[{"publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"citation":{"ama":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. 2023;127(51):10950-10959. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959.","mla":"Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>.","ista":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 127(51), 10950–10959.","ieee":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.","chicago":"Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>.","apa":"Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., &#38; Rivoire, O. (2023). On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>"},"issue":"51","article_type":"original","external_id":{"isi":["001134068000001"],"arxiv":["2312.15940"]},"oa":1,"acknowledgement":"We acknowledge funding from ANR-22-CE06-0037-02. This work has received funding from the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754387.","status":"public","year":"2023","_id":"14831","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":127,"page":"10950-10959","abstract":[{"lang":"eng","text":"Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis."}],"arxiv":1,"date_created":"2024-01-18T07:47:11Z","oa_version":"Preprint","publisher":"American Chemical Society","publication":"The Journal of Physical Chemistry B","department":[{"_id":"AnSa"}],"title":"On kinetic constraints that catalysis imposes on elementary processes","isi":1,"month":"12","language":[{"iso":"eng"}],"day":"13","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.15940","open_access":"1"}],"intvolume":"       127","quality_controlled":"1","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"article_processing_charge":"No","doi":"10.1021/acs.jpcb.3c04627","date_updated":"2024-01-23T07:58:27Z","author":[{"full_name":"Sakref, Yann","first_name":"Yann","last_name":"Sakref"},{"last_name":"Muñoz Basagoiti","orcid":"0000-0003-1483-1457","first_name":"Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","full_name":"Muñoz Basagoiti, Maitane"},{"first_name":"Zorana","last_name":"Zeravcic","full_name":"Zeravcic, Zorana"},{"first_name":"Olivier","last_name":"Rivoire","full_name":"Rivoire, Olivier"}],"date_published":"2023-12-13T00:00:00Z"},{"acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","oa":1,"status":"public","issue":"1","article_type":"original","citation":{"ieee":"S. Stankowski <i>et al.</i>, “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1. Oxford University Press, 2023.","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>.","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>","ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. 2023;2(1). doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>."},"publication_identifier":{"eissn":["2752-938X"]},"volume":2,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14833","has_accepted_license":"1","year":"2023","abstract":[{"text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.","lang":"eng"}],"publication":"Evolutionary Journal of the Linnean Society","department":[{"_id":"NiBa"}],"title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","publisher":"Oxford University Press","date_created":"2024-01-18T07:54:10Z","oa_version":"Published Version","ddc":["570"],"day":"17","month":"08","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","intvolume":"         2","file":[{"file_id":"14875","date_updated":"2024-01-23T08:10:00Z","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","file_size":3408944,"creator":"dernst","access_level":"open_access","relation":"main_file","success":1,"date_created":"2024-01-23T08:10:00Z","content_type":"application/pdf"}],"publication_status":"published","date_published":"2023-08-17T00:00:00Z","author":[{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Zuzanna B","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"last_name":"Montaño-Rendón","first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Mikhailova, Natalia","first_name":"Natalia","last_name":"Mikhailova"},{"full_name":"Blakeslee, April M H","last_name":"Blakeslee","first_name":"April M H"},{"full_name":"Arnason, Einar","first_name":"Einar","last_name":"Arnason"},{"last_name":"Broquet","first_name":"Thomas","full_name":"Broquet, Thomas"},{"last_name":"Morales","first_name":"Hernán E","full_name":"Morales, Hernán E"},{"last_name":"Grahame","first_name":"John W","full_name":"Grahame, John W"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger K","last_name":"Butlin","full_name":"Butlin, Roger K"}],"article_processing_charge":"Yes (via OA deal)","date_updated":"2024-01-23T08:13:43Z","doi":"10.1093/evolinnean/kzad002","quality_controlled":"1","file_date_updated":"2024-01-23T08:10:00Z","article_number":"kzad002","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"}},{"oa_version":"Published Version","date_created":"2024-01-18T10:01:01Z","publisher":"Wiley","title":"Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten","department":[{"_id":"PaSc"}],"publication":"Angewandte Chemie","abstract":[{"lang":"ger","text":"Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht."}],"has_accepted_license":"1","year":"2023","_id":"14835","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":135,"publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"citation":{"short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 135(19), e202219314.","mla":"Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” <i>Angewandte Chemie</i>, vol. 135, no. 19, e202219314, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/ange.202219314\">10.1002/ange.202219314</a>.","ama":"Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. <i>Angewandte Chemie</i>. 2023;135(19). doi:<a href=\"https://doi.org/10.1002/ange.202219314\">10.1002/ange.202219314</a>","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.202219314\">https://doi.org/10.1002/ange.202219314</a>","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” <i>Angewandte Chemie</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/ange.202219314\">https://doi.org/10.1002/ange.202219314</a>.","ieee":"L. M. Becker <i>et al.</i>, “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,” <i>Angewandte Chemie</i>, vol. 135, no. 19. Wiley, 2023."},"article_type":"original","issue":"19","status":"public","acknowledgement":"Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen. Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318 an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität Bordeaux.","oa":1,"tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_number":"e202219314","file_date_updated":"2024-01-23T08:57:01Z","quality_controlled":"1","keyword":["General Medicine"],"date_updated":"2024-01-23T12:23:35Z","doi":"10.1002/ange.202219314","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-05-02T00:00:00Z","author":[{"last_name":"Becker","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie"},{"full_name":"Berbon, Mélanie","first_name":"Mélanie","last_name":"Berbon"},{"last_name":"Vallet","first_name":"Alicia","full_name":"Vallet, Alicia"},{"last_name":"Grelard","first_name":"Axelle","full_name":"Grelard, Axelle"},{"last_name":"Morvan","first_name":"Estelle","full_name":"Morvan, Estelle"},{"full_name":"Bardiaux, Benjamin","first_name":"Benjamin","last_name":"Bardiaux"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"last_name":"Loquet","first_name":"Antoine","full_name":"Loquet, Antoine"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"publication_status":"published","file":[{"file_id":"14876","date_updated":"2024-01-23T08:57:01Z","file_size":1004676,"checksum":"98e68d370159f7be52a3d7c8a8ee1198","file_name":"2023_AngewChem_Becker.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2024-01-23T08:57:01Z","success":1}],"intvolume":"       135","language":[{"iso":"ger"}],"month":"05","day":"02","ddc":["540"]},{"month":"12","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"language":[{"iso":"eng"}],"ddc":["570"],"day":"29","main_file_link":[{"url":"https://doi.org/10.1016/j.bpj.2023.12.020","open_access":"1"}],"publication_status":"inpress","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","quality_controlled":"1","date_published":"2023-12-29T00:00:00Z","author":[{"full_name":"Azadbakht, Ali","last_name":"Azadbakht","first_name":"Ali"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","orcid":"0000-0003-3441-1337","first_name":"Billie"},{"id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","full_name":"Majek, Juraj","last_name":"Majek","first_name":"Juraj"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Kraft, Daniela J.","last_name":"Kraft","first_name":"Daniela J."}],"article_processing_charge":"No","doi":"10.1016/j.bpj.2023.12.020","date_updated":"2024-01-23T09:26:35Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"citation":{"apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., &#38; Kraft, D. J. (n.d.). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>","chicago":"Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>.","ieee":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” <i>Biophysical Journal</i>. Elsevier.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal.","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.).","mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>.","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>"},"publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"acknowledgement":"We gratefully acknowledge useful discussions with Casper van der Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon Idema and George Dadunashvili for initial attempts to simulate the experimental system. D.J.K. would like to thank the physics department at Leiden University for funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).","oa":1,"status":"public","article_type":"original","_id":"14844","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","abstract":[{"text":"Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules.","lang":"eng"}],"ec_funded":1,"date_created":"2024-01-21T23:00:56Z","oa_version":"Published Version","publication":"Biophysical Journal","department":[{"_id":"AnSa"}],"title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","publisher":"Elsevier"},{"status":"public","oa":1,"publication_identifier":{"isbn":["9781839162824"],"eisbn":["9781839165993"]},"citation":{"ama":"Sučec I, Schanda P. Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Hiller S, Liu M, He L, eds. <i>Biophysics of Molecular Chaperones</i>. Vol 29. Royal Society of Chemistry; 2023:136-161. doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00136\">10.1039/bk9781839165986-00136</a>","mla":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 136–61, doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00136\">10.1039/bk9781839165986-00136</a>.","short":"I. Sučec, P. Schanda, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 136–161.","ista":"Sučec I, Schanda P. 2023.Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 136–161.","ieee":"I. Sučec and P. Schanda, “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies,” in <i>Biophysics of Molecular Chaperones</i>, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 136–161.","chicago":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” In <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:136–61. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/bk9781839165986-00136\">https://doi.org/10.1039/bk9781839165986-00136</a>.","apa":"Sučec, I., &#38; Schanda, P. (2023). Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In S. Hiller, M. Liu, &#38; L. He (Eds.), <i>Biophysics of Molecular Chaperones</i> (Vol. 29, pp. 136–161). Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/bk9781839165986-00136\">https://doi.org/10.1039/bk9781839165986-00136</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","volume":29,"page":"136-161","year":"2023","_id":"14847","abstract":[{"text":"Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies.","lang":"eng"}],"publisher":"Royal Society of Chemistry","publication":"Biophysics of Molecular Chaperones","title":"Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies","department":[{"_id":"PaSc"}],"date_created":"2024-01-22T08:04:57Z","oa_version":"Preprint","day":"01","month":"11","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"        29","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2023-rpn28"}],"article_processing_charge":"No","date_updated":"2024-01-23T11:50:10Z","alternative_title":["New Developments in NMR"],"doi":"10.1039/bk9781839165986-00136","date_published":"2023-11-01T00:00:00Z","author":[{"full_name":"Sučec, I.","last_name":"Sučec","first_name":"I."