[{"file_date_updated":"2023-11-07T09:16:23Z","publication":"Forum of Mathematics, Pi","day":"24","_id":"14499","doi":"10.1017/fmp.2023.17","publication_identifier":{"issn":["2050-5086"]},"acknowledgement":"Kwan was supported for part of this work by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-2141064. Sah was supported by the PD Soros Fellowship. Sauermann was supported by NSF Award DMS-2100157, and for part of this work by a Sloan Research Fellowship.","oa":1,"type":"journal_article","department":[{"_id":"MaKw"}],"citation":{"ista":"Kwan MA, Sah A, Sauermann L, Sawhney M. 2023. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 11, e21.","apa":"Kwan, M. A., Sah, A., Sauermann, L., &#38; Sawhney, M. (2023). Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. <i>Forum of Mathematics, Pi</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fmp.2023.17\">https://doi.org/10.1017/fmp.2023.17</a>","short":"M.A. Kwan, A. Sah, L. Sauermann, M. Sawhney, Forum of Mathematics, Pi 11 (2023).","mla":"Kwan, Matthew Alan, et al. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” <i>Forum of Mathematics, Pi</i>, vol. 11, e21, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/fmp.2023.17\">10.1017/fmp.2023.17</a>.","ama":"Kwan MA, Sah A, Sauermann L, Sawhney M. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. <i>Forum of Mathematics, Pi</i>. 2023;11. doi:<a href=\"https://doi.org/10.1017/fmp.2023.17\">10.1017/fmp.2023.17</a>","chicago":"Kwan, Matthew Alan, Ashwin Sah, Lisa Sauermann, and Mehtaab Sawhney. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” <i>Forum of Mathematics, Pi</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/fmp.2023.17\">https://doi.org/10.1017/fmp.2023.17</a>.","ieee":"M. A. Kwan, A. Sah, L. Sauermann, and M. Sawhney, “Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture,” <i>Forum of Mathematics, Pi</i>, vol. 11. Cambridge University Press, 2023."},"publication_status":"published","project":[{"grant_number":"101076777","_id":"bd95085b-d553-11ed-ba76-e55d3349be45","name":"Randomness and structure in combinatorics"}],"article_processing_charge":"Yes","oa_version":"Published Version","file":[{"date_created":"2023-11-07T09:16:23Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"14500","date_updated":"2023-11-07T09:16:23Z","success":1,"file_size":1218719,"file_name":"2023_ForumMathematics_Kwan.pdf","checksum":"54b824098d59073cc87a308d458b0a3e","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper, we study edge statistics in Ramsey graphs, in particular obtaining very precise control of the distribution of the number of edges in a random vertex subset of a C-Ramsey graph. This brings together two ongoing lines of research: the study of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability for low-degree polynomials of independent random variables.\r\n\r\nThe proof proceeds via an ‘additive structure’ dichotomy on the degree sequence and involves a wide range of different tools from Fourier analysis, random matrix theory, the theory of Boolean functions, probabilistic combinatorics and low-rank approximation. In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright theorem on small-ball probability for polynomials of Gaussians, which we believe is of independent interest. One of the consequences of our result is the resolution of an old conjecture of Erdős and McKay, for which Erdős reiterated in several of his open problem collections and for which he offered one of his notorious monetary prizes."}],"scopus_import":"1","year":"2023","arxiv":1,"date_updated":"2025-09-09T13:16:15Z","isi":1,"month":"08","date_published":"2023-08-24T00:00:00Z","publisher":"Cambridge University Press","quality_controlled":"1","title":"Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        11","status":"public","language":[{"iso":"eng"}],"external_id":{"isi":["001123866200001"],"arxiv":["2208.02874"]},"author":[{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567"},{"last_name":"Sah","full_name":"Sah, Ashwin","first_name":"Ashwin"},{"first_name":"Lisa","full_name":"Sauermann, Lisa","last_name":"Sauermann"},{"last_name":"Sawhney","full_name":"Sawhney, Mehtaab","first_name":"Mehtaab"}],"corr_author":"1","article_type":"original","date_created":"2023-11-07T09:02:48Z","ddc":["510"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"e21","keyword":["Discrete Mathematics and Combinatorics","Geometry and Topology","Mathematical Physics","Statistics and Probability","Algebra and Number Theory","Analysis"],"volume":11,"has_accepted_license":"1"},{"author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161"},{"first_name":"Behnam","full_name":"Amiri, Behnam","last_name":"Amiri"},{"orcid":"0000-0001-7149-769X","last_name":"Fäßler","full_name":"Fäßler, Florian","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM"}],"oa":1,"department":[{"_id":"FlSc"}],"type":"software","citation":{"chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>.","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>","mla":"Dimchev, Georgi A., et al. <i>Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023)."},"doi":"10.15479/AT:ISTA:14502","status":"public","tmp":{"short":"GNU AGPLv3  ","name":"GNU Affero General Public License v3.0","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html"},"day":"21","_id":"14502","file_date_updated":"2023-11-21T08:20:23Z","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","publisher":"Institute of Science and Technology Austria","date_published":"2023-11-21T00:00:00Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"10290"}]},"year":"2023","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"month":"11","date_updated":"2025-04-15T08:25:41Z","keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_created":"2023-11-08T20:23:07Z","creator":"fschur","access_level":"open_access","file_id":"14503","success":1,"date_updated":"2023-11-08T20:23:07Z","file_size":347641117,"checksum":"a8b9adeb53a4109dea4d5e39fa1acccf","file_name":"Computational_Toolbox_v1.2.zip","content_type":"application/zip"},{"file_name":"Readme.txt","checksum":"14db2addbfca61a085ba301ed6f2900b","content_type":"text/plain","date_updated":"2023-11-21T08:20:23Z","success":1,"file_size":1522,"file_id":"14586","date_created":"2023-11-21T08:20:23Z","relation":"main_file","access_level":"open_access","creator":"dernst"}],"corr_author":"1","ddc":["570"],"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"date_created":"2023-11-08T19:40:54Z"},{"status":"public","intvolume":"      1042","language":[{"iso":"eng"}],"external_id":{"isi":["001109871200001"],"arxiv":["2202.11071"]},"author":[{"full_name":"Mistakidis, S. I.","first_name":"S. I.","last_name":"Mistakidis"},{"orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"R. E.","full_name":"Barfknecht, R. E.","last_name":"Barfknecht"},{"first_name":"T.","full_name":"Fogarty, T.","last_name":"Fogarty"},{"first_name":"Th","full_name":"Busch, Th","last_name":"Busch"},{"last_name":"Foerster","first_name":"A.","full_name":"Foerster, A."},{"first_name":"P.","full_name":"Schmelcher, P.","last_name":"Schmelcher"},{"first_name":"N. T.","full_name":"Zinner, N. T.","last_name":"Zinner"}],"quality_controlled":"1","title":"Few-body Bose gases in low dimensions - A laboratory for quantum dynamics","page":"1-108","ec_funded":1,"volume":1042,"date_created":"2023-11-12T23:00:54Z","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1016/j.physrep.2023.10.004","publication_identifier":{"issn":["0370-1573"]},"acknowledgement":"This review could not have been written without the many fruitful discussions and great collaborations with colleagues throughout the years, there are too many to mention. Here we acknowledge conversations regarding the context of the review with Joachim Brand, Fabian Brauneis, Adolfo del Campo, Alberto Cappellaro, Panagiotis Giannakeas, Tommaso Macrí, Oleksandr Marchukov, Lukas Rammelmüller and Manuel Valiente. S. I. M. acknowledges support from the NSF through a grant for ITAMP at Harvard University. T.F. acknowledges support from JSPS KAKENHI Grant Number JP23K03290 and T.F. and Th.B. acknowledge support from the Okinawa Institute for Science and Technology Graduate University, and JST Grant Number JPMJPF2221. A.F. and R. E. B. acknowledge support from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) - Edital Universal 406563/2021-7. A. G. V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. P. S. is supported by the Cluster of Excellence ‘Advanced Imaging of Matter’ of the Deutsche Forschungsgemeinschaft (DFG) - EXC2056 - project ID 390715994. N. T. Z. is partially supported by the Independent Research Fund Denmark .","type":"journal_article","department":[{"_id":"MiLe"}],"citation":{"ieee":"S. I. Mistakidis <i>et al.