi Research, Meta.","author":[{"first_name":"Donald","full_name":"Beaver, Donald","last_name":"Beaver"},{"first_name":"Mahimna","last_name":"Kelkar","full_name":"Kelkar, Mahimna"},{"last_name":"Lewi","full_name":"Lewi, Kevin","first_name":"Kevin"},{"last_name":"Nikolaenko","full_name":"Nikolaenko, Valeria","first_name":"Valeria"},{"first_name":"Alberto","full_name":"Sonnino, Alberto","last_name":"Sonnino"},{"last_name":"Chalkias","full_name":"Chalkias, Konstantinos","first_name":"Konstantinos"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Naurois, Ladi De","last_name":"Naurois","first_name":"Ladi De"},{"first_name":"Arnab","full_name":"Roy, Arnab","last_name":"Roy"}],"article_processing_charge":"Yes","title":"STROBE: Streaming Threshold Random Beacons","citation":{"chicago":"Beaver, Donald, Mahimna Kelkar, Kevin Lewi, Valeria Nikolaenko, Alberto Sonnino, Konstantinos Chalkias, Eleftherios Kokoris Kogias, Ladi De Naurois, and Arnab Roy. “STROBE: Streaming Threshold Random Beacons.” In 5th Conference on Advances in Financial Technologies, Vol. 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.AFT.2023.7.","ista":"Beaver D, Kelkar M, Lewi K, Nikolaenko V, Sonnino A, Chalkias K, Kokoris Kogias E, Naurois LD, Roy A. 2023. STROBE: Streaming Threshold Random Beacons. 5th Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, LIPIcs, vol. 282, 7.","mla":"Beaver, Donald, et al. “STROBE: Streaming Threshold Random Beacons.” 5th Conference on Advances in Financial Technologies, vol. 282, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.AFT.2023.7.","short":"D. Beaver, M. Kelkar, K. Lewi, V. Nikolaenko, A. Sonnino, K. Chalkias, E. Kokoris Kogias, L.D. Naurois, A. Roy, in:, 5th Conference on Advances in Financial Technologies, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"D. Beaver et al., “STROBE: Streaming Threshold Random Beacons,” in 5th Conference on Advances in Financial Technologies, Princeton, NJ, United States, 2023, vol. 282.","apa":"Beaver, D., Kelkar, M., Lewi, K., Nikolaenko, V., Sonnino, A., Chalkias, K., … Roy, A. (2023). STROBE: Streaming Threshold Random Beacons. In 5th Conference on Advances in Financial Technologies (Vol. 282). Princeton, NJ, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.AFT.2023.7","ama":"Beaver D, Kelkar M, Lewi K, et al. STROBE: Streaming Threshold Random Beacons. In: 5th Conference on Advances in Financial Technologies. Vol 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.AFT.2023.7"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"7"},{"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105), the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences, and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility.","date_published":"2023-10-20T00:00:00Z","doi":"10.1103/PhysRevApplied.20.044054","date_created":"2023-11-12T23:00:55Z","day":"20","publication":"Physical Review Applied","year":"2023","project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"},{"name":"Open Superconducting Quantum Computers (OpenSuperQPlus)","grant_number":"101080139","_id":"bdb7cfc1-d553-11ed-ba76-d2eaab167738"}],"article_number":"044054","title":"Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses","author":[{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo"},{"last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Trioni","full_name":"Trioni, Andrea","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"article_processing_charge":"No","external_id":{"arxiv":["2206.14104"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied, vol. 20, no. 4, 044054, American Physical Society, 2023, doi:10.1103/PhysRevApplied.20.044054.","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 2023;20(4). doi:10.1103/PhysRevApplied.20.044054","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.20.044054","ieee":"M. Zemlicka et al., “Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses,” Physical Review Applied, vol. 20, no. 4. American Physical Society, 2023.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, Physical Review Applied 20 (2023).","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.20.044054.","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 20(4), 044054."},"month":"10","intvolume":" 20","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2206.14104","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"volume":20,"related_material":{"record":[{"relation":"research_data","status":"public","id":"14520"}]},"issue":"4","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2331-7019"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"14517","department":[{"_id":"JoFi"}],"date_updated":"2023-11-13T09:22:47Z"},{"doi":"10.1103/PhysRevX.13.041017","date_published":"2023-10-26T00:00:00Z","date_created":"2023-11-12T23:00:55Z","day":"26","publication":"Physical Review X","has_accepted_license":"1","year":"2023","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis, and Daan Frenkel for useful discussions and a careful reading of the manuscript, and we thank Age Tjalma for support with obtaining the Gaussian approximation of the chemotaxis system. This work is part of the Dutch Research Council (NWO) and was performed at the research institute AMOLF. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant (024.003.019).","title":"Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories","author":[{"first_name":"Manuel","full_name":"Reinhardt, Manuel","last_name":"Reinhardt"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"last_name":"Ten Wolde","full_name":"Ten Wolde, Pieter Rein","first_name":"Pieter Rein"}],"external_id":{"arxiv":["2203.03461"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.","ista":"Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 13(4), 041017.","mla":"Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.","apa":"Reinhardt, M., Tkačik, G., & Ten Wolde, P. R. (2023). Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.041017","ama":"Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017","short":"M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).","ieee":"M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” Physical Review X, vol. 13, no. 4. American Physical Society, 2023."},"article_number":"041017","issue":"4","volume":13,"file":[{"checksum":"32574aeebcca7347a4152c611b66b3d5","file_id":"14522","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-11-13T09:00:19Z","file_name":"2023_PhysReviewX_Reinhardt.pdf","creator":"dernst","date_updated":"2023-11-13T09:00:19Z","file_size":1595223}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2160-3308"]},"publication_status":"published","month":"10","intvolume":" 13","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger."}],"file_date_updated":"2023-11-13T09:00:19Z","department":[{"_id":"GaTk"}],"ddc":["530"],"date_updated":"2023-11-13T09:03:30Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14515"},{"scopus_import":"1","intvolume":" 131","month":"10","abstract":[{"lang":"eng","text":"The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"14523","status":"public"}]},"issue":"16","volume":131,"publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"1a419e25b762aadffbcc8eb2e609bd97","file_id":"14524","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_PhysRevLetters_Binysh.pdf","date_created":"2023-11-13T09:12:58Z","creator":"dernst","file_size":724098,"date_updated":"2023-11-13T09:12:58Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"14514","department":[{"_id":"ScWa"}],"file_date_updated":"2023-11-13T09:12:58Z","date_updated":"2023-11-13T09:21:30Z","ddc":["530"],"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) through New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1, EP/S022848/1, EP/S029966/1, and EP/P031684/1.","date_created":"2023-11-12T23:00:55Z","doi":"10.1103/PhysRevLett.131.168201","date_published":"2023-10-20T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Physical Review Letters","day":"20","article_number":"168201","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Jack","last_name":"Binysh","full_name":"Binysh, Jack"},{"first_name":"Indrajit","full_name":"Chakraborty, Indrajit","last_name":"Chakraborty"},{"full_name":"Chubynsky, Mykyta V.","last_name":"Chubynsky","first_name":"Mykyta V."},{"last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"},{"first_name":"James E.","last_name":"Sprittles","full_name":"Sprittles, James E."},{"last_name":"Souslov","full_name":"Souslov, Anton","first_name":"Anton"}],"title":"Modeling Leidenfrost levitation of soft elastic solids","citation":{"chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.168201.","ista":"Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 131(16), 168201.","mla":"Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters, vol. 131, no. 16, 168201, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.168201.","apa":"Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J. E., & Souslov, A. (2023). Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.168201","ama":"Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 2023;131(16). doi:10.1103/PhysRevLett.131.168201","ieee":"J. Binysh et al., “Modeling Leidenfrost levitation of soft elastic solids,” Physical Review Letters, vol. 131, no. 16. American Physical Society, 2023.","short":"J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"citation":{"ista":"Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1, Zenodo, 10.5281/ZENODO.8329143.","chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8329143.","apa":"Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J., & Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. Zenodo. https://doi.org/10.5281/ZENODO.8329143","ama":"Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. 2023. doi:10.5281/ZENODO.8329143","short":"J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023).","ieee":"J. Binysh et al., “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1.” Zenodo, 2023.","mla":"Binysh, Jack, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1. Zenodo, 2023, doi:10.5281/ZENODO.8329143."},"date_updated":"2023-11-13T09:21:31Z","department":[{"_id":"ScWa"}],"title":"SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1","author":[{"first_name":"Jack","full_name":"Binysh, Jack","last_name":"Binysh"},{"last_name":"Chakraborty","full_name":"Chakraborty, Indrajit","first_name":"Indrajit"},{"first_name":"Mykyta","full_name":"Chubynsky, Mykyta","last_name":"Chubynsky"},{"first_name":"Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","full_name":"Diaz Melian, Vicente L","last_name":"Diaz Melian"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"},{"first_name":"James","last_name":"Sprittles","full_name":"Sprittles, James"},{"first_name":"Anton","last_name":"Souslov","full_name":"Souslov, Anton"}],"article_processing_charge":"No","_id":"14523","status":"public","type":"research_data_reference","day":"08","year":"2023","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14514"}]},"doi":"10.5281/ZENODO.8329143","date_published":"2023-09-08T00:00:00Z","date_created":"2023-11-13T09:12:11Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"see Readme file"}],"month":"09","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8329143"}],"oa":1},{"ec_funded":1,"volume":372,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":501011,"date_updated":"2023-11-13T10:16:10Z","file_name":"2023_FAIA_Avni.pdf","date_created":"2023-11-13T10:16:10Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"1390ca38480fa4cf286b0f1a42e8c12f","file_id":"14529"}],"publication_status":"published","publication_identifier":{"issn":["0922-6389"],"isbn":["9781643684369"]},"intvolume":" 372","month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets.","lang":"eng"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2023-11-13T10:16:10Z","ddc":["000"],"date_updated":"2023-11-13T10:18:45Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"conference":{"start_date":"2023-09-30","end_date":"2023-10-04","location":"Krakow, Poland","name":"ECAI: European Conference on Artificial Intelligence"},"type":"conference","_id":"14518","date_created":"2023-11-12T23:00:56Z","doi":"10.3233/FAIA230264","date_published":"2023-09-28T00:00:00Z","page":"141-148","publication":"Frontiers in Artificial Intelligence and Applications","day":"28","year":"2023","has_accepted_license":"1","oa":1,"publisher":"IOS Press","quality_controlled":"1","acknowledgement":"This research was supported in part by ISF grant no. 1679/21, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.","title":"Reachability poorman discrete-bidding games","article_processing_charge":"No","external_id":{"arxiv":["2307.15218"]},"author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias"},{"first_name":"Suman","full_name":"Sadhukhan, Suman","last_name":"Sadhukhan"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications. ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.","chicago":"Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde Zikelic. “Reachability Poorman Discrete-Bidding Games.” In Frontiers in Artificial Intelligence and Applications, 372:141–48. IOS Press, 2023. https://doi.org/10.3233/FAIA230264.","ama":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman discrete-bidding games. In: Frontiers in Artificial Intelligence and Applications. Vol 372. IOS Press; 2023:141-148. doi:10.3233/FAIA230264","apa":"Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., & Zikelic, D. (2023). Reachability poorman discrete-bidding games. In Frontiers in Artificial Intelligence and Applications (Vol. 372, pp. 141–148). Krakow, Poland: IOS Press. https://doi.org/10.3233/FAIA230264","short":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.","ieee":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability poorman discrete-bidding games,” in Frontiers in Artificial Intelligence and Applications, Krakow, Poland, 2023, vol. 372, pp. 141–148.","mla":"Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” Frontiers in Artificial Intelligence and Applications, vol. 372, IOS Press, 2023, pp. 141–48, doi:10.3233/FAIA230264."