},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"editor":[{"last_name":"Hiller","first_name":"Sebastian","full_name":"Hiller, Sebastian"},{"first_name":"Maili","last_name":"Liu","full_name":"Liu, Maili"},{"full_name":"He, Lichun","last_name":"He","first_name":"Lichun"}],"quality_controlled":"1"},{"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"quality_controlled":"1","date_published":"2023-11-01T00:00:00Z","author":[{"orcid":"0000-0002-4901-7992","last_name":"Cipolloni","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"},{"full_name":"Xu, Yuanyuan","last_name":"Xu","first_name":"Yuanyuan"}],"article_processing_charge":"No","doi":"10.1214/23-aop1643","date_updated":"2024-01-23T10:56:30Z","intvolume":"        51","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.04448","open_access":"1"}],"publication_status":"published","month":"11","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"day":"01","date_created":"2024-01-22T08:08:41Z","ec_funded":1,"oa_version":"Preprint","publication":"The Annals of Probability","title":"On the rightmost eigenvalue of non-Hermitian random matrices","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","abstract":[{"text":"We establish a precise three-term asymptotic expansion, with an optimal estimate of the error term, for the rightmost eigenvalue of an n×n random matrix with independent identically distributed complex entries as n tends to infinity. All terms in the expansion are universal.","lang":"eng"}],"arxiv":1,"_id":"14849","year":"2023","volume":51,"page":"2192-2242","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. On the rightmost eigenvalue of non-Hermitian random matrices. <i>The Annals of Probability</i>. 2023;51(6):2192-2242. doi:<a href=\"https://doi.org/10.1214/23-aop1643\">10.1214/23-aop1643</a>","ista":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2023. On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. 51(6), 2192–2242.","mla":"Cipolloni, Giorgio, et al. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” <i>The Annals of Probability</i>, vol. 51, no. 6, Institute of Mathematical Statistics, 2023, pp. 2192–242, doi:<a href=\"https://doi.org/10.1214/23-aop1643\">10.1214/23-aop1643</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, The Annals of Probability 51 (2023) 2192–2242.","chicago":"Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” <i>The Annals of Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-aop1643\">https://doi.org/10.1214/23-aop1643</a>.","ieee":"G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “On the rightmost eigenvalue of non-Hermitian random matrices,” <i>The Annals of Probability</i>, vol. 51, no. 6. Institute of Mathematical Statistics, pp. 2192–2242, 2023.","apa":"Cipolloni, G., Erdös, L., Schröder, D. J., &#38; Xu, Y. (2023). On the rightmost eigenvalue of non-Hermitian random matrices. <i>The Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-aop1643\">https://doi.org/10.1214/23-aop1643</a>"},"publication_identifier":{"issn":["0091-1798"]},"oa":1,"status":"public","acknowledgement":"The second and the fourth author were supported by the ERC Advanced Grant\r\n“RMTBeyond” No. 101020331. The third author was supported by Dr. Max Rössler, the\r\nWalter Haefner Foundation and the ETH Zürich Foundation.","issue":"6","external_id":{"arxiv":["2206.04448"]},"article_type":"original"},{"publication_status":"published","intvolume":"        62","main_file_link":[{"url":"https://doi.org/10.1002/anie.202304138","open_access":"1"}],"day":"02","language":[{"iso":"eng"}],"month":"05","article_number":" e202304138","related_material":{"link":[{"relation":"translation","url":"https://doi.org/10.1002/ange.202304138"}],"record":[{"id":"12675","relation":"other","status":"public"}]},"date_updated":"2024-01-23T08:48:14Z","doi":"10.1002/anie.202304138","article_processing_charge":"No","author":[{"first_name":"Lea Marie","orcid":"0000-0002-6401-5151","last_name":"Becker","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"last_name":"Berbon","first_name":"Mélanie","full_name":"Berbon, Mélanie"},{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"last_name":"Grelard","first_name":"Axelle","full_name":"Grelard, Axelle"},{"first_name":"Estelle","last_name":"Morvan","full_name":"Morvan, Estelle"},{"full_name":"Bardiaux, Benjamin","first_name":"Benjamin","last_name":"Bardiaux"},{"full_name":"Lichtenecker, Roman","first_name":"Roman","last_name":"Lichtenecker"},{"first_name":"Matthias","last_name":"Ernst","full_name":"Ernst, Matthias"},{"first_name":"Antoine","last_name":"Loquet","full_name":"Loquet, Antoine"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"}],"date_published":"2023-05-02T00:00:00Z","keyword":["General Chemistry","Catalysis"],"type":"other_academic_publication","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":62,"year":"2023","_id":"14861","issue":"19","status":"public","oa":1,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"citation":{"short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues, Wiley, 2023.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues, Wiley,p.","mla":"Becker, Lea Marie, et al. “Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19, e202304138, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202304138\">10.1002/anie.202304138</a>.","ama":"Becker LM, Berbon M, Vallet A, et al. <i>Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues</i>. Vol 62. Wiley; 2023. doi:<a href=\"https://doi.org/10.1002/anie.202304138\">10.1002/anie.202304138</a>","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). <i>Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues</i>. <i>Angewandte Chemie International Edition</i> (Vol. 62). Wiley. <a href=\"https://doi.org/10.1002/anie.202304138\">https://doi.org/10.1002/anie.202304138</a>","ieee":"L. M. Becker <i>et al.</i>, <i>Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues</i>, vol. 62, no. 19. Wiley, 2023.","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. <i>Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues</i>. <i>Angewandte Chemie International Edition</i>. Vol. 62. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202304138\">https://doi.org/10.1002/anie.202304138</a>."