[{"date_published":"2024-09-01T00:00:00Z","ddc":["000"],"author":[{"full_name":"Braun, Pirmin","last_name":"Braun","first_name":"Pirmin"},{"first_name":"Niklas","last_name":"Hahn","id":"0a01c7b2-b823-11ed-9928-cc3f874f9ffd","full_name":"Hahn, Niklas"},{"first_name":"Martin","full_name":"Hoefer, Martin","last_name":"Hoefer"},{"full_name":"Schecker, Conrad","last_name":"Schecker","first_name":"Conrad"}],"OA_place":"publisher","date_updated":"2025-09-08T08:00:42Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2203.01084"],"isi":["001260448100001"]},"month":"09","oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","doi":"10.1016/j.artint.2024.104171","publication_identifier":{"issn":["0004-3702"]},"acknowledgement":"Hahn gratefully acknowledges the support of GIF grant I-1419-118.4/2017. Hoefer gratefully acknowledges the support of GIF grant I-1419-118.4/2017, DFG Research Unit ADYN (project number 411362735), and DFG grant Ho 3831/9-1 (project number 514505843).","article_number":"104171","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"MoHe"}],"isi":1,"arxiv":1,"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","date_created":"2025-01-09T10:45:24Z","file_name":"2024_ArtificialIntelligence_Braun.pdf","success":1,"creator":"dernst","date_updated":"2025-01-09T10:45:24Z","checksum":"f02a56bc7ea88f41fcc68968e4ceddf3","file_size":772226,"file_id":"18806","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"In a delegation problem, a principal P with commitment power tries to pick one out of 𝑛 options.\r\nEach option is drawn independently from a known distribution. Instead of inspecting the options\r\nherself, P delegates the information acquisition to a rational and self-interested agent A. After\r\ninspection, A proposes one of the options, and P can accept or reject.\r\nDelegation is a classic setting in economic information design with many prominent applications,\r\nbut the computational problems are only poorly understood. In this paper, we study a natural\r\nonline variant of delegation, in which the agent searches through the options in an online fashion.\r\nFor each option, he has to irrevocably decide if he wants to propose the current option or discard\r\nit, before seeing information on the next option(s). How can we design algorithms for P that\r\napproximate the utility of her best option in hindsight?\r\nWe show that in general P can obtain a Θ(1∕𝑛)-approximation and extend this result to ratios\r\nof Θ(𝑘∕𝑛) in case (1) A has a lookahead of 𝑘 rounds, or (2) A can propose up to 𝑘 different\r\noptions. We provide fine-grained bounds independent of 𝑛 based on three parameters. If the ratio\r\nof maximum and minimum utility for A is bounded by a factor đ›Œ, we obtain an Ω(loglog đ›Œâˆ• log đ›Œ)-\r\napproximation algorithm, and we show that this is best possible. Additionally, if P cannot\r\ndistinguish options with the same value for herself, we show that ratios polynomial in 1âˆ•đ›Œ cannot\r\nbe avoided. If there are at most đ›œ different utility values for A, we show a Θ(1âˆ•đ›œ)-approximation.\r\nIf the utilities of P and A for each option are related by a factor đ›Ÿ, we obtain an Ω(1∕ log đ›Ÿ)-\r\napproximation, where 𝑂(log log đ›Ÿâˆ• log đ›Ÿ) is best possible."}],"_id":"17188","intvolume":" 334","status":"public","publication":"Artificial Intelligence","publisher":"Elsevier","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","volume":334,"day":"01","date_created":"2024-06-30T22:01:05Z","year":"2024","corr_author":"1","quality_controlled":"1","article_type":"original","oa":1,"citation":{"apa":"Braun, P., Hahn, N., Hoefer, M., & Schecker, C. (2024). Delegated online search. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2024.104171","chicago":"Braun, Pirmin, Niklas Hahn, Martin Hoefer, and Conrad Schecker. “Delegated Online Search.” Artificial Intelligence. Elsevier, 2024. https://doi.org/10.1016/j.artint.2024.104171.","ama":"Braun P, Hahn N, Hoefer M, Schecker C. Delegated online search. Artificial Intelligence. 2024;334. doi:10.1016/j.artint.2024.104171","ista":"Braun P, Hahn N, Hoefer M, Schecker C. 2024. Delegated online search. Artificial Intelligence. 334, 104171.","short":"P. Braun, N. Hahn, M. Hoefer, C. Schecker, Artificial Intelligence 334 (2024).","ieee":"P. Braun, N. Hahn, M. Hoefer, and C. Schecker, “Delegated online search,” Artificial Intelligence, vol. 334. Elsevier, 2024.","mla":"Braun, Pirmin, et al. “Delegated Online Search.” Artificial Intelligence, vol. 334, 104171, Elsevier, 2024, doi:10.1016/j.artint.2024.104171."},"file_date_updated":"2025-01-09T10:45:24Z","title":"Delegated online search","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"date_published":"2024-09-01T00:00:00Z","author":[{"first_name":"Chris S.","full_name":"Hanson, Chris S.","last_name":"Hanson"},{"first_name":"Srijan B","orcid":"0000-0003-0896-7972","last_name":"Das","full_name":"Das, Srijan B","id":"9ce7c423-dacf-11ed-8942-e09c6cb27149"},{"full_name":"Mani, Prasad","last_name":"Mani","first_name":"Prasad"},{"last_name":"Hanasoge","full_name":"Hanasoge, Shravan","first_name":"Shravan"},{"full_name":"Sreenivasan, Katepalli R.","last_name":"Sreenivasan","first_name":"Katepalli R."}],"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"date_updated":"2025-09-08T08:04:56Z","language":[{"iso":"eng"}],"external_id":{"isi":["001254181700001"]},"month":"09","scopus_import":"1","oa_version":"None","doi":"10.1038/s41550-024-02304-w","publication_identifier":{"eissn":["2397-3366"]},"acknowledgement":"We thank F. J. Simons for the codes for computing Slepian functions,\r\nM. Rempel and R. Cameron for their insights into solar convection, J.\r\nW. Lord for the numerical simulations and J. Naranjo for his help with\r\nthe NYUAD NetDRMS system. This research was carried out with the\r\nHigh Performance Computing resources at NYUAD. The datasets were\r\nprepared in the data centre at the Center for Space Science of NYUAD.\r\nThis research is based upon work supported by Tamkeen under the\r\nNYUAD Research Institute (Grant Nos G1502 and CASS to C.S.H,\r\nS.H. and K.R.S.). S.H. acknowledges funding from the Department\r\nof Atomic Energy, India. K.R.S. and S.H. acknowledge support from\r\nthe Ofice of Sponsored Research of King Abdullah University of\r\nScience and Technology (Award No. OSR-CRG2020-4342). S.B.D.\r\nacknowledges funding from the Elisabeth H. and F. A. Dahlen Award\r\n2022 by the Department of Geosciences, Princeton University. S.B.D.\r\nalso acknowledges funding from the European Union’s Horizon 2020\r\nresearch and innovation programme under a Marie SkƂodowska-Curie\r\ngrant (Grant Agreement No. 101034413). Some data products were\r\nprocessed and downloaded from the German Data Center for SDO,\r\nwhich is funded by the German Aerospace Center (DLR Grant No.\r\n500L1701).","department":[{"_id":"LiBu"}],"isi":1,"publication_status":"published","status":"public","_id":"17189","intvolume":" 8","abstract":[{"text":"Supergranules, which are solar flow features with a lateral scale of 30,000–40,000 km and a lifetime of ~24 h, form a prominent component of the Sun’s convective spectrum. However, their internal flows, which can be probed only by helioseismology, are not well understood. We analyse dopplergrams recorded by the Solar Dynamics Observatory satellite to identify and characterize ~23,000 supergranules. We find that the vertical flows peak at a depth of ~10,000 km, and remain invariant over the full range of lateral supergranular scales, contrary to numerical predictions. We also infer that, within the local seismic resolution (≳5,000 km), downflows are ~40% weaker than upflows, indicating an apparent mass-flux imbalance. This may imply that the descending flows also comprise plumes, which maintain the mass balance but are simply too small to be detected by seismic waves. These results challenge the widely used mixing-length description of solar convection.","lang":"eng"}],"publisher":"Springer Nature","publication":"Nature Astronomy","article_processing_charge":"No","OA_type":"closed access","type":"journal_article","day":"01","page":"1088-1101","volume":8,"year":"2024","date_created":"2024-06-30T22:01:05Z","article_type":"original","quality_controlled":"1","citation":{"apa":"Hanson, C. S., Das, S. B., Mani, P., Hanasoge, S., & Sreenivasan, K. R. (2024). Supergranular-scale solar convection not explained by mixing-length theory. Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-024-02304-w","chicago":"Hanson, Chris S., Srijan B Das, Prasad Mani, Shravan Hanasoge, and Katepalli R. Sreenivasan. “Supergranular-Scale Solar Convection Not Explained by Mixing-Length Theory.” Nature Astronomy. Springer Nature, 2024. https://doi.org/10.1038/s41550-024-02304-w.","ama":"Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. Supergranular-scale solar convection not explained by mixing-length theory. Nature Astronomy. 2024;8:1088-1101. doi:10.1038/s41550-024-02304-w","ista":"Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. 2024. Supergranular-scale solar convection not explained by mixing-length theory. Nature Astronomy. 