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}]},{"_id":"13096","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-11-14T11:49:21Z","file_date_updated":"2023-11-14T11:48:18Z","department":[{"_id":"PaSc"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death."}],"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"intvolume":" 618","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14533","checksum":"0fab69252453bff1de7f0e2eceb76d34","success":1,"date_updated":"2023-11-14T11:48:18Z","file_size":12292188,"creator":"dernst","date_created":"2023-11-14T11:48:18Z","file_name":"2023_Nature_Degen.pdf"}],"publication_status":"published","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"volume":618,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-05991-z.","ista":"Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071.","mla":"Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:10.1038/s41586-023-05991-z.","ieee":"M. Degen et al., “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” Nature, vol. 618. Springer Nature, pp. 1065–1071, 2023.","short":"M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.","apa":"Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-05991-z","ama":"Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 2023;618:1065-1071. doi:10.1038/s41586-023-05991-z"},"title":"Structural basis of NINJ1-mediated plasma membrane rupture in cell death","external_id":{"isi":["000991386800011"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Degen","full_name":"Degen, Morris","first_name":"Morris"},{"first_name":"José Carlos","last_name":"Santos","full_name":"Santos, José Carlos"},{"last_name":"Pluhackova","full_name":"Pluhackova, Kristyna","first_name":"Kristyna"},{"first_name":"Gonzalo","full_name":"Cebrero, Gonzalo","last_name":"Cebrero"},{"full_name":"Ramos, Saray","last_name":"Ramos","first_name":"Saray"},{"first_name":"Gytis","last_name":"Jankevicius","full_name":"Jankevicius, Gytis"},{"full_name":"Hartenian, Ella","last_name":"Hartenian","first_name":"Ella"},{"last_name":"Guillerm","full_name":"Guillerm, Undina","first_name":"Undina","id":"bb74f472-ae54-11eb-9835-bc9c22fb1183"},{"first_name":"Stefania A.","full_name":"Mari, Stefania A.","last_name":"Mari"},{"full_name":"Kohl, Bastian","last_name":"Kohl","first_name":"Bastian"},{"full_name":"Müller, Daniel J.","last_name":"Müller","first_name":"Daniel J."},{"last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"full_name":"Maier, Timm","last_name":"Maier","first_name":"Timm"},{"first_name":"Camilo","last_name":"Perez","full_name":"Perez, Camilo"},{"first_name":"Christian","full_name":"Sieben, Christian","last_name":"Sieben"},{"first_name":"Petr","last_name":"Broz","full_name":"Broz, Petr"},{"first_name":"Sebastian","last_name":"Hiller","full_name":"Hiller, Sebastian"}],"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature","day":"29","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-05-28T22:01:04Z","doi":"10.1038/s41586-023-05991-z","date_published":"2023-06-29T00:00:00Z","page":"1065-1071"},{"acknowledgement":"The authors (N.L.F and R.B.J) would like to acknowledge the funding contributions of Shell and the EPRSC via I–Case studentships (grants no. EP/V519662/1 and EP/R511870/1 respectively). T.I would like to thank the ERC advanced Investigator Grant for CPG (EC H2020 835073). Thank you to Zhen Wang from the University of Cambridge for measuring GPC, the Yusuf Hamied Department of Chemistry's mass spectrometry service for MS measurements and analysis and Dr Andrew Bond from the University of Cambridge for XRD measurement and analysis.","quality_controlled":"1","publisher":"Wiley","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"06","publication":"ChemSusChem","date_published":"2023-07-06T00:00:00Z","doi":"10.1002/cssc.202300128","date_created":"2023-05-21T22:01:05Z","article_number":"e202300128","citation":{"ama":"Farag NL, Jethwa RB, Beardmore AE, et al. Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. 2023;16(13). doi:10.1002/cssc.202300128","apa":"Farag, N. L., Jethwa, R. B., Beardmore, A. E., Insinna, T., O’Keefe, C. A., Klusener, P. A. A., … Wright, D. S. (2023). Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.202300128","short":"N.L. Farag, R.B. Jethwa, A.E. Beardmore, T. Insinna, C.A. O’Keefe, P.A.A. Klusener, C.P. Grey, D.S. Wright, ChemSusChem 16 (2023).","ieee":"N. L. Farag et al., “Triarylamines as catholytes in aqueous organic redox flow batteries,” ChemSusChem, vol. 16, no. 13. Wiley, 2023.","mla":"Farag, Nadia L., et al. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem, vol. 16, no. 13, e202300128, Wiley, 2023, doi:10.1002/cssc.202300128.","ista":"Farag NL, Jethwa RB, Beardmore AE, Insinna T, O’Keefe CA, Klusener PAA, Grey CP, Wright DS. 2023. Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. 16(13), e202300128.","chicago":"Farag, Nadia L., Rajesh B Jethwa, Alice E. Beardmore, Teresa Insinna, Christopher A. O’Keefe, Peter A.A. Klusener, Clare P. Grey, and Dominic S. Wright. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem. Wiley, 2023. https://doi.org/10.1002/cssc.202300128."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Farag, Nadia L.","last_name":"Farag","first_name":"Nadia L."},{"last_name":"Jethwa","full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356","first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f"},{"first_name":"Alice E.","full_name":"Beardmore, Alice E.","last_name":"Beardmore"},{"last_name":"Insinna","full_name":"Insinna, Teresa","first_name":"Teresa"},{"first_name":"Christopher A.","last_name":"O'Keefe","full_name":"O'Keefe, Christopher A."},{"first_name":"Peter A.A.","last_name":"Klusener","full_name":"Klusener, Peter A.A."},{"first_name":"Clare P.","full_name":"Grey, Clare P.","last_name":"Grey"},{"first_name":"Dominic S.","last_name":"Wright","full_name":"Wright, Dominic S."}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["36970847"],"isi":["000985051300001"]},"title":"Triarylamines as catholytes in aqueous organic redox flow batteries","abstract":[{"lang":"eng","text":"A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"07","intvolume":" 16","publication_identifier":{"eissn":["1864-564X"],"issn":["1864-5631"]},"publication_status":"published","file":[{"file_name":"2023_ChemSusChem_Farag.pdf","date_created":"2023-11-14T11:27:16Z","file_size":1168683,"date_updated":"2023-11-14T11:27:16Z","creator":"dernst","success":1,"file_id":"14532","checksum":"efa0713289995af83a2147b3e8e1d6a6","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"13","volume":16,"_id":"13041","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-11-14T11:28:23Z","ddc":["540"],"department":[{"_id":"StFr"}],"file_date_updated":"2023-11-14T11:27:16Z"},{"page":"1280-1285","date_published":"2023-09-01T00:00:00Z","doi":"10.1038/s41567-023-02074-8","date_created":"2023-06-04T22:01:02Z","isi":1,"year":"2023","day":"01","publication":"Nature Physics","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We acknowledge the crucial contribution of the LULI2000 laser and support teams to the success of the experiments. We also thank S. Brygoo and P. Loubeyre for useful discussions. This research was supported by the French National Research Agency (ANR) through the projects POMPEI (grant no. ANR-16-CE31-0008) and SUPER-ICES (grant ANR-15-CE30-008-01), and by the PLAS@PAR Federation. M.F. and R.R. gratefully acknowledge support by the DFG within the Research Unit FOR 2440. M.B. was supported by the European Union within the Marie Skłodowska-Curie actions (xICE grant 894725) and the NOMIS foundation. The DFT-MD calculations were performed at the North-German Supercomputing Alliance facilities.","author":[{"first_name":"J.-A.","last_name":"Hernandez","full_name":"Hernandez, J.-A."},{"first_name":"Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy"},{"first_name":"S.","last_name":"Ninet","full_name":"Ninet, S."},{"last_name":"French","full_name":"French, M.","first_name":"M."},{"full_name":"Benuzzi-Mounaix, A.","last_name":"Benuzzi-Mounaix","first_name":"A."},{"first_name":"F.","last_name":"Datchi","full_name":"Datchi, F."},{"last_name":"Guarguaglini","full_name":"Guarguaglini, M.","first_name":"M."},{"first_name":"F.","full_name":"Lefevre, F.","last_name":"Lefevre"},{"first_name":"F.","full_name":"Occelli, F.","last_name":"Occelli"},{"last_name":"Redmer","full_name":"Redmer, R.","first_name":"R."},{"full_name":"Vinci, T.","last_name":"Vinci","first_name":"T."},{"first_name":"A.","last_name":"Ravasio","full_name":"Ravasio, A."}],"article_processing_charge":"No","external_id":{"isi":["000996921200001"]},"title":"Melting curve of superionic ammonia at planetary interior conditions","citation":{"chicago":"Hernandez, J.-A., Mandy Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix, F. Datchi, M. Guarguaglini, et al. “Melting Curve of Superionic Ammonia at Planetary Interior Conditions.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02074-8.","ista":"Hernandez J-A, Bethkenhagen M, Ninet S, French M, Benuzzi-Mounaix A, Datchi F, Guarguaglini M, Lefevre F, Occelli F, Redmer R, Vinci T, Ravasio A. 2023. Melting curve of superionic ammonia at planetary interior conditions. Nature Physics. 19, 1280–1285.","mla":"Hernandez, J. A., et al. “Melting Curve of Superionic Ammonia at Planetary Interior Conditions.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1280–85, doi:10.1038/s41567-023-02074-8.","short":"J.-A. Hernandez, M. Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix, F. Datchi, M. Guarguaglini, F. Lefevre, F. Occelli, R. Redmer, T. Vinci, A. Ravasio, Nature Physics 19 (2023) 1280–1285.","ieee":"J.-A. Hernandez et al., “Melting curve of superionic ammonia at planetary interior conditions,” Nature Physics, vol. 19. Springer Nature, pp. 1280–1285, 2023.","apa":"Hernandez, J.-A., Bethkenhagen, M., Ninet, S., French, M., Benuzzi-Mounaix, A., Datchi, F., … Ravasio, A. (2023). Melting curve of superionic ammonia at planetary interior conditions. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02074-8","ama":"Hernandez J-A, Bethkenhagen M, Ninet S, et al. Melting curve of superionic ammonia at planetary interior conditions. Nature Physics. 2023;19:1280-1285. doi:10.1038/s41567-023-02074-8"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":19,"related_material":{"link":[{"relation":"erratum","url":"10.1038/s41567-023-02130-3"}]},"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 19","abstract":[{"lang":"eng","text":"Under high pressures and temperatures, molecular systems with substantial polarization charges, such as ammonia and water, are predicted to form superionic phases and dense fluid states with dissociating molecules and high electrical conductivity. This behaviour potentially plays a role in explaining the origin of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain, melting curve and electrical conductivity of these superionic phases is therefore crucial for modelling planetary interiors and dynamos. Here we report the melting curve of superionic ammonia up to 300 GPa from laser-driven shock compression of pre-compressed samples and atomistic calculations. We show that ammonia melts at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical conductivity exceeds that of water at conditions predicted by hot, super-adiabatic models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich dynamo layers."}],"oa_version":"None","department":[{"_id":"BiCh"}],"date_updated":"2023-11-14T12:58:31Z","type":"journal_article","article_type":"original","status":"public","_id":"13118"},{"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14534","checksum":"4887a296e3b6f54e8c0b946cbfd24f49","file_size":8156497,"date_updated":"2023-11-14T13:00:19Z","creator":"dernst","file_name":"2023_Nature_Helson.pdf","date_created":"2023-11-14T13:00:19Z"}],"language":[{"iso":"eng"}],"volume":618,"abstract":[{"text":"A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 618","date_updated":"2023-11-14T13:02:50Z","ddc":["530"],"file_date_updated":"2023-11-14T13:00:19Z","department":[{"_id":"GeKa"}],"_id":"13119","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","isi":1,"has_accepted_license":"1","year":"2023","day":"22","publication":"Nature","page":"716-720","date_published":"2023-06-22T00:00:00Z","doi":"10.1038/s41586-023-06018-3","date_created":"2023-06-04T22:01:03Z","acknowledgement":"Open access funding provided by EPFL Lausanne.We acknowledge discussions with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance in the final stages of the experiment. We acknowledge funding from the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654). F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone Project P 35891-N).