},"publisher":"Wiley","department":[{"_id":"PaSc"}],"title":"Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues","publication":"Angewandte Chemie International Edition","oa_version":"Published Version","date_created":"2024-01-22T11:54:34Z","abstract":[{"lang":"eng","text":"Cover Page"}]},{"article_number":"ckad160.597","file_date_updated":"2024-01-24T11:12:33Z","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_processing_charge":"No","date_updated":"2024-01-24T11:16:09Z","doi":"10.1093/eurpub/ckad160.597","date_published":"2023-10-01T00:00:00Z","author":[{"full_name":"Rella, Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","first_name":"Simon","last_name":"Rella"},{"last_name":"Kulikova","first_name":"Y","full_name":"Kulikova, Y"},{"full_name":"Minnegalieva, Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","first_name":"Aygul","last_name":"Minnegalieva"},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","keyword":["Public Health","Environmental and Occupational Health"],"file":[{"file_name":"2023_EurJourPublicHealth_Rella.pdf","checksum":"98706755bb4cc5d553818ade7660a7d2","file_size":71057,"file_id":"14882","date_updated":"2024-01-24T11:12:33Z","success":1,"date_created":"2024-01-24T11:12:33Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"publication_status":"published","intvolume":"        33","ddc":["570"],"day":"01","month":"10","language":[{"iso":"eng"}],"publisher":"Oxford University Press","publication":"European Journal of Public Health","title":"Complex vaccination strategies prevent the emergence of vaccine resistance","department":[{"_id":"GaTk"}],"date_created":"2024-01-22T12:02:28Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference_abstract","volume":33,"year":"2023","has_accepted_license":"1","_id":"14862","issue":"Supplement_2","oa":1,"status":"public","publication_identifier":{"eissn":["1464-360X"],"issn":["1101-1262"]},"citation":{"ama":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: <i>European Journal of Public Health</i>. Vol 33. Oxford University Press; 2023. doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>","mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” <i>European Journal of Public Health</i>, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>.","ista":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597.","short":"S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.","ieee":"S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in <i>European Journal of Public Health</i>, 2023, vol. 33, no. Supplement_2.","chicago":"Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In <i>European Journal of Public Health</i>, Vol. 33. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>.","apa":"Rella, S., Kulikova, Y., Minnegalieva, A., &#38; Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In <i>European Journal of Public Health</i> (Vol. 33). Oxford University Press. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>"}},{"date_created":"2024-01-22T12:08:12Z","conference":{"location":"Vienna, Austria & Virtual","start_date":"2023-04-23","name":"EGU General Assembly","end_date":"2023-04-28"},"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"European Geosciences Union","article_number":"EGU23-6157","publication":"EGU General Assembly 2023","department":[{"_id":"CaMu"},{"_id":"GradSch"}],"file_date_updated":"2024-01-24T11:19:54Z","title":"Intensification mechanisms of tropical cyclones","article_processing_charge":"No","date_updated":"2024-01-24T11:25:07Z","doi":"10.5194/egusphere-egu23-6157","date_published":"2023-04-13T00:00:00Z","author":[{"full_name":"Polesello, Andrea","id":"74c777f4-32da-11ee-b498-874db0835561","first_name":"Andrea","last_name":"Polesello"},{"full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350"},{"full_name":"Pasquero, Claudia","first_name":"Claudia","last_name":"Pasquero"},{"last_name":"Meroni","first_name":"Agostino N.","full_name":"Meroni, Agostino N."}],"year":"2023","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2024-01-24T11:19:54Z","date_updated":"2024-01-24T11:19:54Z","file_id":"14883","file_size":296769,"file_name":"2023_EGU_Polesello.pdf","checksum":"8cb88c1bc80ccee328478a62064d98f7"}],"publication_status":"published","_id":"14863","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference_abstract","month":"04","language":[{"iso":"eng"}],"citation":{"chicago":"Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In <i>EGU General Assembly 2023</i>. European Geosciences Union, 2023. <a href=\"https://doi.org/10.5194/egusphere-egu23-6157\">https://doi.org/10.5194/egusphere-egu23-6157</a>.","ieee":"A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in <i>EGU General Assembly 2023</i>, Vienna, Austria &#38; Virtual, 2023.","apa":"Polesello, A., Muller, C. J., Pasquero, C., &#38; Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In <i>EGU General Assembly 2023</i>. Vienna, Austria &#38; Virtual: European Geosciences Union. <a href=\"https://doi.org/10.5194/egusphere-egu23-6157\">https://doi.org/10.5194/egusphere-egu23-6157</a>","ama":"Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms of tropical cyclones. In: <i>EGU General Assembly 2023</i>. 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Constructing Hamilton cycles and perfect matchings efficiently. In: <i>Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications</i>. Masaryk University Press; 2023:36-41. doi:<a href=\"https://doi.org/10.5817/cz.muni.eurocomb23-005\">10.5817/cz.muni.eurocomb23-005</a>","mla":"Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.” <i>Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications</i>, Masaryk University Press, 2023, pp. 36–41, doi:<a href=\"https://doi.org/10.5817/cz.muni.eurocomb23-005\">10.5817/cz.muni.eurocomb23-005</a>.","ista":"Anastos M. 2023. Constructing Hamilton cycles and perfect matchings efficiently. Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications. EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications, 36–41.","short":"M. 