8, 1088–1101.","mla":"Hanson, Chris S., et al. “Supergranular-Scale Solar Convection Not Explained by Mixing-Length Theory.” Nature Astronomy, vol. 8, Springer Nature, 2024, pp. 1088–101, doi:10.1038/s41550-024-02304-w.","ieee":"C. S. Hanson, S. B. Das, P. Mani, S. Hanasoge, and K. R. Sreenivasan, “Supergranular-scale solar convection not explained by mixing-length theory,” Nature Astronomy, vol. 8. Springer Nature, pp. 1088–1101, 2024.","short":"C.S. Hanson, S.B. Das, P. Mani, S. Hanasoge, K.R. Sreenivasan, Nature Astronomy 8 (2024) 1088–1101."},"title":"Supergranular-scale solar convection not explained by mixing-length theory","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"oa":1,"citation":{"ista":"Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M. 2024. Brillouin zones of integer lattices and their perturbations. SIAM Journal on Discrete Mathematics. 38(2), 1784–1807.","ama":"Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M. Brillouin zones of integer lattices and their perturbations. SIAM Journal on Discrete Mathematics. 2024;38(2):1784-1807. doi:10.1137/22M1489071","chicago":"Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafaris, Teresa Heiss, Morteza Saghafiant, and Mathijs Wintraecken. “Brillouin Zones of Integer Lattices and Their Perturbations.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/22M1489071.","apa":"Edelsbrunner, H., Garber, A., Ghafaris, M., Heiss, T., Saghafiant, M., & Wintraecken, M. (2024). Brillouin zones of integer lattices and their perturbations. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/22M1489071","short":"H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, M. Wintraecken, SIAM Journal on Discrete Mathematics 38 (2024) 1784–1807.","ieee":"H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, and M. Wintraecken, “Brillouin zones of integer lattices and their perturbations,” SIAM Journal on Discrete Mathematics, vol. 38, no. 2. Society for Industrial and Applied Mathematics, pp. 1784–1807, 2024.","mla":"Edelsbrunner, Herbert, et al. “Brillouin Zones of Integer Lattices and Their Perturbations.” SIAM Journal on Discrete Mathematics, vol. 38, no. 2, Society for Industrial and Applied Mathematics, 2024, pp. 1784–807, doi:10.1137/22M1489071."},"date_created":"2024-06-30T22:01:05Z","year":"2024","corr_author":"1","quality_controlled":"1","article_type":"original","title":"Brillouin zones of integer lattices and their perturbations","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17190","abstract":[{"lang":"eng","text":"For a locally finite set, 𝐮⊆ℝ𝑑\r\n, the 𝑘\r\nth Brillouin zone of 𝑎∈𝐮\r\n is the region of points đ‘„âˆˆâ„đ‘‘\r\n for which â€–đ‘„âˆ’đ‘Žâ€–\r\n is the 𝑘\r\nth smallest among the Euclidean distances between đ‘„\r\n and the points in 𝐮\r\n. If 𝐮\r\n is a lattice, the 𝑘\r\nth Brillouin zones of the points in 𝐮\r\n are translates of each other, and together they tile space. Depending on the value of 𝑘\r\n, they express medium- or long-range order in the set. We study fundamental geometric and combinatorial properties of Brillouin zones, focusing on the integer lattice and its perturbations. Our results include the stability of a Brillouin zone under perturbations, a linear upper bound on the number of chambers in a zone for lattices in ℝ2\r\n, and the convergence of the maximum volume of a chamber to zero for the integer lattice."}],"intvolume":" 38","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.01077"}],"arxiv":1,"publication_status":"published","type":"journal_article","volume":38,"page":"1784-1807","day":"07","publication":"SIAM Journal on Discrete Mathematics","issue":"2","publisher":"Society for Industrial and Applied Mathematics","article_processing_charge":"No","publication_identifier":{"issn":["0895-4801"]},"acknowledgement":"The second author is partially supported by the Alexander von Humboldt Foundation. The sixth author is supported by the European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement 754411, and by Austrian Science Fund(FWF) grant M-3073. All other authors are supported by European Research Council (ERC) grant 788183, by the Wittgenstein Prize, by Austrian Science Fund (FWF) grant Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF) grant I 02979-N35.","doi":"10.1137/22M1489071","isi":1,"department":[{"_id":"HeEd"}],"date_updated":"2025-09-08T08:06:04Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"},{"grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"}],"date_published":"2024-06-07T00:00:00Z","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Garber, Alexey","last_name":"Garber","first_name":"Alexey"},{"first_name":"Mohadese","full_name":"Ghafaris, Mohadese","last_name":"Ghafaris"},{"first_name":"Teresa","orcid":"0000-0002-1780-2689","last_name":"Heiss","full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Morteza","last_name":"Saghafiant","full_name":"Saghafiant, Morteza"},{"last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","first_name":"Mathijs"}],"month":"06","scopus_import":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"external_id":{"isi":["001292728600001"],"arxiv":["2204.01077"]}},{"date_updated":"2025-09-08T08:06:56Z","author":[{"id":"d993a7b2-292f-11ed-aaac-fb045a912e31","last_name":"Lembo","full_name":"Lembo, Sergio","orcid":"0000-0002-2253-8771","first_name":"Sergio"},{"first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"date_published":"2024-06-21T00:00:00Z","oa_version":"None","scopus_import":"1","month":"06","external_id":{"pmid":["38907047"],"isi":["001251509300001"]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1529-2908"],"eissn":["1529-2916"]},"doi":"10.1038/s41590-024-01881-2","department":[{"_id":"MiSi"}],"isi":1,"status":"public","_id":"17191","pmid":1,"abstract":[{"text":"Dendritic cells migrate to and from lymph nodes in response to chemokine gradients.Data now show that steady-state migration of these cells can be triggered by a mechanosensitive pathway.","lang":"eng"}],"intvolume":" 25","publication_status":"published","day":"21","page":"1131–1132 ","volume":25,"type":"journal_article","article_processing_charge":"No","publisher":"Springer Nature","publication":"Nature Immunology","citation":{"mla":"Lembo, Sergio, and Michael K. Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” Nature Immunology, vol. 25, Springer Nature, 2024, pp. 1131–1132, doi:10.1038/s41590-024-01881-2.","short":"S. Lembo, M.K. Sixt, Nature Immunology 25 (2024) 1131–1132.","ieee":"S. Lembo and M. K. Sixt, “Nuclear squeezing wakes up dendritic cells,” Nature Immunology, vol. 25. Springer Nature, pp. 1131–1132, 2024.","apa":"Lembo, S., & Sixt, M. K. (2024). Nuclear squeezing wakes up dendritic cells. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-024-01881-2","chicago":"Lembo, Sergio, and Michael K Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” Nature Immunology. Springer Nature, 2024. https://doi.org/10.1038/s41590-024-01881-2.","ama":"Lembo S, Sixt MK. Nuclear squeezing wakes up dendritic cells. Nature Immunology. 2024;25:1131–1132. doi:10.1038/s41590-024-01881-2","ista":"Lembo S, Sixt MK. 2024. Nuclear squeezing wakes up dendritic cells. Nature Immunology. 25, 1131–1132."},"article_type":"letter_note","corr_author":"1","quality_controlled":"1","year":"2024","date_created":"2024-06-30T22:01:05Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Nuclear squeezing wakes up dendritic cells"},{"external_id":{"isi":["001289270900045"]},"conference":{"location":"Denver, Colorado","start_date":"2024-07-28","end_date":"2024-08-01"},"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","month":"07","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Ly, MickaĂ«l","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"MickaĂ«l"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546"}],"ddc":["516"],"date_published":"2024-07-01T00:00:00Z","date_updated":"2025-09-08T08:29:09Z","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"article_number":"78","isi":1,"department":[{"_id":"ChWo"}],"doi":"10.1145/3658194","acknowledgement":"We thank Gianmarco Cherchi for his help in tailoring the Mesh Booleans code for this project, Stefan Jeschke for his help with the photographs, Malina Strugaru and Aleksei Kalinov for their help with the samples, and the anonymous reviewers as well as the members of the ISTA Visual Computing Group for their feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"article_processing_charge":"Yes (via OA deal)","publisher":"Association for Computing Machinery","issue":"4","publication":"Transactions on Graphics","keyword":["Topology Optimization","Mass Moments","Computational Geometry"],"day":"01","volume":43,"type":"journal_article","file":[{"file_id":"17204","access_level":"open_access","checksum":"0dc9f5a6422b8a49a79026900f349ee5","file_size":7225150,"success":1,"creator":"chafner","date_updated":"2024-07-05T12:05:17Z","content_type":"application/pdf","relation":"main_file","date_created":"2024-07-05T12:05:17Z","file_name":"sif-final.pdf"},{"checksum":"cde433c6a40688d5f1187fb5721f6f94","file_size":397262,"access_level":"open_access","file_id":"17205","file_name":"sif-supp-final.pdf","date_created":"2024-07-05T12:06:03Z","content_type":"application/pdf","relation":"supplementary_material","date_updated":"2024-07-05T12:06:03Z","creator":"chafner"},{"file_id":"17276","access_level":"open_access","title":"Submission Video","file_size":170001305,"checksum":"c0457a09c2ab9a1c2935c995dcc84907","creator":"chafner","date_updated":"2024-07-17T09:29:13Z","relation":"supplementary_material","content_type":"video/mp4","file_name":"sif-video-final.mp4","date_created":"2024-07-17T09:29:13Z"}],"publication_status":"published","status":"public","_id":"17203","intvolume":" 43","abstract":[{"lang":"eng","text":"The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found.