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"ieee":"V. Helson et al., “Density-wave ordering in a unitary Fermi gas with photon-mediated interactions,” Nature, vol. 618. Springer Nature, pp. 716–720, 2023.","short":"V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi, H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.","apa":"Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi, H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06018-3","ama":"Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 2023;618:716-720. doi:10.1038/s41586-023-06018-3","mla":"Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature, vol. 618, Springer Nature, 2023, pp. 716–20, doi:10.1038/s41586-023-06018-3.","ista":"Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H, Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 618, 716–720.","chicago":"Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06018-3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Helson, Victor","last_name":"Helson","first_name":"Victor"},{"first_name":"Timo","full_name":"Zwettler, Timo","last_name":"Zwettler"},{"first_name":"Farokh","last_name":"Mivehvar","full_name":"Mivehvar, Farokh"},{"first_name":"Elvia","full_name":"Colella, Elvia","last_name":"Colella"},{"id":"53f93ea2-803f-11ed-ab7e-b283135794ef","first_name":"Kevin Etienne Robert","full_name":"Roux, Kevin Etienne Robert","last_name":"Roux"},{"first_name":"Hideki","full_name":"Konishi, Hideki","last_name":"Konishi"},{"first_name":"Helmut","last_name":"Ritsch","full_name":"Ritsch, Helmut"},{"full_name":"Brantut, Jean Philippe","last_name":"Brantut","first_name":"Jean Philippe"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001001139300008"]},"title":"Density-wave ordering in a unitary Fermi gas with photon-mediated interactions"},{"department":[{"_id":"RoSe"},{"_id":"JaMa"}],"date_updated":"2023-11-14T13:21:01Z","type":"journal_article","article_type":"original","status":"public","_id":"12911","issue":"4","volume":285,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9792"}]},"ec_funded":1,"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.11217","open_access":"1"}],"month":"08","intvolume":" 285","abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"oa_version":"Preprint","author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario"},{"first_name":"Augusto","full_name":"Gerolin, Augusto","last_name":"Gerolin"},{"last_name":"Portinale","full_name":"Portinale, Lorenzo","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2106.11217"],"isi":["000990804300001"]},"title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","citation":{"chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963.","ista":"Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 285(4), 109963.","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” Journal of Functional Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963.","apa":"Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963","short":"D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis 285 (2023).","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Di erential Systems","grant_number":" F06504"}],"article_number":"109963","date_published":"2023-08-15T00:00:00Z","doi":"10.1016/j.jfa.2023.109963","date_created":"2023-05-07T22:01:02Z","isi":1,"year":"2023","day":"15","publication":"Journal of Functional Analysis","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. The authors also thank J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. Finally, we acknowledge the high quality review done by the anonymous referee of our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813."},{"date_created":"2023-07-02T22:00:43Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1090/proc/14361","page":"3401-3414","publication":"Proceedings of the American Mathematical Society","day":"01","year":"2023","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","acknowledgement":"The second author was supported by the priority program SPP2026 of the German Research Foundation (DFG). The fourth author was supported by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the German Research Foundation (DFG) via RTG 1523/2.","title":"Sobolev-type inequalities and eigenvalue growth on graphs with finite measure","article_processing_charge":"No","external_id":{"isi":["000988204400001"],"arxiv":["1804.08353"]},"author":[{"first_name":"Bobo","full_name":"Hua, Bobo","last_name":"Hua"},{"first_name":"Matthias","full_name":"Keller, Matthias","last_name":"Keller"},{"last_name":"Schwarz","full_name":"Schwarz, Michael","first_name":"Michael"},{"last_name":"Wirth","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and eigenvalue growth on graphs with finite measure,” Proceedings of the American Mathematical Society, vol. 151, no. 8. American Mathematical Society, pp. 3401–3414, 2023.","short":"B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical Society 151 (2023) 3401–3414.","apa":"Hua, B., Keller, M., Schwarz, M., & Wirth, M. (2023). Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/14361","ama":"Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 2023;151(8):3401-3414. doi:10.1090/proc/14361","mla":"Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society, vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:10.1090/proc/14361.","ista":"Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 151(8), 3401–3414.","chicago":"Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/14361."},"issue":"8","volume":151,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"intvolume":" 151","month":"08","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1804.08353"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established.","lang":"eng"}],"department":[{"_id":"JaMa"}],"date_updated":"2023-11-14T13:07:09Z","status":"public","article_type":"original","type":"journal_article","_id":"13177"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"publication_status":"published","issue":"5","volume":52,"ec_funded":1,"oa_version":"None","abstract":[{"text":"n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f\r\n in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m\r\n and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds.","lang":"eng"}],"month":"10","intvolume":" 52","scopus_import":"1","date_updated":"2023-11-20T08:21:07Z","department":[{"_id":"MoHe"}],"_id":"14558","status":"public","type":"journal_article","article_type":"original","day":"01","publication":"SIAM Journal on Computing","year":"2023","date_published":"2023-10-01T00:00:00Z","doi":"10.1137/21M1428649","date_created":"2023-11-19T23:00:56Z","page":"1132-1192","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures (MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council, UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer (ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I 5982-N, and project Z 422-N. The third author was also supported by the Swedish Research Council (Reg. No. 2015-04659). The fourth author was also supported by the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ, 0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023).","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. 2023. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5), 1132–1192.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Xiaowei Wu. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/21M1428649.","short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing 52 (2023) 1132–1192.","ieee":"S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and X. Wu, “Deterministic near-optimal approximation algorithms for dynamic set cover,” SIAM Journal on Computing, vol. 52, no. 5. Society for Industrial and Applied Mathematics, pp. 1132–1192, 2023.","apa":"Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Wu, X. (2023). Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1428649","ama":"Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 2023;52(5):1132-1192. doi:10.1137/21M1428649","mla":"Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” SIAM Journal on Computing, vol. 52, no. 5, Society for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:10.1137/21M1428649."},"title":"Deterministic near-optimal approximation algorithms for dynamic set cover","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"},{"last_name":"Wu","full_name":"Wu, Xiaowei","first_name":"Xiaowei"}],"article_processing_charge":"No","project":[{"grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"}]},{"_id":"14559","type":"conference","conference":{"start_date":"2023-10-24","location":"Singapore, Singapore","end_date":"2023-10-27","name":"ATVA: Automated Technology for Verification and Analysis"},"status":"public","date_updated":"2023-11-20T08:30:20Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"abstract":[{"text":"We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.","lang":"eng"}],"oa_version":"None","scopus_import":"1","alternative_title":["LNCS"],"month":"10","intvolume":" 14215","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031453281"],"eissn":["1611-3349"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":14215,"ec_funded":1,"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"citation":{"ista":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning provably stabilizing neural controllers for discrete-time stochastic systems. 21st International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.","chicago":"Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” In 21st International Symposium on Automated Technology for Verification and Analysis, 14215:357–79. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-45329-8_17.","ama":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably stabilizing neural controllers for discrete-time stochastic systems. In: 21st International Symposium on Automated Technology for Verification and Analysis. Vol 14215. Springer Nature; 2023:357-379. doi:10.1007/978-3-031-45329-8_17","apa":"Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). Learning provably stabilizing neural controllers for discrete-time stochastic systems. In 21st International Symposium on Automated Technology for Verification and Analysis (Vol. 14215, pp. 357–379). Singapore, Singapore: Springer Nature. https://doi.org/10.1007/978-3-031-45329-8_17","short":"M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, 21st International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2023, pp. 357–379.","ieee":"M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “Learning provably stabilizing neural controllers for discrete-time stochastic systems,” in 21st International Symposium on Automated Technology for Verification and Analysis, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.","mla":"Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” 21st International Symposium on Automated Technology for Verification and Analysis, vol. 14215, Springer Nature, 2023, pp. 357–79, doi:10.1007/978-3-031-45329-8_17."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ansaripour, Matin","last_name":"Ansaripour","first_name":"Matin"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publisher":"Springer Nature","quality_controlled":"1","year":"2023","day":"22","publication":"21st International Symposium on Automated Technology for Verification and Analysis","page":"357-379","doi":"10.1007/978-3-031-45329-8_17","date_published":"2023-10-22T00:00:00Z","date_created":"2023-11-19T23:00:56Z"},{"publication_identifier":{"eissn":["2804-7214"],"issn":["2822-7840"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2023-11-20T08:34:57Z","file_size":1508534,"date_created":"2023-11-20T08:34:57Z","file_name":"2023_ESAIM_Cornalba.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14560","checksum":"3aef1475b1882c8dec112df9a5167c39","success":1}],"language":[{"iso":"eng"}],"issue":"5","related_material":{"link":[{"relation":"software","url":"https://github.com/tonyshardlow/RIDK-FD"}]},"volume":57,"ec_funded":1,"abstract":[{"lang":"eng","text":"The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format."}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 57","date_updated":"2023-11-20T08:38:47Z","ddc":["510"],"file_date_updated":"2023-11-20T08:34:57Z","department":[{"_id":"JuFi"}],"_id":"14554","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2023","day":"01","publication":"ESAIM: Mathematical Modelling and Numerical Analysis","page":"3061-3090","doi":"10.1051/m2an/2023077","date_published":"2023-09-01T00:00:00Z","date_created":"2023-11-19T23:00:55Z","acknowledgement":"The authors thank the anonymous referees for their careful reading of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered the first part of this project).","quality_controlled":"1","publisher":"EDP Sciences","oa":1,"citation":{"chicago":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2023. https://doi.org/10.1051/m2an/2023077.","ista":"Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.","mla":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5, EDP Sciences, 2023, pp. 3061–90, doi:10.1051/m2an/2023077.","ieee":"F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime,” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5. EDP Sciences, pp. 3061–3090, 2023.","short":"F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.","apa":"Cornalba, F., & Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2023077","ama":"Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 2023;57(5):3061-3090. doi:10.1051/m2an/2023077"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico","full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149","last_name":"Cornalba"},{"last_name":"Shardlow","full_name":"Shardlow, Tony","first_name":"Tony"}],"article_processing_charge":"Yes (in subscription journal)","title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"_id":"14556","status":"public","type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"ddc":["570"],"date_updated":"2023-11-20T08:51:09Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","abstract":[{"text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.","lang":"eng"}],"month":"11","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1111/jeb.14242","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"publication_status":"epub_ahead","article_number":"14242","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242.","ieee":"E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology. Wiley, 2023.","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023).","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242","chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023. https://doi.org/10.1111/jeb.14242.","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242."