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The case $K=1$ implies that w.h.p. one can build a Hamiltonian graph by choosing $(1+o(1))n$ edges in an online fashion as they appear along the first $(0.5+o(1))n\\log n$ rounds of the random graph process. This answers a question of Frieze, Krivelevich and Michaeli. Observe that the number of rounds is asymptotically optimal as the first $0.5n\\log n$ edges do not span a Hamilton cycle w.h.p. The case $K=\\Theta(\\log n)$ implies that the Hamiltonicity threshold of the corresponding Achlioptas process is at most $(1+o(1))(1+(\\log n)/2K) n$. This matches the $(1-o(1))(1+(\\log n)/2K) n$ lower bound due to Krivelevich, Lubetzky and Sudakov and resolves the problem of determining the Hamiltonicity threshold of the Achlioptas process with $K=\\Theta(\\log n)$. We also show that in the above process one can construct a graph $G$ that spans a matching of size $\\lfloor V(G)/2) \\rfloor$ and $(0.5+o(1))n$ edges within $(1+o(1))(0.5+(\\log n)/2K) n$ rounds w.h.p. Our proof relies on a robust Hamiltonicity property of the strong $4$-core of the binomial random graph which we use as a black-box. This property allows it to absorb paths covering vertices outside the strong $4$-core into a cycle.</jats:p>","lang":"eng"}],"publisher":"Masaryk University Press","title":"Constructing Hamilton cycles and perfect matchings efficiently","department":[{"_id":"MaKw"}],"publication":"Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications","oa_version":"Published Version","date_created":"2024-01-22T12:20:15Z","ec_funded":1,"day":"01","ddc":["510"],"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"09","publication_status":"published","file":[{"file_name":"2023_Eurocomb_Anastos.pdf","checksum":"fb1d9a1e7389d90ec0e5e76934373cf8","file_size":464230,"file_id":"14881","date_updated":"2024-01-24T09:34:43Z","success":1,"date_created":"2024-01-24T09:34:43Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"doi":"10.5817/cz.muni.eurocomb23-005","date_updated":"2024-01-24T09:38:44Z","article_processing_charge":"No","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","full_name":"Anastos, Michael","last_name":"Anastos","first_name":"Michael"}],"date_published":"2023-09-01T00:00:00Z","quality_controlled":"1","file_date_updated":"2024-01-24T09:34:43Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"conference":{"name":"EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications","end_date":"2023-09-01","location":"Prague, Czech Republic","start_date":"2023-08-28"}},{"citation":{"chicago":"Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.10251087\">https://doi.org/10.5281/ZENODO.10251087</a>.","ieee":"D. 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Shaw, P. Buri, M. McCarthy, E. Miles, F. Pellicciotti, (2023).","ista":"Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. 2023. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8277285\">10.5281/ZENODO.8277285</a>.","mla":"Shaw, Thomas, et al. <i>Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8277285\">10.5281/ZENODO.8277285</a>.","ama":"Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8277285\">10.5281/ZENODO.8277285</a>","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E., &#38; Pellicciotti, F. (2023). Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8277285\">https://doi.org/10.5281/ZENODO.8277285</a>","ieee":"T. Shaw, P. Buri, M. McCarthy, E. Miles, and F. Pellicciotti, “Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer.” Zenodo, 2023.","chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan Miles, and Francesca Pellicciotti. “Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8277285\">https://doi.org/10.5281/ZENODO.8277285</a>."},"month":"08","department":[{"_id":"FrPe"}],"title":"Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer","publisher":"Zenodo","oa_version":"Published Version","date_created":"2024-01-31T12:08:26Z","date_published":"2023-08-23T00:00:00Z","author":[{"first_name":"Thomas","last_name":"Shaw","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e"},{"full_name":"Buri, Pascal","id":"317987aa-9421-11ee-ac5a-b941b041abba","first_name":"Pascal","last_name":"Buri"},{"first_name":"Michael","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"first_name":"Evan","last_name":"Miles","full_name":"Miles, Evan"},{"orcid":"0000-0002-5554-8087","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"}],"doi":"10.5281/ZENODO.8277285","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14885"}]},"date_updated":"2024-02-06T08:44:01Z","article_processing_charge":"No","abstract":[{"text":"GLACIER METEOROLOGICAL DATA SWISS ALPS -2022\r\n","lang":"eng"}]},{"author":[{"last_name":"Banerjee","first_name":"Tamajit","full_name":"Banerjee, Tamajit"},{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"first_name":"Kaushik","last_name":"Mallik","orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"},{"full_name":"Schmuck, Anne-Kathrin","last_name":"Schmuck","first_name":"Anne-Kathrin"},{"full_name":"Soudjani, Sadegh","last_name":"Soudjani","first_name":"Sadegh"}],"date_published":"2023-02-24T00:00:00Z","doi":"10.46298/theoretics.23.4","date_updated":"2024-02-05T10:21:51Z","article_processing_charge":"Yes","quality_controlled":"1","file_date_updated":"2024-02-05T10:19:35Z","article_number":"4","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"24","ddc":["000"],"language":[{"iso":"eng"}],"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"month":"02","intvolume":"         2","publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2024-02-05T10:19:35Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":917076,"file_name":"2023_TheoretiCS_Banerjee.pdf","checksum":"2972d531122a6f15727b396110fb3f5c","date_updated":"2024-02-05T10:19:35Z","file_id":"14940"}],"arxiv":1,"abstract":[{"lang":"eng","text":"We consider fixpoint algorithms for two-player games on graphs with $\\omega$-regular winning conditions, where the environment is constrained by a strong transition fairness assumption. Strong transition fairness is a widely occurring special case of strong fairness, which requires that any execution is strongly fair with respect to a specified set of live edges: whenever the\r\nsource vertex of a live edge is visited infinitely often along a play, the edge itself is traversed infinitely often along the play as well. We show that, surprisingly, strong transition fairness retains the algorithmic characteristics of the fixpoint algorithms for $\\omega$-regular games -- the new algorithms have the same alternation depth as the classical algorithms but invoke a new type of predecessor operator. For Rabin games with $k$ pairs, the complexity of the new algorithm is $O(n^{k+2}k!)