\r\n\r\nIn this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes.\r\n\r\nThis insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments","file_date_updated":"2024-07-17T09:29:13Z","article_type":"original","corr_author":"1","quality_controlled":"1","year":"2024","date_created":"2024-07-05T12:08:57Z","citation":{"chicago":"Hafner, Christian, MickaĂ«l Ly, and Chris Wojtan. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658194.","apa":"Hafner, C., Ly, M., & Wojtan, C. (2024). Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. Denver, Colorado: Association for Computing Machinery. https://doi.org/10.1145/3658194","ista":"Hafner C, Ly M, Wojtan C. 2024. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 43(4), 78.","ama":"Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 2024;43(4). doi:10.1145/3658194","ieee":"C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments,” Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024.","short":"C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024).","mla":"Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics, vol. 43, no. 4, 78, Association for Computing Machinery, 2024, doi:10.1145/3658194."},"oa":1},{"language":[{"iso":"eng"}],"external_id":{"pmid":["38941551"],"isi":["001258359900001"]},"month":"06","oa_version":"Published Version","scopus_import":"1","date_published":"2024-06-28T00:00:00Z","author":[{"orcid":"0000-0003-0371-9339","first_name":"Louise","full_name":"Fouqueau, Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","last_name":"Fouqueau"},{"orcid":"0000-0003-0951-3112","first_name":"Jitka","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova"}],"project":[{"name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"date_updated":"2025-09-08T08:08:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"department":[{"_id":"NiBa"}],"doi":"10.1093/jeb/voae067","publication_identifier":{"eissn":["1420-9101"]},"acknowledgement":"This research was funded by the Austrian Science Fund (FWF), project doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896 and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton for their insightful comments on the earlier drafts, and to John Carchrae for his valuable contribution in refining phrasing and enhancing clarity. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","publisher":"Oxford University Press","issue":"6","publication":"Journal of evolutionary biology","article_processing_charge":"No","type":"journal_article","page":"579-587","day":"28","volume":37,"publication_status":"published","status":"public","_id":"17207","intvolume":" 37","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1093/jeb/voae067","open_access":"1"}],"title":"Eco-evolutionary dynamics in changing environments: Integrating theory with data","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","date_created":"2024-07-07T22:01:04Z","article_type":"letter_note","quality_controlled":"1","oa":1,"citation":{"apa":"Fouqueau, L., & Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae067","chicago":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae067.","ama":"Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 2024;37(6):579-587. doi:10.1093/jeb/voae067","ista":"Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.","mla":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:10.1093/jeb/voae067.","ieee":"L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” Journal of evolutionary biology, vol. 37, no. 6. Oxford University Press, pp. 579–587, 2024.","short":"L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587."}},{"citation":{"short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657485.","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Denver, United States, 2024.","chicago":"Chen, Yi-Lu, MickaĂ«l Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657485.","apa":"Chen, Y.-L., Ly, M., & Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Denver, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657485","ista":"Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657485"},"oa":1,"corr_author":"1","quality_controlled":"1","year":"2024","date_created":"2024-07-10T11:06:20Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Primal-dual non-smooth friction for rigid body animation","file_date_updated":"2024-07-10T11:03:58Z","status":"public","_id":"17214","abstract":[{"lang":"eng","text":"Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies."}],"file":[{"date_updated":"2024-07-10T11:03:14Z","creator":"yichen","success":1,"file_name":"sig24_friction_authors.pdf","date_created":"2024-07-10T11:03:14Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"17215","file_size":47309472,"checksum":"b8b203ed09e3995ba0d7e6a76288663a"},{"access_level":"open_access","file_id":"17216","file_size":10518286,"checksum":"89d81b397b4b6469d828808a68b70820","date_updated":"2024-07-10T11:03:12Z","creator":"yichen","success":1,"date_created":"2024-07-10T11:03:12Z","file_name":"sig24_friction_supplementary.pdf","relation":"main_file","content_type":"application/pdf"},{"access_level":"open_access","file_id":"17217","file_size":71789192,"checksum":"7123deed34a5456810e7b5336a31c657","date_updated":"2024-07-10T11:03:51Z","creator":"yichen","success":1,"date_created":"2024-07-10T11:03:51Z","file_name":"friction_paper_extra_video_finished.mp4","content_type":"video/mp4","relation":"main_file"},{"file_size":280610763,"checksum":"e606fc1ae8f2610ce3b4421566800b45","access_level":"open_access","file_id":"17218","file_name":"friction_paper_video_finished.mp4","date_created":"2024-07-10T11:03:58Z","content_type":"video/mp4","relation":"main_file","date_updated":"2024-07-10T11:03:58Z","success":1,"creator":"yichen"}],"publication_status":"published","keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"day":"01","type":"conference","article_processing_charge":"Yes (via OA deal)","publisher":"Association for Computing Machinery","publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","acknowledgement":"We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","publication_identifier":{"isbn":["9798400705250"]},"doi":"10.1145/3641519.3657485","isi":1,"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"date_updated":"2025-09-08T08:54:38Z","author":[{"first_name":"Yi-Lu","last_name":"Chen","full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"last_name":"Ly","full_name":"Ly, MickaĂ«l","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"MickaĂ«l"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546"}],"ddc":["621","531","006"],"date_published":"2024-07-01T00:00:00Z","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","month":"07","external_id":{"isi":["001282218200091"]},"conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","location":"Denver, United States","start_date":"2024-07-28","end_date":"2024-08-01"},"language":[{"iso":"eng"}]},{"isi":1,"department":[{"_id":"VaKa"}],"doi":"10.3934/dcds.2024059","publication_identifier":{"eissn":["1553-5231"],"issn":["1078-0947"]},"language":[{"iso":"eng"}],"external_id":{"isi":["001230091000001"]},"month":"11","oa_version":"Published Version","scopus_import":"1","date_published":"2024-11-01T00:00:00Z","author":[{"first_name":"Corentin","full_name":"Fiorebe, Corentin","id":"06619f18-9070-11eb-847d-d1ee780bd88b","last_name":"Fiorebe"}],"date_updated":"2025-10-16T11:53:22Z","title":"Examples of projective billiards with open sets of periodic orbits","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","date_created":"2024-07-14T22:01:10Z","article_type":"original","quality_controlled":"1","corr_author":"1","oa":1,"citation":{"ista":"Fiorebe C. 2024. Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. 44(11), 3287–3301.","ama":"Fiorebe C. Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. 2024;44(11):3287-3301. doi:10.3934/dcds.2024059","chicago":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” Discrete and Continuous Dynamical Systems- Series A. American Institute of Mathematical Sciences, 2024. https://doi.org/10.3934/dcds.2024059.","apa":"Fiorebe, C. (2024). Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. American Institute of Mathematical Sciences. https://doi.org/10.3934/dcds.2024059","ieee":"C. Fiorebe, “Examples of projective billiards with open sets of periodic orbits,” Discrete and Continuous Dynamical Systems- Series A, vol. 44, no. 11. American Institute of Mathematical Sciences, pp. 3287–3301, 2024.","mla":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” Discrete and Continuous Dynamical Systems- Series A, vol. 44, no. 11, American Institute of Mathematical Sciences, 2024, pp. 3287–301, doi:10.3934/dcds.2024059.","short":"C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024) 3287–3301."},"publisher":"American Institute of Mathematical Sciences","publication":"Discrete and Continuous Dynamical Systems- Series A","issue":"11","article_processing_charge":"No","OA_type":"free access","type":"journal_article","page":"3287-3301","day":"01","volume":44,"publication_status":"published","status":"public","intvolume":" 44","_id":"17231","abstract":[{"lang":"eng","text":"In the class of projective billiards, which contains the usual billiards, we exhibit counter-examples to Ivrii's conjecture, which states that in any planar billiard with smooth boundary the set of periodic orbits has zero measure. The counter-examples are polygons admitting a 2-parameters family of n-periodic orbits, with n being either 3 or any even integer greater than 4."