</i>, “Few-body Bose gases in low dimensions - A laboratory for quantum dynamics,” <i>Physics Reports</i>, vol. 1042. Elsevier, pp. 1–108, 2023.","chicago":"Mistakidis, S. I., Artem Volosniev, R. E. Barfknecht, T. Fogarty, Th Busch, A. Foerster, P. Schmelcher, and N. T. Zinner. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” <i>Physics Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.physrep.2023.10.004\">https://doi.org/10.1016/j.physrep.2023.10.004</a>.","ama":"Mistakidis SI, Volosniev A, Barfknecht RE, et al. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. <i>Physics Reports</i>. 2023;1042:1-108. doi:<a href=\"https://doi.org/10.1016/j.physrep.2023.10.004\">10.1016/j.physrep.2023.10.004</a>","mla":"Mistakidis, S. I., et al. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” <i>Physics Reports</i>, vol. 1042, Elsevier, 2023, pp. 1–108, doi:<a href=\"https://doi.org/10.1016/j.physrep.2023.10.004\">10.1016/j.physrep.2023.10.004</a>.","short":"S.I. Mistakidis, A. Volosniev, R.E. Barfknecht, T. Fogarty, T. Busch, A. Foerster, P. Schmelcher, N.T. Zinner, Physics Reports 1042 (2023) 1–108.","apa":"Mistakidis, S. I., Volosniev, A., Barfknecht, R. E., Fogarty, T., Busch, T., Foerster, A., … Zinner, N. T. (2023). Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. <i>Physics Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physrep.2023.10.004\">https://doi.org/10.1016/j.physrep.2023.10.004</a>","ista":"Mistakidis SI, Volosniev A, Barfknecht RE, Fogarty T, Busch T, Foerster A, Schmelcher P, Zinner NT. 2023. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. 1042, 1–108."},"oa":1,"publication":"Physics Reports","day":"29","_id":"14513","arxiv":1,"date_updated":"2025-09-09T13:16:58Z","month":"11","isi":1,"year":"2023","scopus_import":"1","abstract":[{"lang":"eng","text":"Cold atomic gases have become a paradigmatic system for exploring fundamental physics, which at the same time allows for applications in quantum technologies. The accelerating developments in the field have led to a highly advanced set of engineering techniques that, for example, can tune interactions, shape the external geometry, select among a large set of atomic species with different properties, or control the number of atoms. In particular, it is possible to operate in lower dimensions and drive atomic systems into the strongly correlated regime. In this review, we discuss recent advances in few-body cold atom systems confined in low dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in one dimension and provide an introduction to the static properties before we review the state-of-the-art research into quantum dynamical processes stimulated by the presence of correlations. Besides discussing the fundamental physical phenomena arising in these systems, we also provide an overview of the calculational and numerical tools and methods that are commonly used, thus delivering a balanced and comprehensive overview of the field. We conclude by giving an outlook on possible future directions that are interesting to explore in these correlated systems."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2202.11071"}],"date_published":"2023-11-29T00:00:00Z","publisher":"Elsevier","article_processing_charge":"No","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","oa_version":"Preprint"},{"scopus_import":"1","abstract":[{"lang":"eng","text":"The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines."}],"year":"2023","date_updated":"2025-09-09T13:19:07Z","isi":1,"month":"10","date_published":"2023-10-20T00:00:00Z","publisher":"American Physical Society","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","file":[{"access_level":"open_access","creator":"dernst","date_created":"2023-11-13T09:12:58Z","relation":"main_file","file_id":"14524","file_size":724098,"date_updated":"2023-11-13T09:12:58Z","success":1,"content_type":"application/pdf","file_name":"2023_PhysRevLetters_Binysh.pdf","checksum":"1a419e25b762aadffbcc8eb2e609bd97"}],"oa_version":"Published Version","doi":"10.1103/PhysRevLett.131.168201","acknowledgement":"We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) through New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1, EP/S022848/1, EP/S029966/1, and EP/P031684/1.","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"oa":1,"citation":{"chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.131.168201\">https://doi.org/10.1103/PhysRevLett.131.168201</a>.","ieee":"J. Binysh <i>et al.</i>, “Modeling Leidenfrost levitation of soft elastic solids,” <i>Physical Review Letters</i>, vol. 131, no. 16. American Physical Society, 2023.","apa":"Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J. E., &#38; Souslov, A. (2023). Modeling Leidenfrost levitation of soft elastic solids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.131.168201\">https://doi.org/10.1103/PhysRevLett.131.168201</a>","ista":"Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 131(16), 168201.","ama":"Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation of soft elastic solids. <i>Physical Review Letters</i>. 2023;131(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.168201\">10.1103/PhysRevLett.131.168201</a>","mla":"Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” <i>Physical Review Letters</i>, vol. 131, no. 16, 168201, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.168201\">10.1103/PhysRevLett.131.168201</a>.","short":"J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023)."},"department":[{"_id":"ScWa"}],"type":"journal_article","file_date_updated":"2023-11-13T09:12:58Z","issue":"16","publication":"Physical Review Letters","_id":"14514","day":"20","volume":131,"related_material":{"record":[{"status":"public","relation":"research_data","id":"14523"}]},"has_accepted_license":"1","article_type":"original","date_created":"2023-11-12T23:00:55Z","ddc":["530"],"article_number":"168201","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"intvolume":"       131","status":"public","language":[{"iso":"eng"}],"external_id":{"isi":["001164388300007"],"pmid":["37925690"]},"author":[{"last_name":"Binysh","full_name":"Binysh, Jack","first_name":"Jack"},{"full_name":"Chakraborty, Indrajit","first_name":"Indrajit","last_name":"Chakraborty"},{"last_name":"Chubynsky","full_name":"Chubynsky, Mykyta V.","first_name":"Mykyta V."},{"id":"b6798902-eea0-11ea-9cbc-a8e14286c631","last_name":"Diaz Melian","first_name":"Vicente L","full_name":"Diaz Melian, Vicente L"},{"full_name":"Waitukaitis, Scott R","first_name":"Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James E.","full_name":"Sprittles, James E.","last_name":"Sprittles"},{"last_name":"Souslov","full_name":"Souslov, Anton","first_name":"Anton"}],"quality_controlled":"1","title":"Modeling Leidenfrost levitation of soft elastic solids","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"ddc":["530"],"date_created":"2023-11-12T23:00:55Z","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"041017","volume":13,"has_accepted_license":"1","title":"Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","intvolume":"        13","author":[{"last_name":"Reinhardt","full_name":"Reinhardt, Manuel","first_name":"Manuel"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ten Wolde, Pieter Rein","first_name":"Pieter Rein","last_name":"Ten Wolde"}],"external_id":{"isi":["001122894200001"],"arxiv":["2203.03461"]},"language":[{"iso":"eng"}],"article_processing_charge":"Yes","publication_status":"published","file":[{"file_name":"2023_PhysReviewX_Reinhardt.pdf","checksum":"32574aeebcca7347a4152c611b66b3d5","content_type":"application/pdf","success":1,"date_updated":"2023-11-13T09:00:19Z","file_size":1595223,"file_id":"14522","date_created":"2023-11-13T09:00:19Z","relation":"main_file","access_level":"open_access","creator":"dernst"}],"oa_version":"Published Version","month":"10","isi":1,"arxiv":1,"date_updated":"2025-09-09T13:18:24Z","year":"2023","scopus_import":"1","abstract":[{"text":"Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger.","lang":"eng"}],"publisher":"American Physical Society","date_published":"2023-10-26T00:00:00Z","publication":"Physical Review X","issue":"4","file_date_updated":"2023-11-13T09:00:19Z","_id":"14515","day":"26","acknowledgement":"We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis, and Daan Frenkel for useful discussions and a careful reading of the manuscript, and we thank Age Tjalma for support with obtaining the Gaussian approximation of the chemotaxis system. This work is part of the Dutch Research Council (NWO) and was performed at the research institute AMOLF. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant (024.003.019).","publication_identifier":{"eissn":["2160-3308"]},"doi":"10.1103/PhysRevX.13.041017","type":"journal_article","department":[{"_id":"GaTk"}],"citation":{"chicago":"Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” <i>Physical Review X</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">https://doi.org/10.1103/PhysRevX.13.041017</a>.","ieee":"M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” <i>Physical Review X</i>, vol. 13, no. 4. American Physical Society, 2023.","ista":"Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 13(4), 041017.","apa":"Reinhardt, M., Tkačik, G., &#38; Ten Wolde, P. R. (2023). Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">https://doi.org/10.1103/PhysRevX.13.041017</a>","short":"M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).","mla":"Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” <i>Physical Review X</i>, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">10.1103/PhysRevX.13.041017</a>.","ama":"Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. <i>Physical Review X</i>. 2023;13(4). doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">10.1103/PhysRevX.13.041017</a>"},"oa":1},{"conference":{"end_date":"2023-10-25","name":"AFT: Conference on Advances in Financial Technologies","start_date":"2023-10-23","location":"Princeton, NJ, United States"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"7","corr_author":"1","ddc":["000"],"date_created":"2023-11-12T23:00:55Z","has_accepted_license":"1","volume":282,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"STROBE: Streaming Threshold Random Beacons","quality_controlled":"1","author":[{"last_name":"Beaver","full_name":"Beaver, Donald","first_name":"Donald"},{"full_name":"Kelkar, Mahimna","first_name":"Mahimna","last_name":"Kelkar"},{"first_name":"Kevin","full_name":"Lewi, Kevin","last_name":"Lewi"},{"last_name":"Nikolaenko","full_name":"Nikolaenko, Valeria","first_name":"Valeria"},{"first_name":"Alberto","full_name":"Sonnino, Alberto","last_name":"Sonnino"},{"first_name":"Konstantinos","full_name":"Chalkias, Konstantinos","last_name":"Chalkias"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Naurois","full_name":"Naurois, Ladi De","first_name":"Ladi De"},{"full_name":"Roy, Arnab","first_name":"Arnab","last_name":"Roy"}],"language":[{"iso":"eng"}],"intvolume":"       282","status":"public","file":[{"file_name":"2023_LIPIcs_Beaver.pdf","checksum":"c1f98831cb5149d6c030c41999e6e960","content_type":"application/pdf","date_updated":"2023-11-13T08:44:34Z","success":1,"file_size":793495,"file_id":"14521","date_created":"2023-11-13T08:44:34Z","relation":"main_file","access_level":"open_access","creator":"dernst"}],"oa_version":"Published Version","publication_status":"published","article_processing_charge":"Yes","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2023-10-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1643"}],"scopus_import":"1","year":"2023","abstract":[{"text":"We revisit decentralized random beacons with a focus on practical distributed applications. Decentralized random beacons (Beaver and So, Eurocrypt'93) provide the functionality for n parties to generate an unpredictable sequence of bits in a way that cannot be biased, which is useful for any decentralized protocol requiring trusted randomness. Existing beacon constructions are highly inefficient in practical settings where protocol parties need to rejoin after crashes or disconnections, and more significantly where smart contracts may rely on arbitrary index points in high-volume streams. For this, we introduce a new notion of history-generating decentralized random beacons (HGDRBs). Roughly, the history-generation property of HGDRBs allows for previous beacon outputs to be efficiently generated knowing only the current value and the public key. At application layers, history-generation supports registering a sparser set of on-chain values if desired, so that apps like lotteries can utilize on-chain values without incurring high-frequency costs, enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose chains. Unlike rollups, HG is tailored specifically to recovering and verifying pseudorandom bit sequences and thus enjoys unique optimizations investigated in this work. We introduce STROBE: an efficient HGDRB construction which generalizes the original squaring-based RSA approach of Beaver and So. STROBE enjoys several useful properties that make it suited for practical applications that use beacons: 1) history-generating: it can regenerate and verify high-throughput beacon streams, supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying: NIZK-free, with state and validation employing a single ring element; 3) eco-friendly: stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient: the last beacon suffices to derive all past outputs, thus O(1) storage requirements for nodes serving the whole history.","lang":"eng"}],"alternative_title":["LIPIcs"],"month":"10","date_updated":"2024-10-09T21:07:17Z","day":"01","_id":"14516","file_date_updated":"2023-11-13T08:44:34Z","publication":"5th Conference on Advances in Financial Technologies","oa":1,"type":"conference","citation":{"mla":"Beaver, Donald, et al. “STROBE: Streaming Threshold Random Beacons.” <i>5th Conference on Advances in Financial Technologies</i>, vol. 282, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.AFT.2023.7\">10.4230/LIPIcs.AFT.2023.7</a>.","ama":"Beaver D, Kelkar M, Lewi K, et al. STROBE: Streaming Threshold Random Beacons. In: <i>5th Conference on Advances in Financial Technologies</i>. Vol 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.AFT.2023.7\">10.4230/LIPIcs.AFT.2023.7</a>","short":"D. Beaver, M. Kelkar, K. Lewi, V. Nikolaenko, A. Sonnino, K. Chalkias, E. Kokoris Kogias, L.D. Naurois, A. Roy, in:, 5th Conference on Advances in Financial Technologies, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ista":"Beaver D, Kelkar M, Lewi K, Nikolaenko V, Sonnino A, Chalkias K, Kokoris Kogias E, Naurois LD, Roy A. 2023. STROBE: Streaming Threshold Random Beacons. 5th Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, LIPIcs, vol. 282, 7.","apa":"Beaver, D., Kelkar, M., Lewi, K., Nikolaenko, V., Sonnino, A., Chalkias, K., … Roy, A. (2023). STROBE: Streaming Threshold Random Beacons. In <i>5th Conference on Advances in Financial Technologies</i> (Vol. 282). Princeton, NJ, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.AFT.2023.7\">https://doi.org/10.4230/LIPIcs.AFT.2023.7</a>","ieee":"D. Beaver <i>et al.</i>, “STROBE: Streaming Threshold Random Beacons,” in <i>5th Conference on Advances in Financial Technologies</i>, Princeton, NJ, United States, 2023, vol. 282.","chicago":"Beaver, Donald, Mahimna Kelkar, Kevin Lewi, Valeria Nikolaenko, Alberto Sonnino, Konstantinos Chalkias, Eleftherios Kokoris Kogias, Ladi De Naurois, and Arnab Roy. “STROBE: Streaming Threshold Random Beacons.” In <i>5th Conference on Advances in Financial Technologies</i>, Vol. 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.AFT.2023.7\">https://doi.org/10.4230/LIPIcs.AFT.2023.7</a>."},"department":[{"_id":"ElKo"}],"acknowledgement":"Work done when all the authors were at Novi Research, Meta.","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773034"]},"doi":"10.4230/LIPIcs.AFT.2023.7"},{"author":[{"orcid":"0000-0001-5588-8287","last_name":"Avni","full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","first_name":"Tobias","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer"},{"last_name":"Sadhukhan","first_name":"Suman","full_name":"Sadhukhan, Suman"},{"full_name":"Tkadlec, Josef","first_name":"Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde","full_name":"Zikelic, Dorde"}],"external_id":{"arxiv":["2307.15218"]},"language":[{"iso":"eng"}],"intvolume":"       372","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"page":"141-148","title":"Reachability poorman discrete-bidding games","quality_controlled":"1","has_accepted_license":"1","volume":372,"ec_funded":1,"conference":{"location":"Krakow, Poland","end_date":"2023-10-04","name":"ECAI: European Conference on Artificial Intelligence","start_date":"2023-09-30"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","ddc":["000"],"date_created":"2023-11-12T23:00:56Z","oa":1,"citation":{"short":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.","mla":"Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” <i>Frontiers in Artificial Intelligence and Applications</i>, vol. 372, IOS Press, 2023, pp. 141–48, doi:<a href=\"https://doi.org/10.3233/FAIA230264\">10.3233/FAIA230264</a>.","ama":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman discrete-bidding games. In: <i>Frontiers in Artificial Intelligence and Applications</i>. Vol 372. IOS Press; 2023:141-148. doi:<a href=\"https://doi.org/10.3233/FAIA230264\">10.3233/FAIA230264</a>","apa":"Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., &#38; Zikelic, D. (2023). Reachability poorman discrete-bidding games. In <i>Frontiers in Artificial Intelligence and Applications</i> (Vol. 372, pp. 141–148). Krakow, Poland: IOS Press. <a href=\"https://doi.org/10.3233/FAIA230264\">https://doi.org/10.3233/FAIA230264</a>","ista":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications. ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.","ieee":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability poorman discrete-bidding games,” in <i>Frontiers in Artificial Intelligence and Applications</i>, Krakow, Poland, 2023, vol. 372, pp. 141–148.","chicago":"Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde Zikelic. “Reachability Poorman Discrete-Bidding Games.” In <i>Frontiers in Artificial Intelligence and Applications</i>, 372:141–48. IOS Press, 2023. <a href=\"https://doi.org/10.3233/FAIA230264\">https://doi.org/10.3233/FAIA230264</a>."},"type":"conference","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_identifier":{"issn":["0922-6389"],"isbn":["9781643684369"]},"acknowledgement":"This research was supported in part by ISF grant no. 1679/21, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.","doi":"10.3233/FAIA230264","day":"28","_id":"14518","file_date_updated":"2023-11-13T10:16:10Z","publication":"Frontiers in Artificial Intelligence and Applications","publisher":"IOS Press","date_published":"2023-09-28T00:00:00Z","scopus_import":"1","year":"2023","abstract":[{"lang":"eng","text":"We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets."}],"month":"09","date_updated":"2025-03-31T16:01:09Z","arxiv":1,"oa_version":"Published Version","file":[{"file_id":"14529","date_created":"2023-11-13T10:16:10Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_name":"2023_FAIA_Avni.pdf","checksum":"1390ca38480fa4cf286b0f1a42e8c12f","content_type":"application/pdf","date_updated":"2023-11-13T10:16:10Z","success":1,"file_size":501011}],"publication_status":"published","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"article_processing_charge":"No"},{"day":"08","_id":"14523","title":"SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1","oa":1,"author":[{"last_name":"Binysh","first_name":"Jack","full_name":"Binysh, Jack"},{"last_name":"Chakraborty","first_name":"Indrajit","full_name":"Chakraborty, Indrajit"},{"last_name":"Chubynsky","full_name":"Chubynsky, Mykyta","first_name":"Mykyta"},{"last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L","first_name":"Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R"},{"full_name":"Sprittles, James","first_name":"James","last_name":"Sprittles"},{"full_name":"Souslov, Anton","first_name":"Anton","last_name":"Souslov"}],"department":[{"_id":"ScWa"}],"type":"research_data_reference","citation":{"short":"J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023).","ama":"Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>","mla":"Binysh, Jack, et al. <i>SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>.","apa":"Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J., &#38; Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8329143\">https://doi.org/10.5281/ZENODO.8329143</a>","ista":"Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>.","ieee":"J. Binysh <i>et al.</i>, “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1.” Zenodo, 2023.","chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8329143\">https://doi.org/10.5281/ZENODO.8329143</a>."},"doi":"10.5281/ZENODO.8329143","status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_created":"2023-11-13T09:12:11Z","ddc":["530"],"date_published":"2023-09-08T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8329143"}],"publisher":"Zenodo","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14514"}]},"year":"2023","abstract":[{"text":"see Readme file","lang":"eng"}],"date_updated":"2025-09-09T13:19:07Z","month":"09"},{"intvolume":"        14","status":"public","author":[{"first_name":"Amy","full_name":"Briffa, Amy","last_name":"Briffa"},{"full_name":"Hollwey, Elizabeth","first_name":"Elizabeth","last_name":"Hollwey","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"last_name":"Shahzad","first_name":"Zaigham","full_name":"Shahzad, Zaigham"},{"full_name":"Moore, Jonathan D.","first_name":"Jonathan D.","last_name":"Moore"},{"full_name":"Lyons, David B.","first_name":"David B.","last_name":"Lyons"},{"last_name":"Howard","first_name":"Martin","full_name":"Howard, Martin"},{"first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"external_id":{"pmid":["37944515"],"isi":["001113459100001"]},"language":[{"iso":"eng"}],"title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"953-967","volume":14,"ec_funded":1,"has_accepted_license":"1","article_type":"original","corr_author":"1","ddc":["570"],"date_created":"2023-11-19T23:00:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"acknowledgement":"We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z.","publication_identifier":{"issn":["2405-4712"],"eissn":["2405-4720"]},"doi":"10.1016/j.cels.2023.10.007","oa":1,"department":[{"_id":"DaZi"}],"type":"journal_article","citation":{"ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.","apa":"Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., &#38; Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>","short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","ama":"Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. 2023;14(11):953-967. doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>","mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>.","chicago":"Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>.","ieee":"A. Briffa <i>et al.</i>, “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” <i>Cell Systems</i>, vol. 14, no. 11. Elsevier, pp. 953–967, 2023."},"issue":"11","file_date_updated":"2023-11-20T11:22:52Z","publication":"Cell Systems","day":"15","_id":"14551","scopus_import":"1","abstract":[{"lang":"eng","text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale."}],"year":"2023","isi":1,"month":"11","date_updated":"2025-09-09T13:28:50Z","publisher":"Elsevier","date_published":"2023-11-15T00:00:00Z","publication_status":"published","project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020","grant_number":"725746"}],"article_processing_charge":"Yes (via OA deal)","file":[{"file_size":5587897,"success":1,"date_updated":"2023-11-20T11:22:52Z","content_type":"application/pdf","checksum":"101fdac59e6f1102d68ef91f2b5bd51a","file_name":"2023_CellSystems_Briffa.pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2023-11-20T11:22:52Z","file_id":"14580"}],"oa_version":"Published Version"},{"article_processing_charge":"No","OA_place":"repository","publication_status":"published","oa_version":"Submitted Version","date_updated":"2025-09-09T13:23:56Z","isi":1,"month":"11","scopus_import":"1","year":"2023","abstract":[{"lang":"eng","text":"Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth."}],"date_published":"2023-11-09T00:00:00Z","main_file_link":[{"url":"https://centaur.reading.ac.uk/113962/1/adh8830_CombinedPDF_v6.pdf","open_access":"1"}],"publisher":"AAAS","publication":"Science","issue":"6671","day":"09","_id":"14552","doi":"10.1126/science.adh8830","publication_identifier":{"eissn":["1095-9203"]},"acknowledgement":"The authors acknowledge funding for central project coordination from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution, and Behavior Program at Michigan State University; and AgBioResearch at Michigan State University. Site-specific funding is listed in the supplementary materials.","department":[{"_id":"NiBa"}],"citation":{"apa":"Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R., Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain within-population variability in herbivory. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adh8830\">https://doi.org/10.1126/science.adh8830</a>","ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683.","mla":"Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” <i>Science</i>, vol. 382, no. 6671, AAAS, 2023, pp. 679–83, doi:<a href=\"https://doi.org/10.1126/science.adh8830\">10.1126/science.adh8830</a>.","ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. <i>Science</i>. 2023;382(6671):679-683. doi:<a href=\"https://doi.org/10.1126/science.adh8830\">10.1126/science.adh8830</a>","chicago":"Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead, K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” <i>Science</i>. AAAS, 2023. <a href=\"https://doi.org/10.1126/science.adh8830\">https://doi.org/10.1126/science.adh8830</a>.","ieee":"M. L. Robinson <i>et al.</i>, “Plant size, latitude, and phylogeny explain within-population variability in herbivory,” <i>Science</i>, vol. 382, no. 6671. AAAS, pp. 679–683, 2023."},"type":"journal_article","oa":1,"date_created":"2023-11-19T23:00:54Z","article_type":"original","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":382,"related_material":{"record":[{"status":"public","relation":"research_data","id":"14579"}]},"OA_type":"green","quality_controlled":"1","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","page":"679-683","status":"public","intvolume":"       382","language":[{"iso":"eng"}],"author":[{"last_name":"Robinson","first_name":"M. L.","full_name":"Robinson, M. L."},{"first_name":"P. G.","full_name":"Hahn, P. G.","last_name":"Hahn"},{"full_name":"Inouye, B. D.","first_name":"B. D.","last_name":"Inouye"},{"last_name":"Underwood","full_name":"Underwood, N.","first_name":"N."},{"last_name":"Whitehead","full_name":"Whitehead, S. R.","first_name":"S. R."},{"full_name":"Abbott, K. C.","first_name":"K. C.","last_name":"Abbott"},{"last_name":"Bruna","first_name":"E. M.","full_name":"Bruna, E. M."},{"last_name":"Cacho","full_name":"Cacho, N. I.","first_name":"N. I."},{"last_name":"Dyer","full_name":"Dyer, L. A.","first_name":"L. A."},{"full_name":"Abdala-Roberts, L.","first_name":"L.","last_name":"Abdala-Roberts"},{"last_name":"Allen","first_name":"W. J.","full_name":"Allen, W. J."},{"last_name":"Andrade","full_name":"Andrade, J. F.","first_name":"J. F."},{"full_name":"Angulo, D. F.","first_name":"D. F.","last_name":"Angulo"},{"full_name":"Anjos, D.","first_name":"D.","last_name":"Anjos"},{"full_name":"Anstett, D. N.","first_name":"D. N.","last_name":"Anstett"},{"last_name":"Bagchi","first_name":"R.","full_name":"Bagchi, R."},{"last_name":"Bagchi","first_name":"S.","full_name":"Bagchi, S."},{"last_name":"Barbosa","first_name":"M.","full_name":"Barbosa, M."},{"last_name":"Barrett","first_name":"S.","full_name":"Barrett, S."},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","full_name":"Baskett, Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574"},{"first_name":"E.","full_name":"Ben-Simchon, E.","last_name":"Ben-Simchon"},{"last_name":"Bloodworth","first_name":"K. J.","full_name":"Bloodworth, K. J."},{"full_name":"Bronstein, J. L.","first_name":"J. L.","last_name":"Bronstein"},{"last_name":"Buckley","full_name":"Buckley, Y. M.","first_name":"Y. M."},{"last_name":"Burghardt","full_name":"Burghardt, K. T.","first_name":"K. T."},{"first_name":"C.","full_name":"Bustos-Segura, C.","last_name":"Bustos-Segura"},{"first_name":"E. S.","full_name":"Calixto, E. S.","last_name":"Calixto"},{"last_name":"Carvalho","full_name":"Carvalho, R. L.","first_name":"R. L."},{"last_name":"Castagneyrol","first_name":"B.","full_name":"Castagneyrol, B."},{"last_name":"Chiuffo","first_name":"M. C.","full_name":"Chiuffo, M. C."},{"first_name":"D.","full_name":"Cinoğlu, D.","last_name":"Cinoğlu"},{"last_name":"Cinto Mejía","first_name":"E.","full_name":"Cinto Mejía, E."},{"full_name":"Cock, M. C.","first_name":"M. C.","last_name":"Cock"},{"first_name":"R.","full_name":"Cogni, R.","last_name":"Cogni"},{"full_name":"Cope, O. L.","first_name":"O. L.","last_name":"Cope"},{"last_name":"Cornelissen","full_name":"Cornelissen, T.","first_name":"T."},{"last_name":"Cortez","full_name":"Cortez, D. R.","first_name":"D. R."},{"last_name":"Crowder","first_name":"D. W.","full_name":"Crowder, D. W."},{"last_name":"Dallstream","first_name":"C.","full_name":"Dallstream, C."},{"last_name":"Dáttilo","full_name":"Dáttilo, W.","first_name":"W."},{"full_name":"Davis, J. K.","first_name":"J. K.","last_name":"Davis"},{"last_name":"Dimarco","full_name":"Dimarco, R. D.","first_name":"R. D."},{"last_name":"Dole","first_name":"H. E.","full_name":"Dole, H. E."},{"last_name":"Egbon","first_name":"I. N.","full_name":"Egbon, I. N."},{"last_name":"Eisenring","full_name":"Eisenring, M.","first_name":"M."},{"last_name":"Ejomah","first_name":"A.","full_name":"Ejomah, A."},{"last_name":"Elderd","first_name":"B. D.","full_name":"Elderd, B. D."},{"full_name":"Endara, M. J.","first_name":"M. J.","last_name":"Endara"},{"last_name":"Eubanks","full_name":"Eubanks, M. D.","first_name":"M. D."},{"last_name":"Everingham","first_name":"S. E.","full_name":"Everingham, S. E."},{"last_name":"Farah","first_name":"K. N.","full_name":"Farah, K. N."},{"last_name":"Farias","first_name":"R. P.","full_name":"Farias, R. P."},{"last_name":"Fernandes","full_name":"Fernandes, A. P.","first_name":"A. P."},{"full_name":"Fernandes, G. W.","first_name":"G. W.","last_name":"Fernandes"},{"last_name":"Ferrante","full_name":"Ferrante, M.","first_name":"M."},{"full_name":"Finn, A.","first_name":"A.","last_name":"Finn"},{"full_name":"Florjancic, G. A.","first_name":"G. A.","last_name":"Florjancic"},{"first_name":"M. L.","full_name":"Forister, M. L.","last_name":"Forister"},{"last_name":"Fox","full_name":"Fox, Q. N.","first_name":"Q. N."},{"last_name":"Frago","full_name":"Frago, E.","first_name":"E."},{"first_name":"F. M.","full_name":"França, F. M.","last_name":"França"},{"last_name":"Getman-Pickering","full_name":"Getman-Pickering, A. S.","first_name":"A. S."},{"full_name":"Getman-Pickering, Z.","first_name":"Z.","last_name":"Getman-Pickering"},{"last_name":"Gianoli","full_name":"Gianoli, E.","first_name":"E."},{"last_name":"Gooden","full_name":"Gooden, B.","first_name":"B."},{"last_name":"Gossner","full_name":"Gossner, M. M.","first_name":"M. M."},{"first_name":"K. A.","full_name":"Greig, K. 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P.","first_name":"L. P."},{"last_name":"Weber","first_name":"M. G.","full_name":"Weber, M. G."},{"last_name":"Yamawo","full_name":"Yamawo, A.","first_name":"A."},{"last_name":"Yim","full_name":"Yim, S.","first_name":"S."},{"last_name":"Zarnetske","first_name":"P. L.","full_name":"Zarnetske, P. L."},{"full_name":"Zehr, L. N.","first_name":"L. N.","last_name":"Zehr"},{"full_name":"Zhong, Z.","first_name":"Z.","last_name":"Zhong"},{"last_name":"Wetzel","first_name":"W. C.","full_name":"Wetzel, W. C."}],"external_id":{"pmid":["37943897"],"isi":["001138596500033"]}},{"quality_controlled":"1","title":"Continuous-variable quantum tomography of high-amplitude states","language":[{"iso":"eng"}],"external_id":{"arxiv":["2212.07406"]},"author":[{"last_name":"Fedotova","orcid":"0000-0001-7242-015X","full_name":"Fedotova, Ekaterina","first_name":"Ekaterina","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab"},{"last_name":"Kuznetsov","first_name":"Nikolai","full_name":"Kuznetsov, Nikolai"},{"first_name":"Egor","full_name":"Tiunov, Egor","last_name":"Tiunov"},{"last_name":"Ulanov","full_name":"Ulanov, A. E.","first_name":"A. E."},{"full_name":"Lvovsky, A. I.","first_name":"A. I.","last_name":"Lvovsky"}],"status":"public","intvolume":"       108","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"042430","date_created":"2023-11-19T23:00:54Z","corr_author":"1","article_type":"original","volume":108,"_id":"14553","day":"30","publication":"Physical Review A","issue":"4","type":"journal_article","department":[{"_id":"JoFi"}],"citation":{"ama":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable quantum tomography of high-amplitude states. <i>Physical Review A</i>. 2023;108(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">10.1103/PhysRevA.108.042430</a>","mla":"Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude States.” <i>Physical Review A</i>, vol. 108, no. 4, 042430, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">10.1103/PhysRevA.108.042430</a>.","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023).","ista":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.","apa":"Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., &#38; Lvovsky, A. I. (2023). Continuous-variable quantum tomography of high-amplitude states. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">https://doi.org/10.1103/PhysRevA.108.042430</a>","ieee":"E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable quantum tomography of high-amplitude states,” <i>Physical Review A</i>, vol. 108, no. 4. American Physical Society, 2023.","chicago":"Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">https://doi.org/10.1103/PhysRevA.108.042430</a>."},"oa":1,"doi":"10.1103/PhysRevA.108.042430","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.07406"}],"date_published":"2023-10-30T00:00:00Z","publisher":"American Physical Society","arxiv":1,"date_updated":"2024-10-09T21:07:19Z","month":"10","year":"2023","scopus_import":"1","abstract":[{"text":"Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.","lang":"eng"}]},{"project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"article_processing_charge":"Yes (in subscription journal)","publication_status":"published","oa_version":"Published Version","file":[{"file_id":"14560","date_created":"2023-11-20T08:34:57Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_name":"2023_ESAIM_Cornalba.pdf","checksum":"3aef1475b1882c8dec112df9a5167c39","content_type":"application/pdf","success":1,"date_updated":"2023-11-20T08:34:57Z","file_size":1508534}],"date_updated":"2025-09-09T13:21:05Z","isi":1,"month":"09","scopus_import":"1","abstract":[{"lang":"eng","text":"The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format."}],"year":"2023","date_published":"2023-09-01T00:00:00Z","publisher":"EDP Sciences","publication":"ESAIM: Mathematical Modelling and Numerical Analysis","file_date_updated":"2023-11-20T08:34:57Z","issue":"5","_id":"14554","day":"01","doi":"10.1051/m2an/2023077","publication_identifier":{"eissn":["2804-7214"],"issn":["2822-7840"]},"acknowledgement":"The authors thank the anonymous referees for their careful reading of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered the first part of this project).","type":"journal_article","citation":{"apa":"Cornalba, F., &#38; Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/m2an/2023077\">https://doi.org/10.1051/m2an/2023077</a>","ista":"Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.","short":"F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.","mla":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 57, no. 5, EDP Sciences, 2023, pp. 3061–90, doi:<a href=\"https://doi.org/10.1051/m2an/2023077\">10.1051/m2an/2023077</a>.","ama":"Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. 2023;57(5):3061-3090. doi:<a href=\"https://doi.org/10.1051/m2an/2023077\">10.1051/m2an/2023077</a>","chicago":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences, 2023. <a href=\"https://doi.org/10.1051/m2an/2023077\">https://doi.org/10.1051/m2an/2023077</a>.","ieee":"F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime,” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 57, no. 5. EDP Sciences, pp. 3061–3090, 2023."},"department":[{"_id":"JuFi"}],"oa":1,"date_created":"2023-11-19T23:00:55Z","ddc":["510"],"corr_author":"1","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"volume":57,"related_material":{"link":[{"relation":"software","url":"https://github.com/tonyshardlow/RIDK-FD"}]},"has_accepted_license":"1","quality_controlled":"1","title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime","page":"3061-3090","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","intvolume":"        57","language":[{"iso":"eng"}],"author":[{"first_name":"Federico","full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149","last_name":"Cornalba","id":"2CEB641C-A400-11E9-A717-D712E6697425"},{"first_name":"Tony","full_name":"Shardlow, Tony","last_name":"Shardlow"}],"external_id":{"isi":["001087237700001"]}},{"date_updated":"2025-09-09T13:22:00Z","month":"10","isi":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems."}],"year":"2023","date_published":"2023-10-31T00:00:00Z","publisher":"Frontiers","article_processing_charge":"Yes","publication_status":"published","file":[{"file_id":"14561","access_level":"open_access","creator":"dernst","date_created":"2023-11-20T08:41:15Z","relation":"main_file","content_type":"application/pdf","file_name":"2023_FrontiersCellDevBio_Riedl.pdf","checksum":"61857fc3ebf019354932e7ee684658ce","file_size":2047622,"success":1,"date_updated":"2023-11-20T08:41:15Z"}],"oa_version":"Published Version","doi":"10.3389/fcell.2023.1287420","acknowledgement":"The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.","publication_identifier":{"eissn":["2296-634X"]},"department":[{"_id":"MiSi"}],"type":"journal_article","citation":{"ieee":"M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 11. Frontiers, 2023.","chicago":"Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fcell.2023.1287420\">https://doi.org/10.3389/fcell.2023.1287420</a>.","short":"M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).","mla":"Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 11, 1287420, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fcell.2023.1287420\">10.3389/fcell.2023.1287420</a>.","ama":"Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. <i>Frontiers in Cell and Developmental Biology</i>. 2023;11. doi:<a href=\"https://doi.org/10.3389/fcell.2023.1287420\">10.3389/fcell.2023.1287420</a>","apa":"Riedl, M., &#38; Sixt, M. K. (2023). The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fcell.2023.1287420\">https://doi.org/10.3389/fcell.2023.1287420</a>","ista":"Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11, 1287420."},"oa":1,"publication":"Frontiers in Cell and Developmental Biology","file_date_updated":"2023-11-20T08:41:15Z","day":"31","_id":"14555","volume":11,"has_accepted_license":"1","date_created":"2023-11-19T23:00:55Z","ddc":["570"],"corr_author":"1","article_type":"original","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"1287420","status":"public","intvolume":"        11","language":[{"iso":"eng"}],"author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","first_name":"Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"external_id":{"pmid":["38020899"],"isi":["001100762800001"]},"quality_controlled":"1","title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"_id":"14556","day":"01","file_date_updated":"2024-07-16T08:16:31Z","issue":"12","publication":"Journal of Evolutionary Biology","oa":1,"citation":{"ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 36(12), 14242.","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.14242\">https://doi.org/10.1111/jeb.14242</a>","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology 36 (2023).","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” <i>Journal of Evolutionary Biology</i>, vol. 36, no. 12, 14242, Wiley, 2023, doi:<a href=\"https://doi.org/10.1111/jeb.14242\">10.1111/jeb.14242</a>.","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. <i>Journal of Evolutionary Biology</i>. 2023;36(12). doi:<a href=\"https://doi.org/10.1111/jeb.14242\">10.1111/jeb.14242</a>","chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” <i>Journal of Evolutionary Biology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/jeb.14242\">https://doi.org/10.1111/jeb.14242</a>.","ieee":"E. L. Berdan <i>et al.</i>, “How chromosomal inversions reorient the evolutionary process,” <i>Journal of Evolutionary Biology</i>, vol. 36, no. 12. Wiley, 2023."},"type":"journal_article","department":[{"_id":"NiBa"}],"doi":"10.1111/jeb.14242","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","file":[{"file_id":"17253","access_level":"open_access","creator":"dernst","date_created":"2024-07-16T08:16:31Z","relation":"main_file","content_type":"application/pdf","file_name":"2023_JourEvolutionaryBio_Berdan.pdf","checksum":"93ae4fa700aab8646bc62f0adeed8f8f","file_size":1401726,"date_updated":"2024-07-16T08:16:31Z","success":1}],"oa_version":"Published Version","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-12-01T00:00:00Z","publisher":"Wiley","scopus_import":"1","abstract":[{"lang":"eng","text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach."}],"year":"2023","date_updated":"2025-09-09T13:22:35Z","month":"12","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"quality_controlled":"1","title":"How chromosomal inversions reorient the evolutionary process","language":[{"iso":"eng"}],"external_id":{"pmid":["37942504"],"isi":["001098690500001"]},"author":[{"full_name":"Berdan, Emma L.","first_name":"Emma L.","last_name":"Berdan"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"full_name":"Fragata, Inês","first_name":"Inês","last_name":"Fragata"},{"full_name":"Gilbert, Kimberly J.","first_name":"Kimberly J.","last_name":"Gilbert"},{"last_name":"Jay","first_name":"Paul","full_name":"Jay, Paul"},{"full_name":"Kapun, Martin","first_name":"Martin","last_name":"Kapun"},{"first_name":"Katie E.","full_name":"Lotterhos, Katie E.","last_name":"Lotterhos"},{"last_name":"Mérot","full_name":"Mérot, Claire","first_name":"Claire"},{"full_name":"Durmaz Mitchell, Esra","first_name":"Esra","last_name":"Durmaz Mitchell"},{"first_name":"Marta","full_name":"Pascual, Marta","last_name":"Pascual"},{"last_name":"Peichel","first_name":"Catherine L.","full_name":"Peichel, Catherine L."},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"last_name":"Schaeffer","first_name":"Stephen W.","full_name":"Schaeffer, Stephen W."},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Thomas","full_name":"Flatt, Thomas","last_name":"Flatt"}],"intvolume":"        36","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"14242","pmid":1,"article_type":"review","date_created":"2023-11-19T23:00:55Z","ddc":["570"],"has_accepted_license":"1","volume":36},{"article_type":"original","date_created":"2023-11-19T23:00:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":46,"title":"Epimorphisms and closure operators of categories of semilattices","quality_controlled":"1","page":"191-221","intvolume":"        46","status":"public","author":[{"full_name":"Dikranjan, D.","first_name":"D.","last_name":"Dikranjan"},{"last_name":"Giordano Bruno","full_name":"Giordano Bruno, A.","first_name":"A."},{"first_name":"Nicolò","full_name":"Zava, Nicolò","orcid":"0000-0001-8686-1888","last_name":"Zava","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad"}],"external_id":{"isi":["001098712000006"]},"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Algebraic Footprints of Geometric Features in Homology","_id":"26AD5D90-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I04245"}],"article_processing_charge":"No","oa_version":"None","abstract":[{"text":"Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem.","lang":"eng"}],"year":"2023","scopus_import":"1","month":"11","isi":1,"date_updated":"2025-09-09T13:23:12Z","publisher":"Taylor & Francis","date_published":"2023-11-01T00:00:00Z","issue":"S1","publication":"Quaestiones Mathematicae","_id":"14557","day":"01","acknowledgement":"The first and second named authors are members of GNSAGA – INdAM.\r\nThe third named author was supported by the FWF Grant, Project number I4245–N35","publication_identifier":{"issn":["1607-3606"],"eissn":["1727-933X"]},"doi":"10.2989/16073606.2023.2247731","department":[{"_id":"HeEd"}],"type":"journal_article","citation":{"ista":"Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.","apa":"Dikranjan, D., Giordano Bruno, A., &#38; Zava, N. (2023). Epimorphisms and closure operators of categories of semilattices. <i>Quaestiones Mathematicae</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.2989/16073606.2023.2247731\">https://doi.org/10.2989/16073606.2023.2247731</a>","mla":"Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of Semilattices.” <i>Quaestiones Mathematicae</i>, vol. 46, no. S1, Taylor &#38; Francis, 2023, pp. 191–221, doi:<a href=\"https://doi.org/10.2989/16073606.2023.2247731\">10.2989/16073606.2023.2247731</a>.","ama":"Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of categories of semilattices. <i>Quaestiones Mathematicae</i>. 2023;46(S1):191-221. doi:<a href=\"https://doi.org/10.2989/16073606.2023.2247731\">10.2989/16073606.2023.2247731</a>","short":"D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023) 191–221.","chicago":"Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure Operators of Categories of Semilattices.” <i>Quaestiones Mathematicae</i>. Taylor &#38; Francis, 2023. <a href=\"https://doi.org/10.2989/16073606.2023.2247731\">https://doi.org/10.2989/16073606.2023.2247731</a>.","ieee":"D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators of categories of semilattices,” <i>Quaestiones Mathematicae</i>, vol. 46, no. S1. Taylor &#38; Francis, pp. 191–221, 2023."}},{"article_type":"original","date_created":"2023-11-19T23:00:56Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":52,"ec_funded":1,"title":"Deterministic near-optimal approximation algorithms for dynamic set cover","quality_controlled":"1","page":"1132-1192","intvolume":"        52","status":"public","author":[{"last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan","first_name":"Sayan"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"},{"full_name":"Wu, Xiaowei","first_name":"Xiaowei","last_name":"Wu"}],"external_id":{"isi":["001116719500002"]},"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"},{"grant_number":"Z00422","name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"}],"article_processing_charge":"No","oa_version":"None","year":"2023","abstract":[{"text":"n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1)  O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with  amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f\r\n in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m\r\n and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds.","lang":"eng"}],"scopus_import":"1","isi":1,"month":"10","date_updated":"2025-09-09T13:19:49Z","publisher":"Society for Industrial and Applied Mathematics","date_published":"2023-10-01T00:00:00Z","issue":"5","publication":"SIAM Journal on Computing","_id":"14558","day":"01","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures (MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council, UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer (ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I 5982-N, and project Z 422-N. The third author was also supported by the Swedish Research Council (Reg. No. 2015-04659). The fourth author was also supported by the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ, 0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023).","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"doi":"10.1137/21M1428649","department":[{"_id":"MoHe"}],"type":"journal_article","citation":{"ista":"Bhattacharya S, Henzinger M, Nanongkai D, Wu X. 2023. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5), 1132–1192.","apa":"Bhattacharya, S., Henzinger, M., Nanongkai, D., &#38; Wu, X. (2023). Deterministic near-optimal approximation algorithms for dynamic set cover. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1428649\">https://doi.org/10.1137/21M1428649</a>","short":"S. Bhattacharya, M. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing 52 (2023) 1132–1192.","ama":"Bhattacharya S, Henzinger M, Nanongkai D, Wu X. Deterministic near-optimal approximation algorithms for dynamic set cover. <i>SIAM Journal on Computing</i>. 2023;52(5):1132-1192. doi:<a href=\"https://doi.org/10.1137/21M1428649\">10.1137/21M1428649</a>","mla":"Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” <i>SIAM Journal on Computing</i>, vol. 52, no. 5, Society for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:<a href=\"https://doi.org/10.1137/21M1428649\">10.1137/21M1428649</a>.","chicago":"Bhattacharya, Sayan, Monika Henzinger, Danupon Nanongkai, and Xiaowei Wu. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/21M1428649\">https://doi.org/10.1137/21M1428649</a>.","ieee":"S. Bhattacharya, M. Henzinger, D. Nanongkai, and X. Wu, “Deterministic near-optimal approximation algorithms for dynamic set cover,” <i>SIAM Journal on Computing</i>, vol. 52, no. 5. Society for Industrial and Applied Mathematics, pp. 1132–1192, 2023."}},{"isi":1,"month":"10","date_updated":"2025-09-09T13:20:26Z","arxiv":1,"abstract":[{"text":"We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.","lang":"eng"}],"year":"2023","scopus_import":"1","alternative_title":["LNCS"],"publisher":"Springer Nature","date_published":"2023-10-22T00:00:00Z","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2210.05304","open_access":"1"}],"article_processing_charge":"No","project":[{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"},{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","oa_version":"Preprint","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031453281"]},"doi":"10.1007/978-3-031-45329-8_17","citation":{"short":"M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, 21st International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2023, pp. 357–379.","mla":"Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, vol. 14215, Springer Nature, 2023, pp. 357–79, doi:<a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">10.1007/978-3-031-45329-8_17</a>.","ama":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably stabilizing neural controllers for discrete-time stochastic systems. In: <i>21st International Symposium on Automated Technology for Verification and Analysis</i>. Vol 14215. Springer Nature; 2023:357-379. doi:<a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">10.1007/978-3-031-45329-8_17</a>","ista":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning provably stabilizing neural controllers for discrete-time stochastic systems. 