$ symbolic steps, which is independent of the number of live edges in the strong transition fairness assumption. Further, we show that GR(1) specifications with strong transition fairness assumptions can be solved with a 3-nested fixpoint algorithm, same as the usual algorithm. In contrast, strong fairness necessarily requires increasing the alternation depth depending on the number of fairness assumptions. We get symbolic algorithms for (generalized) Rabin, parity and GR(1) objectives under strong transition fairness assumptions as well as a direct symbolic algorithm for qualitative winning in stochastic\r\n$\\omega$-regular games that runs in $O(n^{k+2}k!)$ symbolic steps, improving the state of the art. Finally, we have implemented a BDD-based synthesis engine based on our algorithm. We show on a set of synthetic and real benchmarks that our algorithm is scalable, parallelizable, and outperforms previous algorithms by orders of magnitude."}],"title":"Fast symbolic algorithms for mega-regular games under strong transition fairness","department":[{"_id":"ToHe"}],"publication":"TheoretiCS","publisher":"EPI Sciences","oa_version":"Published Version","ec_funded":1,"date_created":"2024-01-31T13:40:49Z","acknowledgement":"A previous version of this paper has appeared in TACAS 2022. Authors ordered alphabetically. T. Banerjee was interning with MPI-SWS when this research was conducted. R. Majumdar and A.-K. Schmuck are partially supported by DFG project 389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093.","status":"public","oa":1,"article_type":"original","external_id":{"arxiv":["2202.07480"]},"citation":{"mla":"Banerjee, Tamajit, et al. “Fast Symbolic Algorithms for Mega-Regular Games under Strong Transition Fairness.” <i>TheoretiCS</i>, vol. 2, 4, EPI Sciences, 2023, doi:<a href=\"https://doi.org/10.46298/theoretics.23.4\">10.46298/theoretics.23.4</a>.","ista":"Banerjee T, Majumdar R, Mallik K, Schmuck A-K, Soudjani S. 2023. Fast symbolic algorithms for mega-regular games under strong transition fairness. TheoretiCS. 2, 4.","short":"T. Banerjee, R. Majumdar, K. Mallik, A.-K. Schmuck, S. Soudjani, TheoretiCS 2 (2023).","ama":"Banerjee T, Majumdar R, Mallik K, Schmuck A-K, Soudjani S. Fast symbolic algorithms for mega-regular games under strong transition fairness. <i>TheoretiCS</i>. 2023;2. doi:<a href=\"https://doi.org/10.46298/theoretics.23.4\">10.46298/theoretics.23.4</a>","apa":"Banerjee, T., Majumdar, R., Mallik, K., Schmuck, A.-K., &#38; Soudjani, S. (2023). Fast symbolic algorithms for mega-regular games under strong transition fairness. <i>TheoretiCS</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/theoretics.23.4\">https://doi.org/10.46298/theoretics.23.4</a>","chicago":"Banerjee, Tamajit, Rupak Majumdar, Kaushik Mallik, Anne-Kathrin Schmuck, and Sadegh Soudjani. “Fast Symbolic Algorithms for Mega-Regular Games under Strong Transition Fairness.” <i>TheoretiCS</i>. EPI Sciences, 2023. <a href=\"https://doi.org/10.46298/theoretics.23.4\">https://doi.org/10.46298/theoretics.23.4</a>.","ieee":"T. Banerjee, R. Majumdar, K. Mallik, A.-K. Schmuck, and S. Soudjani, “Fast symbolic algorithms for mega-regular games under strong transition fairness,” <i>TheoretiCS</i>, vol. 2. EPI Sciences, 2023."},"publication_identifier":{"issn":["2751-4838"]},"volume":2,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14920","has_accepted_license":"1","year":"2023"},{"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2305.13165"}],"_id":"14921","year":"2023","publication_status":"inpress","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","citation":{"apa":"Súkeník, P., Mondelli, M., &#38; Lampert, C. (n.d.). Deep neural collapse is provably optimal for the deep unconstrained features model. In <i>37th Annual Conference on Neural Information Processing Systems</i>. New Orleans, LA, United States.","chicago":"Súkeník, Peter, Marco Mondelli, and Christoph Lampert. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” In <i>37th Annual Conference on Neural Information Processing Systems</i>, n.d.","ieee":"P. Súkeník, M. Mondelli, and C. Lampert, “Deep neural collapse is provably optimal for the deep unconstrained features model,” in <i>37th Annual Conference on Neural Information Processing Systems</i>, New Orleans, LA, United States.","mla":"Súkeník, Peter, et al. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” <i>37th Annual Conference on Neural Information Processing Systems</i>.","short":"P. Súkeník, M. Mondelli, C. Lampert, in:, 37th Annual Conference on Neural Information Processing Systems, n.d.","ista":"Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal for the deep unconstrained features model. 37th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, NeurIPS, .","ama":"Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal for the deep unconstrained features model. In: <i>37th Annual Conference on Neural Information Processing Systems</i>."},"month":"12","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"language":[{"iso":"eng"}],"oa":1,"status":"public","acknowledgement":"M. M. is partially supported by the 2019 Lopez-Loreta Prize. The authors would like to thank Eugenia Iofinova, Bernd Prach and Simone Bombari for valuable feedback on the manuscript.","external_id":{"arxiv":["2305.13165"]},"day":"15","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2023-12-16","location":"New Orleans, LA, United States","start_date":"2023-12-10"},"date_created":"2024-02-02T11:17:41Z","oa_version":"Preprint","publication":"37th Annual Conference on Neural Information Processing Systems","department":[{"_id":"MaMo"},{"_id":"ChLa"}],"title":"Deep neural collapse is provably optimal for the deep unconstrained features model","abstract":[{"lang":"eng","text":"Neural collapse (NC) refers to the surprising structure of the last layer of deep neural networks in the terminal phase of gradient descent training. Recently, an increasing amount of experimental evidence has pointed to the propagation of NC to earlier layers of neural networks. However, while