}],"main_file_link":[{"url":"https://doi.org/10.3934/dcds.2024059","open_access":"1"}]},{"status":"public","_id":"17233","intvolume":" 14","pmid":1,"abstract":[{"lang":"eng","text":"CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines GatewayÂź and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite GatewayÂź Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene."}],"file":[{"file_id":"17242","access_level":"open_access","checksum":"c8671c0ad483da6407cb16cc3fef1990","file_size":2896048,"creator":"dernst","success":1,"date_updated":"2024-07-16T06:16:11Z","content_type":"application/pdf","relation":"main_file","file_name":"2024_BioProtocol_Li.pdf","date_created":"2024-07-16T06:16:11Z"}],"publication_status":"published","type":"journal_article","day":"05","volume":14,"publisher":"Bio-Protocol","publication":"Bio-protocol","issue":"13","article_processing_charge":"Yes","oa":1,"citation":{"ama":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 2024;14(13). doi:10.21769/BioProtoc.5029","ista":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. 2024. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 14(13), e5029.","apa":"LI, Z., Huard, J., Bayer, E. M., & Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/BioProtoc.5029","chicago":"LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and ValĂ©rie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” Bio-Protocol. Bio-Protocol, 2024. https://doi.org/10.21769/BioProtoc.5029.","mla":"LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” Bio-Protocol, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:10.21769/BioProtoc.5029.","short":"Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024).","ieee":"Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” Bio-protocol, vol. 14, no. 13. Bio-Protocol, 2024."},"year":"2024","date_created":"2024-07-14T22:01:11Z","article_type":"original","quality_controlled":"1","title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis","file_date_updated":"2024-07-16T06:16:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-03-06T10:28:18Z","ddc":["570"],"date_published":"2024-07-05T00:00:00Z","author":[{"first_name":"Ziqiang","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","last_name":"Li","full_name":"Li, Ziqiang"},{"first_name":"Jennifer","full_name":"Huard, Jennifer","last_name":"Huard"},{"last_name":"Bayer","full_name":"Bayer, Emmanuelle M.","first_name":"Emmanuelle M."},{"last_name":"Wattelet-Boyer","full_name":"Wattelet-Boyer, ValĂ©rie","first_name":"ValĂ©rie"}],"month":"07","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["39007160"]},"publication_identifier":{"eissn":["2331-8325"]},"acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING to E.M.B.).","doi":"10.21769/BioProtoc.5029","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"MiSi"}],"article_number":"e5029"},{"publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"acknowledgement":"We thank the anonymous referee for the helpful comments. B.W. and J.L. acknowledge support from JWST-GO04233.009-A. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project No. 562 (First Light at Cosmic Dawn: Exploiting the James Webb Space Telescope Revolution). This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The JWST data presented in this Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed can be accessed via doi:10.17909/3a4n-9p88. Computations for this research were performed on the Pennsylvania State University’s Institute for Computational and Data Sciences’ Roar supercomputer. This publication made use of the NASA Astrophysical Data System for bibliographic information. \r\nFacilities: HST (ACS, WFC3), JWST (NIRCam, NIRSpec). Software: Astropy (Astropy Collaboration et al. 2013, 2018, 2022), dynesty (Speagle 2020), EAzY (Brammer et al. 2008),\r\nemcee (Foreman-Mackey et al. 2013), Matplotlib (Hunter 2007), msaexp (Brammer 2023b), msafit (de Graaff et al. 2024a), NumPy (Harris et al. 2020), Prospector (Johnson et al. 2021), Python-FSPS (Johnson et al. 2023).","doi":"10.3847/2041-8213/ad55f7","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"JoMa"}],"article_number":"L13","date_updated":"2025-09-08T08:10:21Z","ddc":["520"],"date_published":"2024-07-01T00:00:00Z","author":[{"first_name":"Bingjie","full_name":"Wang, Bingjie","last_name":"Wang"},{"first_name":"Joel","full_name":"Leja, Joel","last_name":"Leja"},{"first_name":"Anna","full_name":"De Graaff, Anna","last_name":"De Graaff"},{"full_name":"Brammer, Gabriel B.","last_name":"Brammer","first_name":"Gabriel B."},{"first_name":"Andrea","full_name":"Weibel, Andrea","last_name":"Weibel"},{"last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter","first_name":"Pieter"},{"first_name":"Josephine F.W.","full_name":"Baggen, Josephine F.W.","last_name":"Baggen"},{"full_name":"Suess, Katherine A.","last_name":"Suess","first_name":"Katherine A."},{"first_name":"Jenny E.","full_name":"Greene, Jenny E.","last_name":"Greene"},{"first_name":"Rachel","full_name":"Bezanson, Rachel","last_name":"Bezanson"},{"last_name":"Cleri","full_name":"Cleri, Nikko J.","first_name":"Nikko J."},{"last_name":"Hirschmann","full_name":"Hirschmann, Michaela","first_name":"Michaela"},{"first_name":"Ivo","last_name":"LabbĂ©","full_name":"LabbĂ©, Ivo"},{"last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"first_name":"Ian","last_name":"Mcconachie","full_name":"Mcconachie, Ian"},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"last_name":"Nelson","full_name":"Nelson, Erica","first_name":"Erica"},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"last_name":"Setton","full_name":"Setton, David J.","first_name":"David J."},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."}],"month":"07","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["2405.01473"],"isi":["001257903200001"]},"oa":1,"citation":{"mla":"Wang, Bingjie, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∌ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” Astrophysical Journal Letters, vol. 969, no. 1, L13, IOP Publishing, 2024, doi:10.3847/2041-8213/ad55f7.","short":"B. Wang, J. Leja, A. De Graaff, G.B. Brammer, A. Weibel, P. Van Dokkum, J.F.W. Baggen, K.A. Suess, J.E. Greene, R. Bezanson, N.J. Cleri, M. Hirschmann, I. LabbĂ©, J.J. Matthee, I. Mcconachie, R.P. Naidu, E. Nelson, P.A. Oesch, D.J. Setton, C.C. Williams, Astrophysical Journal Letters 969 (2024).","ieee":"B. Wang et al., “RUBIES: Evolved stellar populations with extended formation histories at z ∌ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,” Astrophysical Journal Letters, vol. 969, no. 1. IOP Publishing, 2024.","ista":"Wang B, Leja J, De Graaff A, Brammer GB, Weibel A, Van Dokkum P, Baggen JFW, Suess KA, Greene JE, Bezanson R, Cleri NJ, Hirschmann M, LabbĂ© I, Matthee JJ, Mcconachie I, Naidu RP, Nelson E, Oesch PA, Setton DJ, Williams CC. 2024. RUBIES: Evolved stellar populations with extended formation histories at z ∌ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 969(1), L13.","ama":"Wang B, Leja J, De Graaff A, et al. RUBIES: Evolved stellar populations with extended formation histories at z ∌ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 2024;969(1). doi:10.3847/2041-8213/ad55f7","chicago":"Wang, Bingjie, Joel Leja, Anna De Graaff, Gabriel B. Brammer, Andrea Weibel, Pieter Van Dokkum, Josephine F.W. Baggen, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∌ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” Astrophysical Journal Letters. IOP Publishing, 2024. https://doi.org/10.3847/2041-8213/ad55f7.","apa":"Wang, B., Leja, J., De Graaff, A., Brammer, G. B., Weibel, A., Van Dokkum, P., 
 Williams, C. C. (2024). RUBIES: Evolved stellar populations with extended formation histories at z ∌ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ad55f7"},"year":"2024","date_created":"2024-07-14T22:01:11Z","article_type":"original","quality_controlled":"1","title":"RUBIES: Evolved stellar populations with extended formation histories at z ∌ 7-8 in candidate massive galaxies identified with JWST/NIRSpec","file_date_updated":"2024-07-16T06:24:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","_id":"17234","abstract":[{"text":"The identification of red, apparently massive galaxies at z > 7 in early James Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line compared to standard models of galaxy growth. A major uncertainty in the interpretation is whether the red colors are caused by evolved stellar populations, dust, or other effects such as emission lines or active galactic nuclei (AGNs). Here we show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4 ÎŒm and require formation histories extending hundreds of millions of years into the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies also show broad Balmer lines, with HÎČ FWHM > 2500 km s−1, suggesting that dust-reddened AGNs contribute to, or even dominate, the spectral energy distributions of these galaxies at λrest ≳ 0.6 ÎŒm. All three galaxies have relatively narrow [O iii] lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically relaxed, inclined disks. Yet the inferred masses also