},"title":"How chromosomal inversions reorient the evolutionary process","author":[{"first_name":"Emma L.","full_name":"Berdan, Emma L.","last_name":"Berdan"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Inês","full_name":"Fragata, Inês","last_name":"Fragata"},{"first_name":"Kimberly J.","last_name":"Gilbert","full_name":"Gilbert, Kimberly J."},{"first_name":"Paul","last_name":"Jay","full_name":"Jay, Paul"},{"last_name":"Kapun","full_name":"Kapun, Martin","first_name":"Martin"},{"first_name":"Katie E.","last_name":"Lotterhos","full_name":"Lotterhos, Katie E."},{"first_name":"Claire","last_name":"Mérot","full_name":"Mérot, Claire"},{"last_name":"Durmaz Mitchell","full_name":"Durmaz Mitchell, Esra","first_name":"Esra"},{"first_name":"Marta","last_name":"Pascual","full_name":"Pascual, Marta"},{"first_name":"Catherine L.","last_name":"Peichel","full_name":"Peichel, Catherine L."},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Schaeffer","full_name":"Schaeffer, Stephen W.","first_name":"Stephen W."},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Thomas","last_name":"Flatt","full_name":"Flatt, Thomas"}],"article_processing_charge":"No","acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","quality_controlled":"1","publisher":"Wiley","oa":1,"day":"08","publication":"Journal of Evolutionary Biology","has_accepted_license":"1","year":"2023","date_published":"2023-11-08T00:00:00Z","doi":"10.1111/jeb.14242","date_created":"2023-11-19T23:00:55Z"},{"article_number":"1287420","article_processing_charge":"Yes","author":[{"last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","citation":{"mla":"Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology, vol. 11, 1287420, Frontiers, 2023, doi:10.3389/fcell.2023.1287420.","ieee":"M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction,” Frontiers in Cell and Developmental Biology, vol. 11. Frontiers, 2023.","short":"M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).","apa":"Riedl, M., & Sixt, M. K. (2023). The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2023.1287420","ama":"Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 2023;11. doi:10.3389/fcell.2023.1287420","chicago":"Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology. Frontiers, 2023. https://doi.org/10.3389/fcell.2023.1287420.","ista":"Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11, 1287420."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Frontiers","quality_controlled":"1","acknowledgement":"The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.","date_created":"2023-11-19T23:00:55Z","doi":"10.3389/fcell.2023.1287420","date_published":"2023-10-31T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Frontiers in Cell and Developmental Biology","day":"31","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14555","department":[{"_id":"MiSi"}],"file_date_updated":"2023-11-20T08:41:15Z","date_updated":"2023-11-20T08:44:17Z","ddc":["570"],"scopus_import":"1","intvolume":" 11","month":"10","abstract":[{"lang":"eng","text":"The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems."}],"oa_version":"Published Version","volume":11,"publication_status":"published","publication_identifier":{"eissn":["2296-634X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"61857fc3ebf019354932e7ee684658ce","file_id":"14561","creator":"dernst","file_size":2047622,"date_updated":"2023-11-20T08:41:15Z","file_name":"2023_FrontiersCellDevBio_Riedl.pdf","date_created":"2023-11-20T08:41:15Z"}]},{"date_updated":"2023-11-20T10:04:38Z","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"_id":"14542","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.","lang":"eng"}],"month":"10","main_file_link":[{"url":"https://doi.org/10.1142/S0129055X2360005X","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x.","ista":"Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005.","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics, 2360005, World Scientific Publishing, 2023, doi:10.1142/s0129055x2360005x.","short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing, 2023.","ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x","apa":"Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/s0129055x2360005x"},"title":"Universality in low-dimensional BCS theory","external_id":{"arxiv":["2301.05621"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha"},{"first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","last_name":"Lauritsen"},{"last_name":"Roos","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara"}],"article_number":"2360005 ","project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427"}],"publication":"Reviews in Mathematical Physics","day":"31","year":"2023","has_accepted_license":"1","date_created":"2023-11-15T23:48:14Z","date_published":"2023-10-31T00:00:00Z","doi":"10.1142/s0129055x2360005x","acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","oa":1,"quality_controlled":"1","publisher":"World Scientific Publishing"},{"publication":"Physical Review A","day":"30","year":"2023","date_created":"2023-11-19T23:00:54Z","doi":"10.1103/PhysRevA.108.042430","date_published":"2023-10-30T00:00:00Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.","chicago":"Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.108.042430.","ama":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 2023;108(4). doi:10.1103/PhysRevA.108.042430","apa":"Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., & Lvovsky, A. I. (2023). Continuous-variable quantum tomography of high-amplitude states. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.108.042430","ieee":"E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable quantum tomography of high-amplitude states,” Physical Review A, vol. 108, no. 4. American Physical Society, 2023.","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023).","mla":"Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A, vol. 108, no. 4, 042430, American Physical Society, 2023, doi:10.1103/PhysRevA.108.042430."},"title":"Continuous-variable quantum tomography of high-amplitude states","external_id":{"arxiv":["2212.07406"]},"article_processing_charge":"No","author":[{"full_name":"Fedotova, Ekaterina","orcid":"0000-0001-7242-015X","last_name":"Fedotova","first_name":"Ekaterina","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab"},{"first_name":"Nikolai","last_name":"Kuznetsov","full_name":"Kuznetsov, Nikolai"},{"full_name":"Tiunov, Egor","last_name":"Tiunov","first_name":"Egor"},{"first_name":"A. E.","full_name":"Ulanov, A. E.","last_name":"Ulanov"},{"full_name":"Lvovsky, A. I.","last_name":"Lvovsky","first_name":"A. I."}],"article_number":"042430","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"issue":"4","volume":108,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method."}],"intvolume":" 108","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.07406"}],"scopus_import":"1","date_updated":"2023-11-20T10:26:51Z","department":[{"_id":"JoFi"}],"_id":"14553","status":"public","article_type":"original","type":"journal_article"},{"title":"Epimorphisms and closure operators of categories of semilattices","author":[{"first_name":"D.","last_name":"Dikranjan","full_name":"Dikranjan, D."},{"last_name":"Giordano Bruno","full_name":"Giordano Bruno, A.","first_name":"A."},{"last_name":"Zava","orcid":"0000-0001-8686-1888","full_name":"Zava, Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","first_name":"Nicolò"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators of categories of semilattices,” Quaestiones Mathematicae, vol. 46, no. S1. Taylor & Francis, pp. 191–221, 2023.","short":"D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023) 191–221.","ama":"Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 2023;46(S1):191-221. doi:10.2989/16073606.2023.2247731","apa":"Dikranjan, D., Giordano Bruno, A., & Zava, N. (2023). Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. Taylor & Francis. https://doi.org/10.2989/16073606.2023.2247731","mla":"Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of Semilattices.” Quaestiones Mathematicae, vol. 46, no. S1, Taylor & Francis, 2023, pp. 191–221, doi:10.2989/16073606.2023.2247731.","ista":"Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.","chicago":"Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure Operators of Categories of Semilattices.” Quaestiones Mathematicae. Taylor & Francis, 2023. https://doi.org/10.2989/16073606.2023.2247731."},"project":[{"name":"Algebraic Footprints of Geometric Features in Homology","grant_number":"I04245","call_identifier":"FWF","_id":"26AD5D90-B435-11E9-9278-68D0E5697425"}],"date_published":"2023-11-01T00:00:00Z","doi":"10.2989/16073606.2023.2247731","date_created":"2023-11-19T23:00:55Z","page":"191-221","day":"01","publication":"Quaestiones Mathematicae","year":"2023","quality_controlled":"1","publisher":"Taylor & Francis","acknowledgement":"The first and second named authors are members of GNSAGA – INdAM.\r\nThe third named author was supported by the FWF Grant, Project number I4245–N35","department":[{"_id":"HeEd"}],"date_updated":"2023-11-20T09:24:48Z","status":"public","type":"journal_article","article_type":"original","_id":"14557","volume":46,"issue":"S1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1607-3606"],"eissn":["1727-933X"]},"publication_status":"published","month":"11","intvolume":" 46","scopus_import":"1","oa_version":"None","abstract":[{"text":"Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem.","lang":"eng"}]},{"year":"2023","publication":"Science","day":"09","page":"679-683","date_created":"2023-11-19T23:00:54Z","date_published":"2023-11-09T00:00:00Z","doi":"10.1126/science.adh8830","acknowledgement":"The authors acknowledge funding for central project coordination from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution, and Behavior Program at Michigan State University; and AgBioResearch at Michigan State University. Site-specific funding is listed in the supplementary materials.","publisher":"AAAS","quality_controlled":"1","citation":{"ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","chicago":"Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead, K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.","ieee":"M. L. Robinson et al., “Plant size, latitude, and phylogeny explain within-population variability in herbivory,” Science, vol. 382, no. 6671. AAAS, pp. 679–683, 2023.","short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683.","ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 2023;382(6671):679-683. doi:10.1126/science.adh8830","apa":"Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R., Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830","mla":"Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp. 679–83, doi:10.1126/science.adh8830."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37943897"]},"article_processing_charge":"No","author":[{"first_name":"M. L.","last_name":"Robinson","full_name":"Robinson, M. L."},{"first_name":"P. G.","full_name":"Hahn, P. G.","last_name":"Hahn"},{"full_name":"Inouye, B. D.","last_name":"Inouye","first_name":"B. D."},{"first_name":"N.","full_name":"Underwood, N.","last_name":"Underwood"},{"full_name":"Whitehead, S. R.","last_name":"Whitehead","first_name":"S. R."},{"last_name":"Abbott","full_name":"Abbott, K. C.","first_name":"K. C."},{"first_name":"E. M.","full_name":"Bruna, E. M.","last_name":"Bruna"},{"first_name":"N. I.","full_name":"Cacho, N. I.","last_name":"Cacho"},{"full_name":"Dyer, L. A.","last_name":"Dyer","first_name":"L. A."},{"first_name":"L.","last_name":"Abdala-Roberts","full_name":"Abdala-Roberts, L."},{"first_name":"W. J.","full_name":"Allen, W. J.","last_name":"Allen"},{"first_name":"J. F.","full_name":"Andrade, J. F.","last_name":"Andrade"},{"last_name":"Angulo","full_name":"Angulo, D. F.","first_name":"D. F."},{"full_name":"Anjos, D.","last_name":"Anjos","first_name":"D."},{"full_name":"Anstett, D. N.","last_name":"Anstett","first_name":"D. N."},{"last_name":"Bagchi","full_name":"Bagchi, R.","first_name":"R."},{"last_name":"Bagchi","full_name":"Bagchi, S.","first_name":"S."},{"full_name":"Barbosa, M.","last_name":"Barbosa","first_name":"M."},{"first_name":"S.","last_name":"Barrett","full_name":"Barrett, S."},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574"},{"full_name":"Ben-Simchon, E.","last_name":"Ben-Simchon","first_name":"E."},{"full_name":"Bloodworth, K. J.","last_name":"Bloodworth","first_name":"K. J."},{"full_name":"Bronstein, J. L.","last_name":"Bronstein","first_name":"J. L."},{"full_name":"Buckley, Y. M.","last_name":"Buckley","first_name":"Y. M."},{"first_name":"K. T.","full_name":"Burghardt, K. T.","last_name":"Burghardt"},{"full_name":"Bustos-Segura, C.","last_name":"Bustos-Segura","first_name":"C."},{"first_name":"E. S.","last_name":"Calixto","full_name":"Calixto, E. S."},{"last_name":"Carvalho","full_name":"Carvalho, R. L.","first_name":"R. L."},{"first_name":"B.","last_name":"Castagneyrol","full_name":"Castagneyrol, B."},{"first_name":"M. C.","last_name":"Chiuffo","full_name":"Chiuffo, M. C."},{"full_name":"Cinoğlu, D.","last_name":"Cinoğlu","first_name":"D."},{"first_name":"E.","last_name":"Cinto Mejía","full_name":"Cinto Mejía, E."},{"full_name":"Cock, M. C.","last_name":"Cock","first_name":"M. C."},{"first_name":"R.","full_name":"Cogni, R.","last_name":"Cogni"},{"last_name":"Cope","full_name":"Cope, O. L.","first_name":"O. L."},{"first_name":"T.","full_name":"Cornelissen, T.","last_name":"Cornelissen"},{"full_name":"Cortez, D. R.","last_name":"Cortez","first_name":"D. R."},{"full_name":"Crowder, D. W.","last_name":"Crowder","first_name":"D. W."},{"first_name":"C.","last_name":"Dallstream","full_name":"Dallstream, C."},{"first_name":"W.","last_name":"Dáttilo","full_name":"Dáttilo, W."},{"first_name":"J. K.","last_name":"Davis","full_name":"Davis, J. K."