the NC in the last layer is well studied theoretically, much less is known about its multi-layered counterpart - deep neural collapse (DNC). In particular, existing work focuses either on linear layers or only on the last two layers at the price of an extra assumption. Our paper fills this gap by generalizing the established analytical framework for NC - the unconstrained features model - to multiple non-linear layers. Our key technical contribution is to show that, in a deep unconstrained features model, the unique global optimum for binary classification exhibits all the properties typical of DNC. This explains the existing experimental evidence of DNC. We also empirically show that (i) by optimizing deep unconstrained features models via gradient descent, the resulting solution agrees well with our theory, and (ii) trained networks recover the unconstrained features suitable for the occurrence of DNC, thus supporting the validity of this modeling principle."}],"quality_controlled":"1","date_published":"2023-12-15T00:00:00Z","author":[{"last_name":"Súkeník","first_name":"Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","full_name":"Súkeník, Peter"},{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"arxiv":1,"article_processing_charge":"No","date_updated":"2024-09-10T13:03:19Z","alternative_title":["NeurIPS"]},{"external_id":{"arxiv":["2303.07245"]},"day":"30","oa":1,"acknowledgement":"The authors are partially supported by the 2019 Lopez-Loreta Prize. They would also like to thank Professor Jan Maas for providing valuable suggestions and comments on an early version of the work.","status":"public","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"language":[{"iso":"eng"}],"month":"06","citation":{"apa":"Esposito, A. R., &#38; Mondelli, M. (n.d.). Concentration without independence via information measures. In <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>. Taipei, Taiwan: IEEE. <a href=\"https://doi.org/10.1109/isit54713.2023.10206899\">https://doi.org/10.1109/isit54713.2023.10206899</a>","chicago":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” In <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>. IEEE, n.d. <a href=\"https://doi.org/10.1109/isit54713.2023.10206899\">https://doi.org/10.1109/isit54713.2023.10206899</a>.","ieee":"A. R. Esposito and M. Mondelli, “Concentration without independence via information measures,” in <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>, Taipei, Taiwan.","mla":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>, IEEE, doi:<a href=\"https://doi.org/10.1109/isit54713.2023.10206899\">10.1109/isit54713.2023.10206899</a>.","ista":"Esposito AR, Mondelli M. Concentration without independence via information measures. Proceedings of 2023 IEEE International Symposium on Information Theory. ISIT: IEEE International Symposium on Information Theory.","short":"A.R. Esposito, M. Mondelli, in:, Proceedings of 2023 IEEE International Symposium on Information Theory, IEEE, n.d.","ama":"Esposito AR, Mondelli M. Concentration without independence via information measures. In: <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>. IEEE. doi:<a href=\"https://doi.org/10.1109/isit54713.2023.10206899\">10.1109/isit54713.2023.10206899</a>"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"inpress","year":"2023","_id":"14922","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.07245"}],"date_updated":"2024-02-14T14:24:25Z","doi":"10.1109/isit54713.2023.10206899","article_processing_charge":"No","arxiv":1,"date_published":"2023-06-30T00:00:00Z","author":[{"full_name":"Esposito, Amedeo Roberto","id":"9583e921-e1ad-11ec-9862-cef099626dc9","first_name":"Amedeo Roberto","last_name":"Esposito"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco"}],"quality_controlled":"1","abstract":[{"text":"We propose a novel approach to concentration for non-independent random variables. The main idea is to ``pretend'' that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid's inequality) when the random variables are independent. Furthermore, in a ``large deviations'' regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide.","lang":"eng"}],"publisher":"IEEE","title":"Concentration without independence via information measures","department":[{"_id":"MaMo"}],"publication":"Proceedings of 2023 IEEE International Symposium on Information Theory","oa_version":"Preprint","date_created":"2024-02-02T11:18:40Z","conference":{"location":"Taipei, Taiwan","start_date":"2023-06-25","name":"ISIT: IEEE International Symposium on Information Theory","end_date":"2023-06-30"}},{"department":[{"_id":"MaMo"}],"title":"Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise","publication":"Proceedings of 2023 IEEE International Symposium on Information Theory","publisher":"IEEE","oa_version":"Preprint","conference":{"name":"ISIT: IEEE International Symposium on Information Theory","end_date":"2023-06-30","location":"Taipei, Taiwan","start_date":"2023-06-25"},"date_created":"2024-02-02T11:20:39Z","arxiv":1,"date_published":"2023-06-30T00:00:00Z","author":[{"last_name":"Fu","first_name":"Teng","full_name":"Fu, Teng"},{"full_name":"Liu, YuHao","first_name":"YuHao","last_name":"Liu"},{"last_name":"Barbier","first_name":"Jean","full_name":"Barbier, Jean"},{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"full_name":"Liang, ShanSuo","first_name":"ShanSuo","last_name":"Liang"},{"last_name":"Hou","first_name":"TianQi","full_name":"Hou, TianQi"}],"doi":"10.1109/isit54713.2023.10206671","date_updated":"2024-02-14T14:34:03Z","article_processing_charge":"No","abstract":[{"text":"We study the performance of a Bayesian statistician who estimates a rank-one signal corrupted by non-symmetric rotationally invariant noise with a generic distribution of singular values. As the signal-to-noise ratio and the noise structure are unknown, a Gaussian setup is incorrectly assumed. We derive the exact analytic expression for the error of the mismatched Bayes estimator and also provide the analysis of an approximate message passing (AMP) algorithm. The first result exploits the asymptotic behavior of spherical integrals for rectangular matrices and of low-rank matrix perturbations; the second one relies on the design and analysis of an auxiliary AMP. The numerical experiments show that there is a performance gap between the AMP and Bayes estimators, which is due to the incorrect estimation of the signal norm.","lang":"eng"}],"quality_controlled":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14923","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.03306","open_access":"1"}],"publication_status":"inpress","year":"2023","oa":1,"status":"public","day":"30","external_id":{"arxiv":["2302.03306"]},"citation":{"ista":"Fu T, Liu Y, Barbier J, Mondelli M, Liang S, Hou T. Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise. Proceedings of 2023 IEEE International Symposium on Information Theory. ISIT: IEEE International Symposium on Information Theory.","mla":"Fu, Teng, et al. “Mismatched Estimation of Non-Symmetric Rank-One Matrices Corrupted by Structured Noise.” <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>, IEEE, doi:<a href=\"https://doi.org/10.1109/isit54713.2023.10206671\">10.1109/isit54713.2023.10206671</a>.","short":"T. Fu, Y. Liu, J. Barbier, M. Mondelli, S. Liang, T. Hou, in:, Proceedings of 2023 IEEE International Symposium on Information Theory, IEEE, n.d.","ama":"Fu T, Liu Y, Barbier J, Mondelli M, Liang S, Hou T. Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise. In: <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>. IEEE. doi:<a href=\"https://doi.org/10.1109/isit54713.2023.10206671\">10.1109/isit54713.2023.10206671</a>","apa":"Fu, T., Liu, Y., Barbier, J., Mondelli, M., Liang, S., &#38; Hou, T. (n.d.). Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise. In <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>. Taipei, Taiwan: IEEE. <a href=\"https://doi.org/10.1109/isit54713.2023.10206671\">https://doi.org/10.1109/isit54713.2023.10206671</a>","chicago":"Fu, Teng, YuHao Liu, Jean Barbier, Marco Mondelli, ShanSuo Liang, and TianQi Hou. “Mismatched Estimation of Non-Symmetric Rank-One Matrices Corrupted by Structured Noise.” In <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>. IEEE, n.d. <a href=\"https://doi.org/10.1109/isit54713.2023.10206671\">https://doi.org/10.1109/isit54713.2023.10206671</a>.","ieee":"T. Fu, Y. Liu, J. Barbier, M. Mondelli, S. Liang, and T. Hou, “Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise,” in <i>Proceedings of 2023 IEEE International Symposium on Information Theory</i>, Taipei, Taiwan."},"language":[{"iso":"eng"}],"month":"06"},{"date_created":"2024-02-02T11:21:56Z","oa_version":"Published Version","publication":"Transactions on Machine Learning Research","department":[{"_id":"MaMo"}],"title":"Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence","publisher":"ML Research Press","abstract":[{"lang":"eng","text":"The stochastic heavy ball method (SHB), also known as stochastic gradient descent (SGD) with Polyak's momentum, is widely used in training neural networks. However, despite the remarkable success of such algorithm in practice, its theoretical characterization remains limited. In this paper, we focus on neural networks with two and three layers and provide a rigorous understanding of the properties of the solutions found by SHB: \\emph{(i)} stability after dropping out part of the neurons, \\emph{(ii)} connectivity along a low-loss path, and \\emph{(iii)} convergence to the global optimum.\r\nTo achieve this goal, we take a mean-field view and relate the SHB dynamics to a certain partial differential equation in the limit of large network widths. This mean-field perspective has inspired a recent line of work focusing on SGD while, in contrast, our paper considers an algorithm with momentum. More specifically, after proving existence and uniqueness of the limit differential equations, we show convergence to the global optimum and give a quantitative bound between the mean-field limit and the SHB dynamics of a finite-width network. Armed with this last bound, we are able to establish the dropout-stability and connectivity of SHB solutions."}],"arxiv":1,"_id":"14924","year":"2023","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","citation":{"ista":"Wu D, Kungurtsev V, Mondelli M. 2023. Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence. Transactions on Machine Learning Research. , TMLR, .","mla":"Wu, Diyuan, et al. “Mean-Field Analysis for Heavy Ball Methods: Dropout-Stability, Connectivity, and Global Convergence.” <i>Transactions on Machine Learning Research</i>, ML Research Press, 2023.","short":"D. Wu, V. Kungurtsev, M. Mondelli, in:, Transactions on Machine Learning Research, ML Research Press, 2023.","ama":"Wu D, Kungurtsev V, Mondelli M. Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence. In: <i>Transactions on Machine Learning Research</i>. ML Research Press; 2023.","apa":"Wu, D., Kungurtsev, V., &#38; Mondelli, M. (2023). Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence. In <i>Transactions on Machine Learning Research</i>. ML Research Press.","chicago":"Wu, Diyuan, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis for Heavy Ball Methods: Dropout-Stability, Connectivity, and Global Convergence.” In <i>Transactions on Machine Learning Research</i>. ML Research Press, 2023.","ieee":"D. Wu, V. Kungurtsev, and M. Mondelli, “Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence,” in <i>Transactions on Machine Learning Research</i>, 2023."},"status":"public","oa":1,"acknowledgement":"D. Wu and M. Mondelli are partially supported by the 2019 Lopez-Loreta Prize. V. Kungurtsev was supported by the OP VVV project CZ.02.1.01/0.0/0.0/16_019/0000765 \"Research Center for Informatics\".","external_id":{"arxiv":["2210.06819"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","date_published":"2023-02-28T00:00:00Z","author":[{"first_name":"Diyuan","last_name":"Wu","full_name":"Wu, Diyuan","id":"1a5914c2-896a-11ed-bdf8-fb80621a0635"},{"first_name":"Vyacheslav","last_name":"Kungurtsev","full_name":"Kungurtsev, Vyacheslav"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco"}],"article_processing_charge":"No","date_updated":"2024-09-10T13:03:20Z","alternative_title":["TMLR"],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06819","open_access":"1"}],"publication_status":"published","month":"02","language":[{"iso":"eng"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"day":"28"}]