remain highly uncertain. We model the high-quality spectra using Prospector to decompose the continuum into stellar and AGN components and explore limiting cases in stellar/AGN contribution. This produces a wide range of possible stellar masses, spanning M⋆ ∌ 109−1011M⊙. Nevertheless, all fits suggest a very early and rapid formation, most of which follow with a truncation in star formation. Potential origins and evolutionary tracks for these objects are discussed, from the cores of massive galaxies to low-mass galaxies with overmassive black holes. Intriguingly, we find all of these explanations to be incomplete; deeper and redder data are needed to understand the physics of these systems.","lang":"eng"}],"intvolume":" 969","arxiv":1,"file":[{"file_size":3273303,"checksum":"bb1a6725586df12e745d091b5778bb2b","access_level":"open_access","file_id":"17243","file_name":"2024_AstrophysicalJourn_Wang.pdf","date_created":"2024-07-16T06:24:29Z","content_type":"application/pdf","relation":"main_file","date_updated":"2024-07-16T06:24:29Z","success":1,"creator":"dernst"}],"publication_status":"published","DOAJ_listed":"1","type":"journal_article","day":"01","volume":969,"publisher":"IOP Publishing","issue":"1","publication":"Astrophysical Journal Letters","article_processing_charge":"Yes"},{"quality_controlled":"1","article_type":"original","date_created":"2024-07-14T22:01:11Z","year":"2024","citation":{"ama":"KohopÀÀ K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting thin films. APL Materials. 2024;12(7). doi:10.1063/5.0202851","ista":"KohopÀÀ K, Ronzani A, Jabdaraghi RN, Bera A, Ribeiro M, Hazra D, Senior JL, Prunnila M, Govenius J, Lehtinen JS, Kemppinen A. 2024. Effect of ion irradiation on superconducting thin films. APL Materials. 12(7), 071101.","apa":"KohopÀÀ, K., Ronzani, A., Jabdaraghi, R. N., Bera, A., Ribeiro, M., Hazra, D., 
 Kemppinen, A. (2024). Effect of ion irradiation on superconducting thin films. APL Materials. AIP Publishing. https://doi.org/10.1063/5.0202851","chicago":"KohopÀÀ, Katja, Alberto Ronzani, Robab Najafi Jabdaraghi, Arijit Bera, MĂĄrio Ribeiro, Dibyendu Hazra, Jorden L Senior, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” APL Materials. AIP Publishing, 2024. https://doi.org/10.1063/5.0202851.","ieee":"K. KohopÀÀ et al., “Effect of ion irradiation on superconducting thin films,” APL Materials, vol. 12, no. 7. AIP Publishing, 2024.","short":"K. KohopÀÀ, A. Ronzani, R.N. Jabdaraghi, A. Bera, M. Ribeiro, D. Hazra, J.L. Senior, M. Prunnila, J. Govenius, J.S. Lehtinen, A. Kemppinen, APL Materials 12 (2024).","mla":"KohopÀÀ, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” APL Materials, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:10.1063/5.0202851."},"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-07-16T06:30:30Z","title":"Effect of ion irradiation on superconducting thin films","ec_funded":1,"publication_status":"published","file":[{"file_name":"2024_APLMaterial_Kohopaa.pdf","date_created":"2024-07-16T06:30:30Z","relation":"main_file","content_type":"application/pdf","date_updated":"2024-07-16T06:30:30Z","creator":"dernst","success":1,"file_size":9408198,"checksum":"32a5cdf0ea9c937f806b6039f3219917","access_level":"open_access","file_id":"17244"}],"_id":"17235","abstract":[{"lang":"eng","text":"We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors."}],"intvolume":" 12","status":"public","article_processing_charge":"Yes","publication":"APL Materials","issue":"7","publisher":"AIP Publishing","volume":12,"day":"01","type":"journal_article","doi":"10.1063/5.0202851","acknowledgement":"We thank J. A. Sauls for useful discussions. For funding of our research project, we acknowledge the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement Nos. 862660/Quantum e-leaps, 899558/aCryComm, 766853/EFINED, and ECSEL programme 101007322/MatQu. This project has also received funding from Business Finland through Quantum Technologies Industrial (QuTI) Project No. 128291 and from Research Council of Finland through Grant Nos. 310909, 350220 and Finnish Quantum Flagship project 359284. This work was performed as part of the Research Council of Finland Centres of Excellence program (Project Nos. 336817, 336819, 352934, and 352935). We also acknowledge funding from an internal strategic innovation project of VTT related to the development of quantum computing technologies. This research was supported by the Scientific Service Units of IST Austria through resources provided by Electron Microscopy Facility. J. Senior acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie SkƂodowska-Curie Grant Agreement No. 754411. A. Ronzani acknowledges funding from Research Council of Finland (Research Fellowship Project No. 356542).","publication_identifier":{"eissn":["2166-532X"]},"article_number":"071101","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"AnHi"}],"isi":1,"author":[{"first_name":"Katja","full_name":"KohopÀÀ, Katja","last_name":"KohopÀÀ"},{"first_name":"Alberto","full_name":"Ronzani, Alberto","last_name":"Ronzani"},{"first_name":"Robab Najafi","last_name":"Jabdaraghi","full_name":"Jabdaraghi, Robab Najafi"},{"full_name":"Bera, Arijit","last_name":"Bera","first_name":"Arijit"},{"last_name":"Ribeiro","full_name":"Ribeiro, MĂĄrio","first_name":"MĂĄrio"},{"first_name":"Dibyendu","last_name":"Hazra","full_name":"Hazra, Dibyendu"},{"orcid":"0000-0002-0672-9295","first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L"},{"first_name":"Mika","last_name":"Prunnila","full_name":"Prunnila, Mika"},{"first_name":"Joonas","last_name":"Govenius","full_name":"Govenius, Joonas"},{"full_name":"Lehtinen, Janne S.","last_name":"Lehtinen","first_name":"Janne S."},{"first_name":"Antti","last_name":"Kemppinen","full_name":"Kemppinen, Antti"}],"date_published":"2024-07-01T00:00:00Z","ddc":["530"],"date_updated":"2025-09-08T08:10:58Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"external_id":{"isi":["001260942200003"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"07"},{"doi":"10.1145/3626183.3659969","publication_identifier":{"issn":["1548-6109"],"isbn":["9798400704161"]},"department":[{"_id":"VlKo"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"ddc":["510"],"date_published":"2024-06-17T00:00:00Z","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"}],"date_updated":"2026-01-21T09:46:25Z","OA_place":"publisher","conference":{"start_date":"2024-06-17","end_date":"2024-06-21","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Nantes, France"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2307.00115"],"isi":["001253331900044"]},"month":"06","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","year":"2024","date_created":"2024-07-14T22:01:11Z","corr_author":"1","quality_controlled":"1","oa":1,"citation":{"ista":"Kolmogorov V. 2024. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 403–414.","ama":"Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In: Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2024:403-414. doi:10.1145/3626183.3659969","chicago":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” In Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, 403–14. Association for Computing Machinery, 2024. https://doi.org/10.1145/3626183.3659969.","apa":"Kolmogorov, V. (2024). A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 403–414). Nantes, France: Association for Computing Machinery. https://doi.org/10.1145/3626183.3659969","short":"V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–414.","mla":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–14, doi:10.1145/3626183.3659969.","ieee":"V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut,” in Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Nantes, France, 2024, pp. 403–414."},"title":"A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut","file_date_updated":"2024-07-16T06:38:08Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"relation":"extended_version","id":"21007","status":"public"}]},"arxiv":1,"file":[{"checksum":"6ca18ac8508719dbd5d5735f4c991af2","file_size":1116166,"access_level":"open_access","file_id":"17245","file_name":"2024_SPAA_Kolmogorov.pdf","date_created":"2024-07-16T06:38:08Z","relation":"main_file","content_type":"application/pdf","date_updated":"2024-07-16T06:38:08Z","success":1,"creator":"dernst"}],"publication_status":"published","status":"public","_id":"17236","abstract":[{"text":"Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/Δ)-approximation using O(nΔ logO(1) n) maxflows for any Δ∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain \"chaining\" algorithm that combines results of multiple calls to the maxflow algorithm.\r\nWe present an alternative approach that avoids solving the multicommodity flow problem and instead computes \"violating paths\". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/Δ)-approximation via O(logO(1) n) maxflows using O(nΔ) processors.