},{"full_name":"Dimarco, R. D.","last_name":"Dimarco","first_name":"R. D."},{"last_name":"Dole","full_name":"Dole, H. E.","first_name":"H. E."},{"last_name":"Egbon","full_name":"Egbon, I. N.","first_name":"I. N."},{"full_name":"Eisenring, M.","last_name":"Eisenring","first_name":"M."},{"last_name":"Ejomah","full_name":"Ejomah, A.","first_name":"A."},{"first_name":"B. D.","full_name":"Elderd, B. D.","last_name":"Elderd"},{"first_name":"M. J.","last_name":"Endara","full_name":"Endara, M. J."},{"full_name":"Eubanks, M. D.","last_name":"Eubanks","first_name":"M. D."},{"full_name":"Everingham, S. E.","last_name":"Everingham","first_name":"S. E."},{"first_name":"K. N.","last_name":"Farah","full_name":"Farah, K. N."},{"full_name":"Farias, R. P.","last_name":"Farias","first_name":"R. P."},{"first_name":"A. P.","last_name":"Fernandes","full_name":"Fernandes, A. P."},{"first_name":"G. W.","full_name":"Fernandes, G. W.","last_name":"Fernandes"},{"full_name":"Ferrante, M.","last_name":"Ferrante","first_name":"M."},{"first_name":"A.","last_name":"Finn","full_name":"Finn, A."},{"last_name":"Florjancic","full_name":"Florjancic, G. A.","first_name":"G. A."},{"first_name":"M. L.","full_name":"Forister, M. L.","last_name":"Forister"},{"first_name":"Q. N.","full_name":"Fox, Q. N.","last_name":"Fox"},{"first_name":"E.","full_name":"Frago, E.","last_name":"Frago"},{"last_name":"França","full_name":"França, F. M.","first_name":"F. M."},{"full_name":"Getman-Pickering, A. S.","last_name":"Getman-Pickering","first_name":"A. S."},{"full_name":"Getman-Pickering, Z.","last_name":"Getman-Pickering","first_name":"Z."},{"first_name":"E.","last_name":"Gianoli","full_name":"Gianoli, E."},{"first_name":"B.","last_name":"Gooden","full_name":"Gooden, B."},{"full_name":"Gossner, M. M.","last_name":"Gossner","first_name":"M. M."},{"first_name":"K. A.","full_name":"Greig, K. A.","last_name":"Greig"},{"full_name":"Gripenberg, S.","last_name":"Gripenberg","first_name":"S."},{"full_name":"Groenteman, R.","last_name":"Groenteman","first_name":"R."},{"first_name":"P.","full_name":"Grof-Tisza, P.","last_name":"Grof-Tisza"},{"first_name":"N.","last_name":"Haack","full_name":"Haack, N."},{"first_name":"L.","full_name":"Hahn, L.","last_name":"Hahn"},{"first_name":"S. M.","full_name":"Haq, S. M.","last_name":"Haq"},{"full_name":"Helms, A. M.","last_name":"Helms","first_name":"A. M."},{"first_name":"J.","full_name":"Hennecke, J.","last_name":"Hennecke"},{"first_name":"S. L.","last_name":"Hermann","full_name":"Hermann, S. L."},{"last_name":"Holeski","full_name":"Holeski, L. M.","first_name":"L. M."},{"last_name":"Holm","full_name":"Holm, S.","first_name":"S."},{"first_name":"M. C.","last_name":"Hutchinson","full_name":"Hutchinson, M. C."},{"first_name":"E. E.","full_name":"Jackson, E. E.","last_name":"Jackson"},{"last_name":"Kagiya","full_name":"Kagiya, S.","first_name":"S."},{"full_name":"Kalske, A.","last_name":"Kalske","first_name":"A."},{"last_name":"Kalwajtys","full_name":"Kalwajtys, M.","first_name":"M."},{"last_name":"Karban","full_name":"Karban, R.","first_name":"R."},{"first_name":"R.","last_name":"Kariyat","full_name":"Kariyat, R."},{"first_name":"T.","last_name":"Keasar","full_name":"Keasar, T."},{"first_name":"M. F.","full_name":"Kersch-Becker, M. F.","last_name":"Kersch-Becker"},{"first_name":"H. M.","last_name":"Kharouba","full_name":"Kharouba, H. M."},{"first_name":"T. N.","full_name":"Kim, T. N.","last_name":"Kim"},{"full_name":"Kimuyu, D. M.","last_name":"Kimuyu","first_name":"D. M."},{"last_name":"Kluse","full_name":"Kluse, J.","first_name":"J."},{"full_name":"Koerner, S. E.","last_name":"Koerner","first_name":"S. E."},{"first_name":"K. J.","last_name":"Komatsu","full_name":"Komatsu, K. J."},{"first_name":"S.","last_name":"Krishnan","full_name":"Krishnan, S."},{"first_name":"M.","full_name":"Laihonen, M.","last_name":"Laihonen"},{"first_name":"L.","full_name":"Lamelas-López, L.","last_name":"Lamelas-López"},{"first_name":"M. C.","last_name":"Lascaleia","full_name":"Lascaleia, M. C."},{"last_name":"Lecomte","full_name":"Lecomte, N.","first_name":"N."},{"last_name":"Lehn","full_name":"Lehn, C. R.","first_name":"C. R."},{"first_name":"X.","full_name":"Li, X.","last_name":"Li"},{"last_name":"Lindroth","full_name":"Lindroth, R. L.","first_name":"R. L."},{"last_name":"Lopresti","full_name":"Lopresti, E. F.","first_name":"E. F."},{"full_name":"Losada, M.","last_name":"Losada","first_name":"M."},{"last_name":"Louthan","full_name":"Louthan, A. M.","first_name":"A. M."},{"last_name":"Luizzi","full_name":"Luizzi, V. J.","first_name":"V. J."},{"first_name":"S. C.","last_name":"Lynch","full_name":"Lynch, S. C."},{"first_name":"J. S.","last_name":"Lynn","full_name":"Lynn, J. S."},{"first_name":"N. J.","full_name":"Lyon, N. J.","last_name":"Lyon"},{"first_name":"L. F.","last_name":"Maia","full_name":"Maia, L. F."},{"first_name":"R. A.","last_name":"Maia","full_name":"Maia, R. A."},{"first_name":"T. L.","full_name":"Mannall, T. L.","last_name":"Mannall"},{"first_name":"B. S.","full_name":"Martin, B. S.","last_name":"Martin"},{"last_name":"Massad","full_name":"Massad, T. J.","first_name":"T. J."},{"last_name":"Mccall","full_name":"Mccall, A. C.","first_name":"A. C."},{"last_name":"Mcgurrin","full_name":"Mcgurrin, K.","first_name":"K."},{"first_name":"A. C.","last_name":"Merwin","full_name":"Merwin, A. C."},{"first_name":"Z.","last_name":"Mijango-Ramos","full_name":"Mijango-Ramos, Z."},{"first_name":"C. H.","full_name":"Mills, C. H.","last_name":"Mills"},{"first_name":"A. T.","last_name":"Moles","full_name":"Moles, A. T."},{"full_name":"Moore, C. M.","last_name":"Moore","first_name":"C. M."},{"last_name":"Moreira","full_name":"Moreira, X.","first_name":"X."},{"first_name":"C. R.","full_name":"Morrison, C. R.","last_name":"Morrison"},{"full_name":"Moshobane, M. C.","last_name":"Moshobane","first_name":"M. C."},{"first_name":"A.","full_name":"Muola, A.","last_name":"Muola"},{"first_name":"R.","full_name":"Nakadai, R.","last_name":"Nakadai"},{"first_name":"K.","full_name":"Nakajima, K.","last_name":"Nakajima"},{"first_name":"S.","last_name":"Novais","full_name":"Novais, S."},{"last_name":"Ogbebor","full_name":"Ogbebor, C. O.","first_name":"C. O."},{"last_name":"Ohsaki","full_name":"Ohsaki, H.","first_name":"H."},{"last_name":"Pan","full_name":"Pan, V. S.","first_name":"V. S."},{"first_name":"N. A.","last_name":"Pardikes","full_name":"Pardikes, N. A."},{"first_name":"M.","full_name":"Pareja, M.","last_name":"Pareja"},{"full_name":"Parthasarathy, N.","last_name":"Parthasarathy","first_name":"N."},{"first_name":"R. R.","full_name":"Pawar, R. R.","last_name":"Pawar"},{"first_name":"Q.","full_name":"Paynter, Q.","last_name":"Paynter"},{"full_name":"Pearse, I. S.","last_name":"Pearse","first_name":"I. S."},{"first_name":"R. M.","full_name":"Penczykowski, R. M.","last_name":"Penczykowski"},{"full_name":"Pepi, A. A.","last_name":"Pepi","first_name":"A. A."},{"last_name":"Pereira","full_name":"Pereira, C. C.","first_name":"C. C."},{"last_name":"Phartyal","full_name":"Phartyal, S. S.","first_name":"S. S."},{"full_name":"Piper, F. I.","last_name":"Piper","first_name":"F. I."},{"full_name":"Poveda, K.","last_name":"Poveda","first_name":"K."},{"first_name":"E. G.","full_name":"Pringle, E. G.","last_name":"Pringle"},{"first_name":"J.","full_name":"Puy, J.","last_name":"Puy"},{"first_name":"T.","full_name":"Quijano, T.","last_name":"Quijano"},{"first_name":"C.","last_name":"Quintero","full_name":"Quintero, C."},{"full_name":"Rasmann, S.","last_name":"Rasmann","first_name":"S."},{"last_name":"Rosche","full_name":"Rosche, C.","first_name":"C."},{"first_name":"L. Y.","last_name":"Rosenheim","full_name":"Rosenheim, L. Y."},{"first_name":"J. A.","full_name":"Rosenheim, J. A.","last_name":"Rosenheim"},{"first_name":"J. B.","last_name":"Runyon","full_name":"Runyon, J. B."},{"full_name":"Sadeh, A.","last_name":"Sadeh","first_name":"A."},{"full_name":"Sakata, Y.","last_name":"Sakata","first_name":"Y."},{"last_name":"Salcido","full_name":"Salcido, D. M.","first_name":"D. M."},{"last_name":"Salgado-Luarte","full_name":"Salgado-Luarte, C.","first_name":"C."},{"last_name":"Santos","full_name":"Santos, B. A.","first_name":"B. A."},{"first_name":"Y.","full_name":"Sapir, Y.","last_name":"Sapir"},{"full_name":"Sasal, Y.","last_name":"Sasal","first_name":"Y."},{"first_name":"Y.","full_name":"Sato, Y.","last_name":"Sato"},{"first_name":"M.","last_name":"Sawant","full_name":"Sawant, M."},{"full_name":"Schroeder, H.","last_name":"Schroeder","first_name":"H."},{"full_name":"Schumann, I.","last_name":"Schumann","first_name":"I."},{"full_name":"Segoli, M.","last_name":"Segoli","first_name":"M."},{"first_name":"H.","last_name":"Segre","full_name":"Segre, H."},{"last_name":"Shelef","full_name":"Shelef, O.","first_name":"O."},{"first_name":"N.","full_name":"Shinohara, N.","last_name":"Shinohara"},{"last_name":"Singh","full_name":"Singh, R. P.","first_name":"R. P."},{"first_name":"D. S.","last_name":"Smith","full_name":"Smith, D. S."},{"full_name":"Sobral, M.","last_name":"Sobral","first_name":"M."},{"last_name":"Stotz","full_name":"Stotz, G. C.","first_name":"G. C."},{"last_name":"Tack","full_name":"Tack, A. J.M.","first_name":"A. J.M."},{"full_name":"Tayal, M.","last_name":"Tayal","first_name":"M."},{"full_name":"Tooker, J. F.","last_name":"Tooker","first_name":"J. F."},{"first_name":"D.","last_name":"Torrico-Bazoberry","full_name":"Torrico-Bazoberry, D."},{"first_name":"K.","full_name":"Tougeron, K.","last_name":"Tougeron"},{"first_name":"A. M.","last_name":"Trowbridge","full_name":"Trowbridge, A. M."},{"last_name":"Utsumi","full_name":"Utsumi, S.","first_name":"S."},{"last_name":"Uyi","full_name":"Uyi, O.","first_name":"O."},{"full_name":"Vaca-Uribe, J. L.","last_name":"Vaca-Uribe","first_name":"J. L."},{"full_name":"Valtonen, A.","last_name":"Valtonen","first_name":"A."},{"first_name":"L. J.A.","full_name":"Van Dijk, L. J.A.","last_name":"Van Dijk"},{"first_name":"V.","last_name":"Vandvik","full_name":"Vandvik, V."},{"full_name":"Villellas, J.","last_name":"Villellas","first_name":"J."},{"last_name":"Waller","full_name":"Waller, L. P.","first_name":"L. P."},{"first_name":"M. G.","full_name":"Weber, M. G.","last_name":"Weber"},{"first_name":"A.","full_name":"Yamawo, A.","last_name":"Yamawo"},{"full_name":"Yim, S.","last_name":"Yim","first_name":"S."},{"first_name":"P. L.","full_name":"Zarnetske, P. L.","last_name":"Zarnetske"},{"last_name":"Zehr","full_name":"Zehr, L. N.","first_name":"L. N."},{"last_name":"Zhong","full_name":"Zhong, Z.","first_name":"Z."},{"first_name":"W. C.","last_name":"Wetzel","full_name":"Wetzel, W. C."}],"title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"volume":382,"related_material":{"record":[{"relation":"research_data","id":"14579","status":"public"}]},"issue":"6671","abstract":[{"lang":"eng","text":"Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth."}],"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 382","month":"11","date_updated":"2023-11-20T11:17:34Z","department":[{"_id":"NiBa"}],"_id":"14552","article_type":"original","type":"journal_article","status":"public"},{"citation":{"chicago":"Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.","ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.","mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007.","short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","ieee":"A. Briffa et al., “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems, vol. 14, no. 11. Elsevier, pp. 953–967, 2023.","apa":"Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., & Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier. https://doi.org/10.1016/j.cels.2023.10.007","ama":"Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Briffa, Amy","last_name":"Briffa","first_name":"Amy"},{"first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","last_name":"Hollwey","full_name":"Hollwey, Elizabeth"},{"full_name":"Shahzad, Zaigham","last_name":"Shahzad","first_name":"Zaigham"},{"first_name":"Jonathan D.","full_name":"Moore, Jonathan D.","last_name":"Moore"},{"first_name":"David B.","last_name":"Lyons","full_name":"Lyons, David B."