21st International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.","apa":"Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., &#38; Zikelic, D. (2023). Learning provably stabilizing neural controllers for discrete-time stochastic systems. In <i>21st International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 14215, pp. 357–379). Singapore, Singapore: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">https://doi.org/10.1007/978-3-031-45329-8_17</a>","ieee":"M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “Learning provably stabilizing neural controllers for discrete-time stochastic systems,” in <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.","chicago":"Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” In <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, 14215:357–79. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">https://doi.org/10.1007/978-3-031-45329-8_17</a>."},"type":"conference","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"oa":1,"publication":"21st International Symposium on Automated Technology for Verification and Analysis","day":"22","_id":"14559","ec_funded":1,"volume":14215,"date_created":"2023-11-19T23:00:56Z","corr_author":"1","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2023-10-27","start_date":"2023-10-24","location":"Singapore, Singapore"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","intvolume":"     14215","external_id":{"isi":["001456127300017"],"arxiv":["2210.05304"]},"author":[{"last_name":"Ansaripour","full_name":"Ansaripour, Matin","first_name":"Matin"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner"},{"last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","quality_controlled":"1","page":"357-379"},{"corr_author":"1","ddc":["570"],"date_created":"2023-11-20T09:22:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","first_name":"Florian","contributor_type":"researcher","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Javoor","contributor_type":"researcher","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Julia","contributor_type":"researcher","orcid":"0000-0002-3616-8580","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hermann","contributor_type":"researcher","last_name":"Döring"},{"first_name":"Florian","contributor_type":"researcher","last_name":"Hofer","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev"},{"first_name":"Victor-Valentin","contributor_type":"researcher","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Faix","first_name":"Jan","contributor_type":"researcher"},{"last_name":"Rottner","first_name":"Klemens","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12334"}]},"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-sa/4.0/","title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"status":"public","author":[{"first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"oa_version":"Published 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of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n"}],"month":"11","date_updated":"2025-04-23T08:46:21Z","publisher":"Institute of Science and Technology Austria","date_published":"2023-11-21T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"file_date_updated":"2023-11-20T11:49:58Z","day":"21","_id":"14562","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","doi":"10.15479/AT:ISTA:14562","oa":1,"citation":{"short":"F.K. Schur, (2023).","mla":"Schur, Florian KM. <i>Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>."},"department":[{"_id":"FlSc"}],"type":"research_data"},{"has_accepted_license":"1","volume":15,"keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"article_number":"e2022MS003391","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","ddc":["550"],"date_created":"2023-11-20T09:18:21Z","external_id":{"isi":["001106311000001"]},"author":[{"last_name":"Khouider","full_name":"Khouider, B.","first_name":"B."},{"last_name":"GOSWAMI","orcid":"0000-0001-8602-3083","first_name":"BIDYUT B","full_name":"GOSWAMI, BIDYUT B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b"},{"full_name":"Phani, R.","first_name":"R.","last_name":"Phani"},{"last_name":"Majda","first_name":"A. J.","full_name":"Majda, A. J."}],"language":[{"iso":"eng"}],"intvolume":"        15","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","quality_controlled":"1","publisher":"American Geophysical Union","date_published":"2023-11-01T00:00:00Z","year":"2023","scopus_import":"1","abstract":[{"text":"Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized.","lang":"eng"}],"month":"11","isi":1,"date_updated":"2025-09-09T13:29:45Z","file":[{"access_level":"open_access","creator":"dernst","date_created":"2023-11-20T11:29:16Z","relation":"main_file","file_id":"14582","file_size":6435697,"date_updated":"2023-11-20T11:29:16Z","success":1,"content_type":"application/pdf","file_name":"2023_JAMES_Khoulder.pdf","checksum":"e30329dd985559de0ddc7021ca7382b4"}],"oa_version":"Published Version","publication_status":"published","article_processing_charge":"Yes","oa":1,"citation":{"short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023).","mla":"Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2022ms003391\">10.1029/2022ms003391</a>.","ama":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. <i>Journal of Advances in Modeling Earth Systems</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1029/2022ms003391\">10.1029/2022ms003391</a>","apa":"Khouider, B., GOSWAMI, B. B., Phani, R., &#38; Majda, A. J. (2023). A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2022ms003391\">https://doi.org/10.1029/2022ms003391</a>","ista":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.","ieee":"B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 11. American Geophysical Union, 2023.","chicago":"Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2022ms003391\">https://doi.org/10.1029/2022ms003391</a>."},"department":[{"_id":"CaMu"}],"type":"journal_article","publication_identifier":{"eissn":["1942-2466"]},"acknowledgement":"The research of B.K. is supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020). This research was conducted during the visits of P.M. Krishna to the Center for Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November 2018 to June 2019 and July 2019 and October 2019, respectively. The authors are very grateful to the three anonymous reviewers who provided very thoughtful and constructive comments during the review process that helped greatly improve and shape the final version of the manuscript.","doi":"10.1029/2022ms003391","_id":"14564","day":"01","issue":"11","file_date_updated":"2023-11-20T11:29:16Z","publication":"Journal of Advances in Modeling Earth Systems"},{"day":"11","_id":"14579","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","department":[{"_id":"NiBa"}],"citation":{"ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>.","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133117\">https://doi.org/10.5281/ZENODO.8133117</a>","short":"W. Wetzel, (2023).","mla":"Wetzel, William. <i>HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>.","ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133117\">https://doi.org/10.5281/ZENODO.8133117</a>.","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023."},"type":"research_data_reference","oa":1,"author":[{"last_name":"Wetzel","first_name":"William","full_name":"Wetzel, William"}],"status":"public","doi":"10.5281/ZENODO.8133117","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-11-20T11:07:45Z","article_processing_charge":"No","ddc":["570"],"date_published":"2023-07-11T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133118"}],"publisher":"Zenodo","date_updated":"2025-09-09T13:23:55Z","month":"07","related_material":{"record":[{"id":"14552","status":"public","relation":"used_in_publication"}]},"year":"2023","abstract":[{"text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n","lang":"eng"}]}]