\r\nWe also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.","lang":"eng"}],"publisher":"Association for Computing Machinery","publication":"Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","type":"conference","day":"17","page":"403-414"},{"date_updated":"2025-06-04T07:23:23Z","date_published":"2024-06-01T00:00:00Z","author":[{"full_name":"Reynes, Lauric","last_name":"Reynes","first_name":"Lauric"},{"last_name":"Fouqueau","full_name":"Fouqueau, Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise","orcid":"0000-0003-0371-9339"},{"first_name":"Didier","last_name":"Aurelle","full_name":"Aurelle, Didier"},{"first_name":"Stephane","last_name":"Mauger","full_name":"Mauger, Stephane"},{"last_name":"Destombe","full_name":"Destombe, Christophe","first_name":"Christophe"},{"first_name":"Myriam","full_name":"Valero, Myriam","last_name":"Valero"}],"month":"06","oa_version":"Preprint","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["38629140"],"arxiv":["2404.14003"]},"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"acknowledgement":"This work was funded by the EU project MARFOR Biodiversa/004/2015. L.F. was additionally funded by the Region Bretagne (ARED 2017 REEALG) and the NOMIS Foundation. The project leading to this publication has received funding from the EC2CO (CNRS) fund and from the European FEDER Fund under project 1166-39417.\r\nThis work is especially dedicated to the memory of Gernot Glöckner who contributed to the sequencing of Laminaria digitata genome and passed away in very recent time. The authors thank the ABiMS platform of the Roscoff biological station (http://abims.sb-roscoff.fr) for providing the HPC resources that contributed to the search results reported in this document. We also acknowledge the staff of the “Cluster de calcul intensif HPC” Platform of the OSU Institut PythĂ©as (Aix-Marseille UniversitĂ©, INSU-CNRS) for providing the computing facilities.","doi":"10.1093/jeb/voae048","department":[{"_id":"NiBa"}],"status":"public","pmid":1,"_id":"17237","abstract":[{"lang":"eng","text":"The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change."}],"intvolume":" 37","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2404.14003"}],"arxiv":1,"publication_status":"published","type":"journal_article","page":"677-692","day":"01","volume":37,"publisher":"Oxford University Press","issue":"6","publication":"Journal of Evolutionary Biology","article_processing_charge":"No","oa":1,"citation":{"ieee":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, and M. Valero, “Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations,” Journal of Evolutionary Biology, vol. 37, no. 6. Oxford University Press, pp. 677–692, 2024.","short":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal of Evolutionary Biology 37 (2024) 677–692.","mla":"Reynes, Lauric, et al. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:10.1093/jeb/voae048.","apa":"Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., & Valero, M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. Journal of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae048","chicago":"Reynes, Lauric, Louise Fouqueau, Didier Aurelle, Stephane Mauger, Christophe Destombe, and Myriam Valero. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” Journal of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae048.","ama":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. Journal of Evolutionary Biology. 2024;37(6):677-692. doi:10.1093/jeb/voae048","ista":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. 2024. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. Journal of Evolutionary Biology. 37(6), 677–692."},"year":"2024","date_created":"2024-07-14T22:01:12Z","article_type":"original","quality_controlled":"1","title":"Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","file":[{"file_size":1194263,"checksum":"94e6b68bddf6cadcec29c7f41647359f","file_id":"17241","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2024-07-15T09:45:25Z","file_name":"2024_JourEvolutionaryBiology_Barton.pdf","success":1,"creator":"dernst","date_updated":"2024-07-15T09:45:25Z"}],"_id":"17238","pmid":1,"intvolume":" 37","abstract":[{"lang":"eng","text":"We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace."}],"status":"public","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Evolutionary Biology","issue":"6","publisher":"Oxford University Press","volume":37,"page":"605-615","day":"01","type":"journal_article","corr_author":"1","quality_controlled":"1","article_type":"review","date_created":"2024-07-14T22:01:12Z","year":"2024","citation":{"apa":"Barton, N. H. (2024). Limits to species’ range: The tension between local and global adaptation. Journal of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae052","chicago":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” Journal of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae052.","ama":"Barton NH. Limits to species’ range: The tension between local and global adaptation. Journal of Evolutionary Biology. 2024;37(6):605-615. doi:10.1093/jeb/voae052","ista":"Barton NH. 2024. Limits to species’ range: The tension between local and global adaptation. Journal of Evolutionary Biology. 37(6), 605–615.","short":"N.H. Barton, Journal of Evolutionary Biology 37 (2024) 605–615.","mla":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 605–15, doi:10.1093/jeb/voae052.","ieee":"N. H. Barton, “Limits to species’ range: The tension between local and global adaptation,” Journal of Evolutionary Biology, vol. 37, no. 6. Oxford University Press, pp. 605–615, 2024."},"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-07-15T09:45:25Z","title":"Limits to species' range: The tension between local and global adaptation","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"date_published":"2024-06-01T00:00:00Z","ddc":["570"],"date_updated":"2025-09-08T08:08:41Z","project":[{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"external_id":{"pmid":["38683160"],"isi":["001225323900001"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"06","doi":"10.1093/jeb/voae052","acknowledgement":"This work was supported by a grant from the ERC, 101055327, “HaplotypeStructure”. I thank Himani Sachdeva, Michal Hledik, Jitka Polechova, and the reviewers for their helpful comments.","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"department":[{"_id":"NiBa"}]},{"acknowledgement":"We are grateful to Nancy Forde (Simon Fraser University) for her motivating comments. Financial support from the Ministerio de Ciencia, InnovaciĂłn y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged. A.Ć . and K.K. acknowledge support from the Royal Society University Research Fellowship and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant No. 585 80296).","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"doi":"10.1021/acsnano.4c03839","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"AnSa"}],"date_updated":"2025-12-16T09:01:10Z","project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"OA_place":"publisher","author":[{"full_name":"Garcia-Sacristan, Clara","last_name":"Garcia-Sacristan","first_name":"Clara"},{"full_name":"Gisbert, Victor G.","last_name":"Gisbert","first_name":"Victor G."},{"full_name":"Klein, Kevin","last_name":"Klein","id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398","first_name":"Kevin"},{"full_name":"Ć arić, Anđela","last_name":"Ć arić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Garcia","full_name":"Garcia, Ricardo","first_name":"Ricardo"}],"ddc":["540"],"date_published":"2024-07-16T00:00:00Z","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","month":"07","external_id":{"pmid":["38958189"],"isi":["001263155500001"]},"language":[{"iso":"eng"}],"citation":{"chicago":"Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Ć arić, and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” ACS Nano. American Chemical Society, 2024. https://doi.org/10.1021/acsnano.4c03839.","apa":"Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Ć arić, A., & Garcia, R. (2024). In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.4c03839","ista":"Garcia-Sacristan C, Gisbert VG, Klein K, Ć arić A, Garcia R. 2024. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 18(28), 18485–18492.","ama":"Garcia-Sacristan C, Gisbert VG, Klein K, Ć arić A, Garcia R. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 2024;18(28):18485-18492. doi:10.1021/acsnano.4c03839","mla":"Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” ACS Nano, vol. 18, no. 28, American Chemical Society, 2024, pp. 18485–92, doi:10.1021/acsnano.4c03839.","ieee":"C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Ć arić, and R. Garcia, “In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,” ACS Nano, vol. 18, no. 28. American Chemical Society, pp. 18485–18492, 2024.","short":"C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Ć arić, R. Garcia, ACS Nano 18 (2024) 18485–18492."