},{"first_name":"Martin","full_name":"Howard, Martin","last_name":"Howard"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"external_id":{"pmid":["37944515"]},"article_processing_charge":"Yes (via OA deal)","title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746"}],"has_accepted_license":"1","year":"2023","day":"15","publication":"Cell Systems","page":"953-967","date_published":"2023-11-15T00:00:00Z","doi":"10.1016/j.cels.2023.10.007","date_created":"2023-11-19T23:00:54Z","acknowledgement":"We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z.","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_updated":"2023-11-20T11:24:34Z","ddc":["570"],"file_date_updated":"2023-11-20T11:22:52Z","department":[{"_id":"DaZi"}],"_id":"14551","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"publication_status":"published","file":[{"success":1,"file_id":"14580","checksum":"101fdac59e6f1102d68ef91f2b5bd51a","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_CellSystems_Briffa.pdf","date_created":"2023-11-20T11:22:52Z","file_size":5587897,"date_updated":"2023-11-20T11:22:52Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":14,"issue":"11","ec_funded":1,"abstract":[{"text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 14"},{"_id":"14579","type":"research_data_reference","status":"public","date_updated":"2023-11-20T11:17:33Z","citation":{"ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117.","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.","short":"W. Wetzel, (2023).","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/10.5281/ZENODO.8133117","mla":"Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Wetzel, William","last_name":"Wetzel","first_name":"William"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","abstract":[{"lang":"eng","text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n"}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133118"}],"oa":1,"month":"07","year":"2023","day":"11","date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133117","related_material":{"record":[{"relation":"used_in_publication","id":"14552","status":"public"}]},"date_created":"2023-11-20T11:07:45Z"},{"volume":9,"related_material":{"record":[{"relation":"research_data","id":"14562","status":"public"}]},"issue":"3","publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"12335","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_ScienceAdvances_Faessler.pdf","date_created":"2023-01-23T07:45:54Z","creator":"dernst","file_size":1756234,"date_updated":"2023-01-23T07:45:54Z"}],"scopus_import":"1","intvolume":" 9","month":"01","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version","file_date_updated":"2023-01-23T07:45:54Z","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"date_updated":"2023-11-21T08:05:35Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Multidisciplinary"],"status":"public","_id":"12334","date_created":"2023-01-23T07:26:42Z","date_published":"2023-01-20T00:00:00Z","doi":"10.1126/sciadv.add6495","year":"2023","has_accepted_license":"1","isi":1,"publication":"Science Advances","day":"20","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","article_processing_charge":"No","external_id":{"isi":["000964550100015"]},"author":[{"orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"last_name":"Javoor","full_name":"Javoor, Manjunath","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"last_name":"Datler","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Döring","full_name":"Döring, Hermann","first_name":"Hermann"},{"full_name":"Hofer, Florian","last_name":"Hofer","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","citation":{"ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 2023;9(3). doi:10.1126/sciadv.add6495","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","ieee":"F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495.","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"article_number":"add6495"},{"_id":"14562","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"status":"public","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-21T08:05:34Z","citation":{"ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","short":"F.K. Schur, (2023).","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562","mla":"Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562."},"file_date_updated":"2023-11-20T11:49:58Z","department":[{"_id":"FlSc"}],"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","author":[{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"month":"11","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"checksum":"e9bab797b44614f144a5b02d9636f8c3","file_id":"14570","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2023-11-20T10:27:17Z","file_name":"Figure2.zip","creator":"fschur","date_updated":"2023-11-20T10:27:17Z","file_size":1581687449},{"checksum":"4efd388cccd03c549fc90f6e46d37006","file_id":"14571","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2023-11-20T10:29:18Z","file_name":"SupplementaryFigure3.zip","creator":"fschur","date_updated":"2023-11-20T10:29:18Z","file_size":116088565},{"creator":"fschur","file_size":5154614201,"date_updated":"2023-11-20T10:44:39Z","file_name":"Figure5.zip","date_created":"2023-11-20T10:44:39Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"file_id":"14572","checksum":"bdeb232dc94d0c22a3f7e0d18189ce89"},{"checksum":"83aee17d621a05d865f68f39c8892d27","file_id":"14573","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2023-11-20T10:46:00Z","file_name":"SupplementaryFigure7.zip","creator":"fschur","date_updated":"2023-11-20T10:46:00Z","file_size":1277893286},{"success":1,"file_id":"14574","checksum":"fb9beb6fe15c8dac6679dd02044d2ea6","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"SupplementaryFigure9.zip","date_created":"2023-11-20T10:46:08Z","file_size":228485124,"date_updated":"2023-11-20T10:46:08Z","creator":"fschur"},{"creator":"fschur","date_updated":"2023-11-20T10:46:32Z","file_size":1226788198,"date_created":"2023-11-20T10:46:32Z","file_name":"SupplementaryFigure10.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"4f3644e5feabe4824486d56885bb79fe","file_id":"14575","success":1},{"date_created":"2023-11-20T10:46:17Z","file_name":"SupplementaryFigure11.zip","creator":"fschur","date_updated":"2023-11-20T10:46:17Z","file_size":277577131,"file_id":"14576","checksum":"96167f722ed0ca78e30681cd1573b9d7","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"file_size":591483468,"date_updated":"2023-11-20T10:46:29Z","creator":"fschur","file_name":"SupplementaryFigure15.zip","date_created":"2023-11-20T10:46:29Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"checksum":"d1e03c9805c18cfbc2e9fdf38a9f556f","file_id":"14577"},{"date_created":"2023-11-20T10:47:00Z","file_name":"SupplementaryFigure17.zip","creator":"fschur","date_updated":"2023-11-20T10:47:00Z","file_size":1709528579,"checksum":"4d437c04fdb3c1e699618063c4bd21c3","file_id":"14578","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"creator":"fschur","file_size":1920765280,"date_updated":"2023-11-20T11:26:36Z","file_name":"SupplementaryFigure4.zip","date_created":"2023-11-20T11:26:36Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"checksum":"967b5378a4f16c43f490eae328afe50e","file_id":"14581"},{"file_size":3013566196,"date_updated":"2023-11-20T11:38:12Z","creator":"fschur","file_name":"Figure1_partA.zip","date_created":"2023-11-20T11:38:12Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"checksum":"11899986cf0b471d258fe168ee33a3ea","file_id":"14583"},{"checksum":"c452afe1ab506d58d32e601d5b3878bb","file_id":"14584","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2023-11-20T11:43:23Z","file_name":"Figure1_partB.zip","creator":"fschur","date_updated":"2023-11-20T11:43:23Z","file_size":3250260203},{"date_created":"2023-11-20T11:49:58Z","file_name":"ReadMe.rtf","creator":"fschur","date_updated":"2023-11-20T11:49:58Z","file_size":1460,"checksum":"223c98eceecbe65dd268f4f363a620d8","file_id":"14585","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/rtf"}],"day":"21","has_accepted_license":"1","year":"2023","doi":"10.15479/AT:ISTA:14562","related_material":{"record":[{"id":"12334","status":"public","relation":"used_in_publication"}]},"date_published":"2023-11-21T00:00:00Z","contributor":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","contributor_type":"researcher","orcid":"0000-0001-7149-769X","last_name":"Fäßler"},{"first_name":"Manjunath","contributor_type":"researcher","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Julia","orcid":"0000-0002-3616-8580","last_name":"Datler"},{"last_name":"Döring","first_name":"Hermann","contributor_type":"researcher"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","contributor_type":"researcher","last_name":"Hofer"},{"contributor_type":"researcher","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","last_name":"Dimchev"},{"last_name":"Hodirnau","contributor_type":"researcher","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","first_name":"Jan","last_name":"Faix"},{"first_name":"Klemens","contributor_type":"researcher","last_name":"Rottner"},{"contributor_type":"researcher","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078"}],"date_created":"2023-11-20T09:22:33Z"},{"date_published":"2023-11-21T00:00:00Z","related_material":{"record":[{"status":"public","id":"10290","relation":"used_for_analysis_in"}]},"doi":"10.15479/AT:ISTA:14502","date_created":"2023-11-08T19:40:54Z","has_accepted_license":"1","year":"2023","day":"21","file":[{"date_created":"2023-11-08T20:23:07Z","file_name":"Computational_Toolbox_v1.2.zip","creator":"fschur","date_updated":"2023-11-08T20:23:07Z","file_size":347641117,"checksum":"a8b9adeb53a4109dea4d5e39fa1acccf","file_id":"14503","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"date_created":"2023-11-21T08:20:23Z","file_name":"Readme.txt","date_updated":"2023-11-21T08:20:23Z","file_size":1522,"creator":"dernst","file_id":"14586","checksum":"14db2addbfca61a085ba301ed6f2900b","success":1,"content_type":"text/plain","access_level":"open_access","relation":"main_file"}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"11","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"author":[{"last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler"},{"first_name":"Martin","full_name":"Falcke, Martin","last_name":"Falcke"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","department":[{"_id":"FlSc"}],"file_date_updated":"2023-11-21T08:20:23Z","citation":{"apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:10.15479/AT:ISTA:14502","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","mla":"Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14502.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14502."},"date_updated":"2023-11-21T08:36:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"type":"software","tmp":{"short":"GNU AGPLv3 ","name":"GNU Affero General Public License v3.0","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html"},"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"status":"public","keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"_id":"14502"},{"title":"Stress granules plug and stabilize damaged endolysosomal membranes","author":[{"last_name":"Bussi","full_name":"Bussi, Claudio","first_name":"Claudio"},{"full_name":"Mangiarotti, Agustín","last_name":"Mangiarotti","first_name":"Agustín"},{"full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"full_name":"Aylan, Beren","last_name":"Aylan","first_name":"Beren"},{"first_name":"Enrica","full_name":"Pellegrino, Enrica","last_name":"Pellegrino"},{"first_name":"Natalia","full_name":"Athanasiadi, Natalia","last_name":"Athanasiadi"},{"last_name":"Fearns","full_name":"Fearns, Antony","first_name":"Antony"},{"first_name":"Angela","full_name":"Rodgers, Angela","last_name":"Rodgers"},{"last_name":"Franzmann","full_name":"Franzmann, Titus M.","first_name":"Titus M."},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Dimova","full_name":"Dimova, Rumiana","first_name":"Rumiana"},{"first_name":"Maximiliano G.","last_name":"Gutierrez","full_name":"Gutierrez, Maximiliano G."}],"external_id":{"pmid":["37968398"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w","short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature (2023).","ieee":"C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal membranes,” Nature. Springer Nature, 2023.","chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w.","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature."},"date_published":"2023-11-15T00:00:00Z","doi":"10.1038/s41586-023-06726-w","date_created":"2023-11-27T07:56:37Z","day":"15","publication":"Nature","year":"2023","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","department":[{"_id":"AnSa"}],"date_updated":"2023-11-27T09:05:08Z","status":"public","keyword":["Multidisciplinary"],"article_type":"original","type":"journal_article","_id":"14610","related_material":{"record":[{"status":"public","id":"14472","relation":"research_data"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication_status":"epub_ahead","month":"11","main_file_link":[{"url":"https://doi.org/10.1038/s41586-023-06726-w","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host."}]},{"date_created":"2023-10-30T16:38:32Z","date_published":"2023-10-31T00:00:00Z","doi":"10.15479/AT:ISTA:14472","related_material":{"record":[{"status":"public","id":"14610","relation":"used_in_publication"}]},"file":[{"success":1,"file_id":"14473","checksum":"a18706e952e8660c51ede52a167270b7","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"SGporecondensation-main.zip","date_created":"2023-10-30T16:31:08Z","file_size":62821432,"date_updated":"2023-10-30T16:31:08Z","creator":"ipalaia"},{"success":1,"checksum":"389eab31c6509dbc05795017fb618758","file_id":"14474","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_name":"README.txt","date_created":"2023-10-31T08:57:50Z","file_size":1697,"date_updated":"2023-10-31T08:57:50Z","creator":"dernst"}],"day":"31","year":"2023","has_accepted_license":"1","month":"10","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w."}],"file_date_updated":"2023-10-31T08:57:50Z","department":[{"_id":"AnSa"}],"title":"Stress granules plug and stabilize damaged endolysosomal membranes","article_processing_charge":"No","author":[{"last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-27T09:05:07Z","citation":{"ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.","chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.","ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472","apa":"Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","short":"C.E. Vanhille-Campos, A. Šarić, (2023).","mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472."},"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"14472"},{"status":"public","type":"journal_article","article_type":"original","_id":"14605","department":[{"_id":"BiCh"}],"date_updated":"2023-11-28T07:48:55Z","month":"11","intvolume":" 108","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments."}],"volume":108,"issue":"17","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"article_number":"174302","title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","author":[{"first_name":"Niuchang","last_name":"Ouyang","full_name":"Ouyang, Niuchang"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","full_name":"Zeng, Zezhu","last_name":"Zeng"},{"first_name":"Chen","full_name":"Wang, Chen","last_name":"Wang"},{"first_name":"Qi","last_name":"Wang","full_name":"Wang, Qi"},{"first_name":"Yue","full_name":"Chen, Yue","last_name":"Chen"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.174302.","ista":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 108(17), 174302.","mla":"Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B, vol. 108, no. 17, 174302, American Physical Society, 2023, doi:10.1103/PhysRevB.108.174302.","ama":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 2023;108(17). doi:10.1103/PhysRevB.108.174302","apa":"Ouyang, N., Zeng, Z., Wang, C., Wang, Q., & Chen, Y. (2023). Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.174302","ieee":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),” Physical Review B, vol. 108, no. 17. American Physical Society, 2023.","short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023)."},"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (Grants No. 17318122 and No. 17306721). The authors are grateful for the research computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","date_published":"2023-11-01T00:00:00Z","doi":"10.1103/PhysRevB.108.174302","date_created":"2023-11-26T23:00:54Z","day":"01","publication":"Physical Review B","year":"2023"},{"project":[{"name":"Secure Network and Hardware for Efficient Blockchains","grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"citation":{"apa":"Das, S., Xiang, Z., Kokoris Kogias, E., & Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In 32nd USENIX Security Symposium (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix.","ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: 32nd USENIX Security Symposium. Vol 8. Usenix; 2023:5359-5376.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in 32nd USENIX Security Symposium, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.","short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376.","mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” 32nd USENIX Security Symposium, vol. 8, Usenix, 2023, pp. 5359–76.","ista":"Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In 32nd USENIX Security Symposium, 8:5359–76. Usenix, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Das","full_name":"Das, Sourav","first_name":"Sourav"},{"first_name":"Zhuolun","full_name":"Xiang, Zhuolun","last_name":"Xiang"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Ren","full_name":"Ren, Ling","first_name":"Ling"}],"title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","acknowledgement":"The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.","oa":1,"quality_controlled":"1","publisher":"Usenix","year":"2023","has_accepted_license":"1","publication":"32nd USENIX Security Symposium","day":"15","page":"5359-5376","date_created":"2023-11-26T23:00:55Z","date_published":"2023-08-15T00:00:00Z","_id":"14609","conference":{"start_date":"2023-08-09","location":"Anaheim, CA, United States","end_date":"2023-08-11","name":"USENIX Security Symposium"},"type":"conference","status":"public","date_updated":"2023-11-28T09:17:38Z","ddc":["000"],"department":[{"_id":"ElKo"}],"file_date_updated":"2023-11-28T09:14:34Z","abstract":[{"text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://eprint.iacr.org/2022/1389","open_access":"1"}],"scopus_import":"1","intvolume":" 8","month":"08","publication_status":"published","publication_identifier":{"isbn":["9781713879497"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-11-28T09:14:34Z","file_size":704331,"creator":"dernst","date_created":"2023-11-28T09:14:34Z","file_name":"2023_USENIX_Das.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14621","checksum":"1a730765930138e23c6efd2575872641","success":1}],"volume":8},{"issue":"18","volume":159,"related_material":{"record":[{"status":"public","id":"14619","relation":"research_data"}]},"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"publication_status":"published","file":[{"success":1,"checksum":"f668ee0d07096eef81159d05bc27aabc","file_id":"14620","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","date_created":"2023-11-28T08:39:06Z","creator":"dernst","file_size":6276059,"date_updated":"2023-11-28T08:39:06Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"11","intvolume":" 159","abstract":[{"text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"BiCh"}],"file_date_updated":"2023-11-28T08:39:06Z","date_updated":"2023-11-28T08:39:23Z","ddc":["530","540"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14603","date_published":"2023-11-14T00:00:00Z","doi":"10.1063/5.0173341","date_created":"2023-11-26T23:00:54Z","has_accepted_license":"1","year":"2023","day":"14","publication":"Journal of Chemical Physics","publisher":"AIP Publishing","quality_controlled":"1","oa":1,"acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","author":[{"first_name":"Aleks","full_name":"Reinhardt, Aleks","last_name":"Reinhardt"},{"last_name":"Chew","full_name":"Chew, Pin Yu","first_name":"Pin Yu"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2308.10886"]},"title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","citation":{"mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 2023;159(18). doi:10.1063/5.0173341","apa":"Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” Journal of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.","ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"184110"},{"acknowledgement":"All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript.","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","publication":"Evolution","day":"02","year":"2023","has_accepted_license":"1","date_created":"2023-11-26T23:00:54Z","date_published":"2023-11-02T00:00:00Z","doi":"10.1093/evolut/qpad169","page":"2504-2511","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpad169.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169","apa":"Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023."},"title":"The X chromosome of insects likely predates the origin of class Insecta","external_id":{"pmid":["37738212"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"intvolume":" 77","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"b66dc10edae92d38918d534e64dda77c","file_id":"14618","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-11-28T08:12:15Z","file_name":"2023_Evolution_Toups.pdf","date_updated":"2023-11-28T08:12:15Z","file_size":1399102,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1558-5646"]},"related_material":{"record":[{"relation":"research_data","status":"public","id":"14616"},{"relation":"research_data","status":"public","id":"14617"}],"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}]},"issue":"11","volume":77,"_id":"14604","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-11-28T08:25:28Z","department":[{"_id":"BeVi"}],"file_date_updated":"2023-11-28T08:12:15Z"},{"_id":"14616","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","citation":{"mla":"Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT.","apa":"Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5061/DRYAD.HX3FFBGKT","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","short":"M.A. Toups, B. Vicoso, (2023).","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT."},"date_updated":"2023-11-28T08:17:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","author":[{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.hx3ffbgkt"}],"oa":1,"publisher":"Dryad","month":"09","year":"2023","has_accepted_license":"1","day":"15","date_created":"2023-11-28T08:01:53Z","related_material":{"record":[{"status":"public","id":"14604","relation":"used_in_publication"}]},"doi":"10.5061/DRYAD.HX3FFBGKT","date_published":"2023-09-15T00:00:00Z"},{"author":[{"last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"article_processing_charge":"No","department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","citation":{"ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","short":"M.A. Toups, B. Vicoso, (2023).","apa":"Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5281/ZENODO.8138705","mla":"Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705.","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705."},"date_updated":"2023-11-28T08:25:28Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","status":"public","_id":"14617","date_published":"2023-09-15T00:00:00Z","related_material":{"record":[{"status":"public","id":"14604","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.8138705","date_created":"2023-11-28T08:04:03Z","has_accepted_license":"1","year":"2023","day":"15","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8138705"}],"oa":1,"month":"09","other_data_license":"MIT License","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"oa_version":"Published Version"},{"related_material":{"record":[{"id":"14603","status":"public","relation":"used_in_publication"}]},"date_published":"2023-10-02T00:00:00Z","doi":"10.5281/ZENODO.8398094","date_created":"2023-11-28T08:32:18Z","has_accepted_license":"1","year":"2023","day":"02","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8398094","open_access":"1"}],"month":"10","abstract":[{"text":"Data underlying the publication \"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals\" (DOI https://doi.org/10.1063/5.0173341).","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"}],"article_processing_charge":"No","title":"BingqingCheng/solubility: V1.0","department":[{"_id":"BiCh"}],"citation":{"ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.","chicago":"Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.","short":"B. Cheng, (2023).","ama":"Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094","apa":"Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094","mla":"Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094."},"date_updated":"2023-11-28T08:39:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"type":"research_data_reference","status":"public","_id":"14619"},{"citation":{"ieee":"B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11. American Geophysical Union, 2023.","short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023).","apa":"Khouider, B., GOSWAMI, B. B., Phani, R., & Majda, A. J. (2023). A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. American Geophysical Union. https://doi.org/10.1029/2022ms003391","ama":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 2023;15(11). doi:10.1029/2022ms003391","mla":"Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:10.1029/2022ms003391.","ista":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.","chicago":"Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems. American Geophysical Union, 2023. https://doi.org/10.1029/2022ms003391."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"B.","full_name":"Khouider, B.","last_name":"Khouider"},{"orcid":"0000-0001-8602-3083","full_name":"GOSWAMI, BIDYUT B","last_name":"GOSWAMI","first_name":"BIDYUT B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b"},{"last_name":"Phani","full_name":"Phani, R.","first_name":"R."},{"first_name":"A. J.","full_name":"Majda, A. J.","last_name":"Majda"}],"article_processing_charge":"Yes","title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","article_number":"e2022MS003391","has_accepted_license":"1","year":"2023","day":"01","publication":"Journal of Advances in Modeling Earth Systems","doi":"10.1029/2022ms003391","date_published":"2023-11-01T00:00:00Z","date_created":"2023-11-20T09:18:21Z","acknowledgement":"The research of B.K. is supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020). This research was conducted during the visits of P.M. Krishna to the Center for Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November 2018 to June 2019 and July 2019 and October 2019, respectively. The authors are very grateful to the three anonymous reviewers who provided very thoughtful and constructive comments during the review process that helped greatly improve and shape the final version of the manuscript.","publisher":"American Geophysical Union","quality_controlled":"1","oa":1,"date_updated":"2023-11-28T12:04:42Z","ddc":["550"],"file_date_updated":"2023-11-20T11:29:16Z","department":[{"_id":"CaMu"}],"_id":"14564","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"publication_identifier":{"eissn":["1942-2466"]},"publication_status":"published","file":[{"file_name":"2023_JAMES_Khoulder.pdf","date_created":"2023-11-20T11:29:16Z","file_size":6435697,"date_updated":"2023-11-20T11:29:16Z","creator":"dernst","success":1,"checksum":"e30329dd985559de0ddc7021ca7382b4","file_id":"14582","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":15,"issue":"11","abstract":[{"lang":"eng","text":"Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized."}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 15"},{"day":"01","publication":"Physical Review E","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-03-01T00:00:00Z","doi":"10.1103/PhysRevE.107.034901","date_created":"2023-04-02T22:01:10Z","acknowledgement":"This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901.","short":"N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).","ieee":"N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” Physical Review E, vol. 107, no. 3. American Physical Society, 2023.","apa":"Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.034901","ama":"Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901","chicago":"Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901.","ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901."},"title":"Accurate determination of the shapes of granular charge distributions","author":[{"full_name":"Mujica, Nicolás","last_name":"Mujica","first_name":"Nicolás"},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R"}],"article_processing_charge":"No","external_id":{"isi":["000992142700001"]},"article_number":"034901","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"file":[{"checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","file_id":"14612","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-11-27T09:51:48Z","file_name":"PhysRevE.107.034901 (1).pdf","creator":"swaituka","date_updated":"2023-11-27T09:51:48Z","file_size":1428631}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"publication_status":"published","volume":107,"issue":"3","ec_funded":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.","lang":"eng"}],"month":"03","intvolume":" 107","scopus_import":"1","ddc":["530"],"date_updated":"2023-11-28T09:22:25Z","file_date_updated":"2023-11-27T09:51:48Z","department":[{"_id":"ScWa"}],"_id":"12789","status":"public","type":"journal_article","article_type":"original"},{"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information and Communication Complexity , Springer Nature, 2023, pp. 576–594.","ieee":"S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation,” in SIROCCO 2023: Structural Information and Communication Complexity , Alcala de Henares, Spain, 2023, vol. 13892, pp. 576–594.","ama":"Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023: Structural Information and Communication Complexity . Vol 13892. Springer Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26","apa":"Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In SIROCCO 2023: Structural Information and Communication Complexity (Vol. 13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26","mla":"Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94, doi:10.1007/978-3-031-32733-9_26.","ista":"Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023: Structural Information and Communication Complexity . SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 576–594.","chicago":"Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” In SIROCCO 2023: Structural Information and Communication Complexity , 13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26."},"title":"Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation","author":[{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"external_id":{"arxiv":["2204.13459"]},"article_processing_charge":"No","acknowledgement":"We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful discussions about different variants of the problem. This work is supported by the European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025, the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant 470029389 (FlexNets), 2021–2024.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"25","publication":"SIROCCO 2023: Structural Information and Communication Complexity ","year":"2023","doi":"10.1007/978-3-031-32733-9_26","date_published":"2023-05-25T00:00:00Z","date_created":"2023-07-16T22:01:12Z","page":"576-594","_id":"13238","status":"public","type":"conference","conference":{"name":"SIROCCO: Structural Information and Communication Complexity","start_date":"2023-06-06","location":"Alcala de Henares, Spain","end_date":"2023-06-09"},"date_updated":"2023-11-30T10:54:51Z","department":[{"_id":"KrPi"},{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."}],"month":"05","intvolume":" 13892","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.13459"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783031327322"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"14506","relation":"dissertation_contains"}]},"volume":13892,"ec_funded":1},{"file_date_updated":"2023-11-23T10:30:08Z","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"ddc":["000"],"supervisor":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"date_updated":"2023-11-30T10:54:51Z","status":"public","type":"dissertation","_id":"14506","related_material":{"record":[{"id":"9969","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"13238"},{"id":"14490","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"file_name":"thesis_yeo.zip","date_created":"2023-11-23T10:29:55Z","creator":"cchlebak","file_size":3037720,"date_updated":"2023-11-23T10:29:55Z","checksum":"521c72818d720a52b377207b2ee87b6a","file_id":"14598","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed"},{"file_name":"thesis_yeo.pdf","date_created":"2023-11-23T10:30:08Z","file_size":2717256,"date_updated":"2023-11-23T10:30:08Z","creator":"cchlebak","success":1,"checksum":"0ed5d16899687aecf13d843c9878c9f2","file_id":"14599","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios.","lang":"eng"}],"title":"Advances in efficiency and privacy in payment channel network analysis","author":[{"last_name":"Yeo","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506","apa":"Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506","chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria."},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_published":"2023-11-10T00:00:00Z","doi":"10.15479/14506","date_created":"2023-11-10T08:10:43Z","page":"162","day":"10","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","oa":1},{"acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant 2020388). It was also partially supported by NCN Grant 2019/35/B/ST6/04138 and ERC Grant 885666.","oa":1,"quality_controlled":"1","publisher":"IEEE","publication":"43rd International Conference on Distributed Computing Systems","day":"11","year":"2023","date_created":"2023-11-05T23:00:54Z","date_published":"2023-10-11T00:00:00Z","doi":"10.1109/ICDCS57875.2023.00037","page":"603-613","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13, doi:10.1109/ICDCS57875.2023.00037.","short":"Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.","ieee":"Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation games,” in 43rd International Conference on Distributed Computing Systems, Hong Kong, China, 2023, vol. 2023, pp. 603–613.","apa":"Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning creation games. In 43rd International Conference on Distributed Computing Systems (Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037","ama":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In: 43rd International Conference on Distributed Computing Systems. Vol 2023. IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037","chicago":"Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo. “Lightning Creation Games.” In 43rd International Conference on Distributed Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037.","ista":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games. 43rd International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems vol. 2023, 603–613."},"title":"Lightning creation games","article_processing_charge":"No","external_id":{"arxiv":["2306.16006"]},"author":[{"full_name":"Avarikioti, Zeta","last_name":"Avarikioti","first_name":"Zeta"},{"full_name":"Lizurej, Tomasz","last_name":"Lizurej","first_name":"Tomasz"},{"full_name":"Michalak, Tomasz","last_name":"Michalak","first_name":"Tomasz"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"oa_version":"Preprint","abstract":[{"text":"Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium.","lang":"eng"}],"intvolume":" 2023","month":"10","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.16006","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9798350339864"],"eissn":["2575-8411"]},"related_material":{"record":[{"status":"public","id":"14506","relation":"dissertation_contains"}]},"volume":2023,"_id":"14490","status":"public","conference":{"location":"Hong Kong, China","end_date":"2023-07-21","start_date":"2023-07-18","name":"ICDCS: International Conference on Distributed Computing Systems"},"type":"conference","date_updated":"2023-11-30T10:54:51Z","department":[{"_id":"KrPi"}]},{"supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"date_updated":"2023-11-30T10:55:13Z","ddc":["530"],"file_date_updated":"2023-11-24T11:57:46Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"_id":"12726","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"12745","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","relation":"main_file","access_level":"closed","content_type":"application/pdf","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_name":"Thesis_Riedl_2023.pdf","date_created":"2023-03-23T12:49:23Z","creator":"cchlebak","file_size":63734746,"date_updated":"2023-11-24T11:57:46Z"},{"creator":"cchlebak","file_size":339473651,"date_updated":"2023-09-24T22:30:03Z","file_name":"Thesis_Riedl_2023_source.rar","date_created":"2023-03-23T12:54:34Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/octet-stream","file_id":"12746","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"10703","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10791","status":"public"},{"status":"public","id":"7932","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"461","status":"public"},{"relation":"new_edition","status":"public","id":"14530"}]},"abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"None","alternative_title":["ISTA Thesis"],"month":"03","citation":{"mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"article_processing_charge":"No","title":"Synchronization in collectively moving active matter","has_accepted_license":"1","year":"2023","day":"23","page":"260","date_published":"2023-03-23T00:00:00Z","doi":"10.15479/at:ista:12726","date_created":"2023-03-15T13:22:13Z","publisher":"Institute of Science and Technology Austria"},{"page":"260","date_created":"2023-11-15T09:59:03Z","doi":"10.15479/14530","date_published":"2023-11-16T00:00:00Z","year":"2023","has_accepted_license":"1","day":"16","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl"}],"title":"Synchronization in collectively moving active matter","citation":{"chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"10703","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10791","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7932"},{"status":"public","id":"461","relation":"part_of_dissertation"},{"relation":"old_edition","status":"public","id":"12726"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"14536","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-11-15T09:52:54Z","file_name":"Thesis_Riedl_2023_corr.pdf","date_updated":"2023-11-15T09:52:54Z","file_size":36743942,"creator":"mriedl"}],"alternative_title":["ISTA Thesis"],"month":"11","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. ","lang":"eng"}],"oa_version":"Updated Version","file_date_updated":"2023-11-15T09:52:54Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"date_updated":"2023-11-30T10:55:13Z","supervisor":[{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"ddc":["530","570"],"type":"dissertation","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"status":"public","_id":"14530"},{"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"file_date_updated":"2023-11-22T09:46:06Z","ddc":["530"],"date_updated":"2023-11-30T10:56:04Z","supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","_id":"14547","related_material":{"record":[{"id":"10851","status":"public","relation":"part_of_dissertation"},{"id":"13264","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"db0c37d213bc002125bd59690e9db246","file_id":"14548","creator":"pduc","date_updated":"2023-11-22T09:46:06Z","file_size":34828019,"date_created":"2023-11-17T13:36:44Z","file_name":"Phan_Thesis_pdfa.pdf"},{"creator":"pduc","date_updated":"2023-11-17T13:47:54Z","file_size":279319709,"date_created":"2023-11-17T13:44:53Z","file_name":"dissertation_src.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","file_id":"14549"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"title":"Resonant microwave spectroscopy of Al-InAs","article_processing_charge":"No","author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","full_name":"Phan, Duc T","last_name":"Phan"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547","apa":"Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","mla":"Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547.","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547."},"date_created":"2023-11-17T13:45:26Z","doi":"10.15479/14547","date_published":"2023-11-16T00:00:00Z","page":"80","day":"16","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"article_number":"064032","title":"Gate-tunable superconductor-semiconductor parametric amplifier","article_processing_charge":"No","external_id":{"isi":["001012022600004"],"arxiv":["2206.05746"]},"author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan","full_name":"Phan, Duc T"},{"id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","first_name":"Paul","last_name":"Falthansl-Scheinecker","full_name":"Falthansl-Scheinecker, Paul"},{"full_name":"Mishra, Umang","last_name":"Mishra","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","first_name":"Umang"},{"last_name":"Strickland","full_name":"Strickland, W. M.","first_name":"W. M."},{"full_name":"Langone, D.","last_name":"Langone","first_name":"D."},{"first_name":"J.","last_name":"Shabani","full_name":"Shabani, J."},{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","ieee":"D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical Society, 2023.","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.19.064032","ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:10.1103/PhysRevApplied.19.064032.","ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.19.064032."},"oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","date_created":"2023-07-23T22:01:12Z","date_published":"2023-06-09T00:00:00Z","doi":"10.1103/PhysRevApplied.19.064032","publication":"Physical Review Applied","day":"09","year":"2023","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"13264","department":[{"_id":"AnHi"},{"_id":"OnHo"}],"date_updated":"2023-11-30T10:56:03Z","intvolume":" 19","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.05746"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"issue":"6","related_material":{"record":[{"relation":"dissertation_contains","id":"14547","status":"public"}]},"volume":19,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2331-7019"]}}]