},"oa":1,"article_type":"original","quality_controlled":"1","year":"2024","date_created":"2024-07-14T22:01:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"title":"In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures","file_date_updated":"2025-01-09T12:06:48Z","status":"public","abstract":[{"text":"Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes.","lang":"eng"}],"_id":"17239","intvolume":" 18","pmid":1,"file":[{"file_id":"18808","access_level":"open_access","checksum":"b7e9ce718e92f568bcb3810e8e28e458","file_size":10036838,"success":1,"creator":"dernst","date_updated":"2025-01-09T12:06:48Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_ACSNano_GarciaSacristan.pdf","date_created":"2025-01-09T12:06:48Z"}],"publication_status":"published","page":"18485-18492","day":"16","volume":18,"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","publisher":"American Chemical Society","publication":"ACS Nano","issue":"28"},{"OA_place":"repository","date_updated":"2025-09-08T08:28:31Z","project":[{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288"},{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022"}],"author":[{"last_name":"Vercruysse","full_name":"Vercruysse, ElĂ©onore","first_name":"ElĂ©onore"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"BrĂŒckner","full_name":"BrĂŒckner, David","orcid":"0000-0001-7205-2975","first_name":"David"},{"first_name":"Manuel","last_name":"GĂłmez-GonzĂĄlez","full_name":"GĂłmez-GonzĂĄlez, Manuel"},{"first_name":"Alexandre","last_name":"Remson","full_name":"Remson, Alexandre"},{"first_name":"Marine","last_name":"Luciano","full_name":"Luciano, Marine"},{"first_name":"Yohalie","last_name":"Kalukula","full_name":"Kalukula, Yohalie"},{"full_name":"Rossetti, Leone","last_name":"Rossetti","first_name":"Leone"},{"first_name":"Xavier","full_name":"Trepat, Xavier","last_name":"Trepat"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"last_name":"Gabriele","full_name":"Gabriele, Sylvain","first_name":"Sylvain"}],"date_published":"2024-09-01T00:00:00Z","scopus_import":"1","oa_version":"Preprint","month":"09","external_id":{"isi":["001250246200004"]},"language":[{"iso":"eng"}],"acknowledgement":"M.L., E.V. and S.G. acknowledge funding from the European Regional Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS; Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23), the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen, ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow (Aspirant FNRS) and Postdoctoral Researcher (ChargĂ©e de Recherches FNRS), respectively. E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund for Research Training in Industry and Agriculture (FRIA). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie SkƂodowska-Curie Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS foundation as a NOMIS fellow and by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen Center for Physics, which is supported by the National Science Foundation (Grant No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia (Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research Council (Grant No. Adv-883739), FundaciĂł la MaratĂł de TV3 (201903-30-31-32), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade and Business.","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"doi":"10.1038/s41567-024-02532-x","department":[{"_id":"EdHa"}],"isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.07.17.500364"}],"abstract":[{"text":"The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments.","lang":"eng"}],"_id":"17269","intvolume":" 20","status":"public","publication_status":"published","volume":20,"page":"1492-1500","day":"01","type":"journal_article","OA_type":"green","article_processing_charge":"No","publication":"Nature Physics","publisher":"Springer Nature","citation":{"mla":"Vercruysse, ElĂ©onore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:10.1038/s41567-024-02532-x.","ieee":"E. Vercruysse et al., “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” Nature Physics, vol. 20. Springer Nature, pp. 1492–1500, 2024.","short":"E. Vercruysse, D. BrĂŒckner, M. GĂłmez-GonzĂĄlez, A. Remson, M. Luciano, Y. Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20 (2024) 1492–1500.","ista":"Vercruysse E, BrĂŒckner D, GĂłmez-GonzĂĄlez M, Remson A, Luciano M, Kalukula Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.","ama":"Vercruysse E, BrĂŒckner D, GĂłmez-GonzĂĄlez M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 2024;20:1492-1500. doi:10.1038/s41567-024-02532-x","chicago":"Vercruysse, ElĂ©onore, David BrĂŒckner, Manuel GĂłmez-GonzĂĄlez, Alexandre Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02532-x.","apa":"Vercruysse, E., BrĂŒckner, D., GĂłmez-GonzĂĄlez, M., Remson, A., Luciano, M., Kalukula, Y., 
 Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02532-x"},"oa":1,"corr_author":"1","quality_controlled":"1","article_type":"original","date_created":"2024-07-16T12:32:17Z","year":"2024","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/a-railroad-of-cells/"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","ec_funded":1},{"title":"Stability for the logarithmic Sobolev inequality","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","date_created":"2024-07-21T22:01:00Z","article_type":"original","quality_controlled":"1","corr_author":"1","oa":1,"citation":{"ieee":"G. Brigati, J. Dolbeault, and N. Simonov, “Stability for the logarithmic Sobolev inequality,” Journal of Functional Analysis, vol. 287, no. 8. Elsevier, 2024.","mla":"Brigati, Giovanni, et al. “Stability for the Logarithmic Sobolev Inequality.” Journal of Functional Analysis, vol. 287, no. 8, 110562, Elsevier, 2024, doi:10.1016/j.jfa.2024.110562.","short":"G. Brigati, J. Dolbeault, N. Simonov, Journal of Functional Analysis 287 (2024).","ama":"Brigati G, Dolbeault J, Simonov N. Stability for the logarithmic Sobolev inequality. Journal of Functional Analysis. 2024;287(8). doi:10.1016/j.jfa.2024.110562","ista":"Brigati G, Dolbeault J, Simonov N. 2024. Stability for the logarithmic Sobolev inequality. Journal of Functional Analysis. 287(8), 110562.","apa":"Brigati, G., Dolbeault, J., & Simonov, N. (2024). Stability for the logarithmic Sobolev inequality. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110562","chicago":"Brigati, Giovanni, Jean Dolbeault, and Nikita Simonov. “Stability for the Logarithmic Sobolev Inequality.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110562."},"publisher":"Elsevier","publication":"Journal of Functional Analysis","issue":"8","article_processing_charge":"No","OA_type":"green","type":"journal_article","day":"15","volume":287,"arxiv":1,"publication_status":"published","status":"public","_id":"17277","abstract":[{"lang":"eng","text":"This paper is devoted to stability results for the Gaussian logarithmic Sobolev inequality, with explicit stability constants.\r\n\r\n"}],"intvolume":" 287","main_file_link":[{"open_access":"1","url":"10.48550/arXiv.2303.12926"}],"article_number":"110562","isi":1,"department":[{"_id":"JaMa"}],"doi":"10.1016/j.jfa.2024.110562","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"acknowledgement":"The authors thank Max Fathi and Pierre Cardaliaguet for fruitful discussions and Emanuel Indrei for stimulating interactions. They also thank an anonymous referee for useful comments and suggestions which have led to an improvement of the manuscript. They also want to express their gratitude to the managing editor, L. Gross, for his encouragements and questions. G.B. has been funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 754362. This work has been (partially) supported by the Project Conviviality ANR-23-CE40-0003 of the French National Research Agency.","language":[{"iso":"eng"}],"external_id":{"isi":["001271814000001"],"arxiv":["2303.12926"]},"month":"10","oa_version":"Preprint","scopus_import":"1","date_published":"2024-10-15T00:00:00Z","author":[{"first_name":"Giovanni","full_name":"Brigati, Giovanni","last_name":"Brigati","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1"},{"first_name":"Jean","last_name":"Dolbeault","full_name":"Dolbeault, Jean"},{"full_name":"Simonov, Nikita","last_name":"Simonov","first_name":"Nikita"}],"date_updated":"2025-09-08T08:25:34Z","OA_place":"repository"},{"acknowledgement":"B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No. EP/P020259/1).","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"doi":"10.1063/5.0217232","isi":1,"department":[{"_id":"BiCh"},{"_id":"GradSch"}],"article_number":"034111","date_updated":"2025-09-08T08:26:09Z","author":[{"first_name":"Xiaoyu","id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","full_name":"Wang, Xiaoyu","last_name":"Wang"},{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"}],"date_published":"2024-07-14T00:00:00Z","oa_version":"Preprint","scopus_import":"1","month":"07","external_id":{"isi":["001281819100016"],"pmid":["39007379"],"arxiv":["2405.02216"]},"language":[{"iso":"eng"}],"citation":{"short":"X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).","ieee":"X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures,” Journal of Chemical Physics, vol. 161, no. 3. AIP Publishing, 2024.","mla":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal of Chemical Physics, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:10.1063/5.0217232.","ama":"Wang X, Cheng B. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 2024;161(3). doi:10.1063/5.0217232","ista":"Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 161(3), 034111.","apa":"Wang, X., & Cheng, B. (2024). Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0217232","chicago":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0217232."},"oa":1,"article_type":"original","corr_author":"1","quality_controlled":"1","year":"2024","date_created":"2024-07-21T22:01:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"link":[{"url":"https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0","relation":"software"}]},"title":"Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.02216"}],"status":"public","_id":"17278","pmid":1,"abstract":[{"text":"An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult due to the complexities and convergence problems of Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes, or lack thereof, in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes and reveal that they tend to form when the mixture components have similar boiling points and strong interactions.","lang":"eng"}],"intvolume":" 161","publication_status":"published","arxiv":1,"day":"14","volume":161,"type":"journal_article","article_processing_charge":"No","publisher":"AIP Publishing","publication":"Journal of Chemical Physics","issue":"3"},{"title":"Rescuing T cells from stiff tumors","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-21T22:01:00Z","year":"2024","corr_author":"1","quality_controlled":"1","article_type":"review","citation":{"apa":"Avellaneda SarriĂł, M., & Sixt, M. K. (2024). Rescuing T cells from stiff tumors. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2024.06.011","chicago":"Avellaneda SarriĂł, Mario, and Michael K Sixt. “Rescuing T Cells from Stiff Tumors.” Cell Chemical Biology. Elsevier, 2024. https://doi.org/10.1016/j.chembiol.2024.06.011.","ama":"Avellaneda SarriĂł M, Sixt MK. Rescuing T cells from stiff tumors. Cell Chemical Biology. 2024;31(7):1242-1243. doi:10.1016/j.chembiol.2024.06.011","ista":"Avellaneda SarriĂł M, Sixt MK. 2024. Rescuing T cells from stiff tumors. Cell Chemical Biology. 31(7), 1242–1243.","ieee":"M. Avellaneda SarriĂł and M. K. Sixt, “Rescuing T cells from stiff tumors,” Cell Chemical Biology, vol. 31, no. 7. Elsevier, pp. 1242–1243, 2024.","mla":"Avellaneda SarriĂł, Mario, and Michael K. Sixt. “Rescuing T Cells from Stiff Tumors.” Cell Chemical Biology, vol. 31, no. 7, Elsevier, 2024, pp. 1242–43, doi:10.1016/j.chembiol.2024.06.011.","short":"M. Avellaneda SarriĂł, M.K. Sixt, Cell Chemical Biology 31 (2024) 1242–1243."},"publication":"Cell Chemical Biology","issue":"7","publisher":"Elsevier","article_processing_charge":"No","type":"journal_article","volume":31,"day":"18","page":"1242-1243","publication_status":"published","_id":"17279","intvolume":" 31","pmid":1,"abstract":[{"lang":"eng","text":"In a recent issue of Cell, Zhang et al.1 demonstrate that mechanical features of a solid tumor can drive T cells into dysfunctionality and identify pathways that revert this “exhausted” state."}],"status":"public","department":[{"_id":"MiSi"}],"isi":1,"doi":"10.1016/j.chembiol.2024.06.011","publication_identifier":{"issn":["2451-9456"],"eissn":["2451-9448"]},"language":[{"iso":"eng"}],"external_id":{"pmid":["39029454"],"isi":["001275725000001"]},"month":"07","scopus_import":"1","oa_version":"None","date_published":"2024-07-18T00:00:00Z","author":[{"full_name":"Avellaneda SarriĂł, Mario","last_name":"Avellaneda SarriĂł","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","orcid":"0000-0001-6406-524X","first_name":"Mario"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"date_updated":"2025-09-08T08:27:03Z"},{"publication_identifier":{"eissn":["2375-2548"]},"acknowledgement":"Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration with Pawel Pelczar at the center for transgenic models at the University of Basel, Switzerland. We thank the imaging core facility (IMCF, University of Basel) and in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM microscope.\r\nThis work was supported by a grant from the Swiss National Science Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1, 16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative Medicines Initiatives from the European Commission joint undertaking under grant agreement No 777394.","doi":"10.1126/sciadv.adk5462","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"department":[{"_id":"RySh"},{"_id":"PreCl"}],"article_number":"adk5462","date_updated":"2025-09-08T08:15:54Z","OA_place":"publisher","ddc":["570"],"date_published":"2024-07-12T00:00:00Z","author":[{"last_name":"FrĂŒh","full_name":"FrĂŒh, Simon","first_name":"Simon"},{"first_name":"Sami","full_name":"Boudkkazi, Sami","last_name":"Boudkkazi"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","first_name":"Peter","orcid":"0000-0002-3509-1948"},{"last_name":"Sereikaite","full_name":"Sereikaite, Vita","first_name":"Vita"},{"full_name":"Chen, Li Yuan","last_name":"Chen","first_name":"Li Yuan"},{"first_name":"Diego","full_name":"Fernandez-Fernandez, Diego","last_name":"Fernandez-Fernandez"},{"last_name":"Rem","full_name":"Rem, Pascal D.","first_name":"Pascal D."},{"last_name":"Ulrich","full_name":"Ulrich, Daniel","first_name":"Daniel"},{"first_name":"Jochen","last_name":"Schwenk","full_name":"Schwenk, Jochen"},{"first_name":"Ziyang","last_name":"Chen","full_name":"Chen, Ziyang"},{"last_name":"Monnier","full_name":"Monnier, Elodie Le","first_name":"Elodie Le"},{"full_name":"Fritzius, Thorsten","last_name":"Fritzius","first_name":"Thorsten"},{"full_name":"Innocenti, Sabrina M.","last_name":"Innocenti","first_name":"Sabrina M."},{"last_name":"Besseyrias","full_name":"Besseyrias, ValĂ©rie","first_name":"ValĂ©rie"},{"first_name":"Luca","full_name":"TrovĂČ, Luca","last_name":"TrovĂČ"},{"full_name":"Stawarski, Michal","last_name":"Stawarski","first_name":"Michal"},{"first_name":"Emanuela","last_name":"Argilli","full_name":"Argilli, Emanuela"},{"full_name":"Sherr, Elliott H.","last_name":"Sherr","first_name":"Elliott H."},{"first_name":"Bregje","last_name":"Van Bon","full_name":"Van Bon, Bregje"},{"first_name":"Erik Jan","full_name":"Kamsteeg, Erik Jan","last_name":"Kamsteeg"},{"last_name":"Iascone","full_name":"Iascone, Maria","first_name":"Maria"},{"full_name":"Pilotta, Alba","last_name":"Pilotta","first_name":"Alba"},{"first_name":"Maria R.","full_name":"CutrĂŹ, Maria R.","last_name":"CutrĂŹ"},{"last_name":"Azamian","full_name":"Azamian, Mahshid S.","first_name":"Mahshid S."},{"last_name":"HernĂĄndez-GarcĂ­a","full_name":"HernĂĄndez-GarcĂ­a, AndrĂ©s","first_name":"AndrĂ©s"},{"first_name":"Seema R.","full_name":"Lalani, Seema R.","last_name":"Lalani"},{"first_name":"Jill A.","last_name":"Rosenfeld","full_name":"Rosenfeld, Jill A."},{"last_name":"Zhao","full_name":"Zhao, Xiaonan","first_name":"Xiaonan"},{"first_name":"Tiphanie P.","last_name":"Vogel","full_name":"Vogel, Tiphanie P."},{"first_name":"Herda","last_name":"Ona","full_name":"Ona, Herda"},{"full_name":"Scott, Daryl A.","last_name":"Scott","first_name":"Daryl A."},{"last_name":"Scheiffele","full_name":"Scheiffele, Peter","first_name":"Peter"},{"first_name":"Kristian","last_name":"StrĂžmgaard","full_name":"StrĂžmgaard, Kristian"},{"first_name":"Mehdi","last_name":"Tafti","full_name":"Tafti, Mehdi"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"first_name":"Bernd","last_name":"Fakler","full_name":"Fakler, Bernd"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"Bernhard","full_name":"Bettler, Bernhard","last_name":"Bettler"}],"month":"07","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001280159000022"],"pmid":["38985877"]},"oa":1,"citation":{"ama":"FrĂŒh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 2024;10(28). doi:10.1126/sciadv.adk5462","ista":"FrĂŒh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM, Besseyrias V, TrovĂČ L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ, Iascone M, Pilotta A, CutrĂŹ MR, Azamian MS, HernĂĄndez-GarcĂ­a A, Lalani SR, Rosenfeld JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, StrĂžmgaard K, Tafti M, Gassmann M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 10(28), adk5462.","apa":"FrĂŒh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez, D., 
 Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk5462","chicago":"FrĂŒh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk5462.","short":"S. FrĂŒh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez, P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti, V. Besseyrias, L. TrovĂČ, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J. Kamsteeg, M. Iascone, A. Pilotta, M.R. CutrĂŹ, M.S. Azamian, A. HernĂĄndez-GarcĂ­a, S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele, K. StrĂžmgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science Advances 10 (2024).","ieee":"S. FrĂŒh et al., “Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release,” Science Advances, vol. 10, no. 28. American Association for the Advancement of Science, 2024.","mla":"FrĂŒh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” Science Advances, vol. 10, no. 28, adk5462, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk5462."},"year":"2024","date_created":"2024-07-21T22:01:01Z","article_type":"original","quality_controlled":"1","title":"Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release","file_date_updated":"2024-07-22T06:29:27Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","_id":"17280","intvolume":" 10","abstract":[{"text":"Adherens junction–associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to Îł-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function AJAP1 variants.","lang":"eng"}],"pmid":1,"file":[{"creator":"dernst","success":1,"date_updated":"2024-07-22T06:29:27Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_ScienceAdv_FrĂŒh.pdf","date_created":"2024-07-22T06:29:27Z","file_id":"17287","access_level":"open_access","checksum":"9cbc4501fcd4ba1c0811fd244031422b","file_size":7241489}],"publication_status":"published","DOAJ_listed":"1","type":"journal_article","day":"12","volume":10,"publisher":"American Association for the Advancement of Science","publication":"Science Advances","issue":"28","article_processing_charge":"Yes","OA_type":"gold"}]