[{"keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"degree_awarded":"PhD","article_processing_charge":"No","date_updated":"2024-03-25T23:30:25Z","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"14591","relation":"part_of_dissertation","status":"public"},{"id":"9887","relation":"part_of_dissertation","status":"public"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:14510","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","first_name":"Nataliia"}],"date_published":"2023-11-10T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-11-23T13:10:55Z","month":"11","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["570"],"day":"10","file":[{"file_name":"Thesis_Gnyliukh_final_08_11_23.docx","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_size":20824903,"file_id":"14567","date_updated":"2023-11-20T09:18:51Z","date_created":"2023-11-20T09:18:51Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"ngnyliuk","relation":"source_file"},{"file_size":24871844,"checksum":"bfc96d47fc4e7e857dd71656097214a4","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_updated":"2023-11-23T13:10:55Z","file_id":"14568","embargo":"2024-11-23","embargo_to":"open_access","content_type":"application/pdf","date_created":"2023-11-20T09:23:11Z","relation":"main_file","creator":"ngnyliuk","access_level":"closed"}],"publication_status":"published","ec_funded":1,"date_created":"2023-11-10T09:10:06Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"citation":{"mla":"Gnyliukh, Nataliia. <i>Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>","apa":"Gnyliukh, N. (2023). <i>Mechanism of clathrin-coated vesicle  formation during endocytosis in plants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>."},"status":"public","has_accepted_license":"1","year":"2023","supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"_id":"14510","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","page":"180"},{"day":"29","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"11","intvolume":"      1042","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2202.11071","open_access":"1"}],"publication_status":"published","date_published":"2023-11-29T00:00:00Z","author":[{"last_name":"Mistakidis","first_name":"S. I.","full_name":"Mistakidis, S. I."},{"first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barfknecht","first_name":"R. E.","full_name":"Barfknecht, R. E."},{"last_name":"Fogarty","first_name":"T.","full_name":"Fogarty, T."},{"first_name":"Th","last_name":"Busch","full_name":"Busch, Th"},{"last_name":"Foerster","first_name":"A.","full_name":"Foerster, A."},{"full_name":"Schmelcher, P.","first_name":"P.","last_name":"Schmelcher"},{"full_name":"Zinner, N. T.","last_name":"Zinner","first_name":"N. T."}],"doi":"10.1016/j.physrep.2023.10.004","date_updated":"2023-11-13T08:01:57Z","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","oa":1,"status":"public","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 .","article_type":"original","external_id":{"arxiv":["2202.11071"]},"citation":{"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>","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>.","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.","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.","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>"},"publication_identifier":{"issn":["0370-1573"]},"page":"1-108","volume":1042,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14513","year":"2023","arxiv":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."}],"department":[{"_id":"MiLe"}],"title":"Few-body Bose gases in low dimensions - A laboratory for quantum dynamics","publication":"Physics Reports","publisher":"Elsevier","oa_version":"Preprint","ec_funded":1,"date_created":"2023-11-12T23:00:54Z"},{"abstract":[{"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.","lang":"eng"}],"publication":"Physical Review Letters","title":"Modeling Leidenfrost levitation of soft elastic solids","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","date_created":"2023-11-12T23:00:55Z","oa_version":"Published Version","oa":1,"acknowledgement":"We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) through New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1, EP/S022848/1, EP/S029966/1, and EP/P031684/1.","status":"public","issue":"16","article_type":"original","citation":{"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.","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>.","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>","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>.","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.","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)."},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"volume":131,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14514","year":"2023","has_accepted_license":"1","date_published":"2023-10-20T00:00:00Z","author":[{"last_name":"Binysh","first_name":"Jack","full_name":"Binysh, Jack"},{"last_name":"Chakraborty","first_name":"Indrajit","full_name":"Chakraborty, Indrajit"},{"full_name":"Chubynsky, Mykyta V.","first_name":"Mykyta V.","last_name":"Chubynsky"},{"id":"b6798902-eea0-11ea-9cbc-a8e14286c631","full_name":"Diaz Melian, Vicente L","last_name":"Diaz Melian","first_name":"Vicente L"},{"first_name":"Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sprittles, James E.","first_name":"James E.","last_name":"Sprittles"},{"first_name":"Anton","last_name":"Souslov","full_name":"Souslov, Anton"}],"article_processing_charge":"Yes (in subscription journal)","doi":"10.1103/PhysRevLett.131.168201","related_material":{"record":[{"status":"public","relation":"research_data","id":"14523"}]},"date_updated":"2023-11-13T09:21:30Z","scopus_import":"1","quality_controlled":"1","file_date_updated":"2023-11-13T09:12:58Z","article_number":"168201","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530"],"day":"20","month":"10","language":[{"iso":"eng"}],"intvolume":"       131","file":[{"checksum":"1a419e25b762aadffbcc8eb2e609bd97","file_name":"2023_PhysRevLetters_Binysh.pdf","file_size":724098,"date_updated":"2023-11-13T09:12:58Z","file_id":"14524","date_created":"2023-11-13T09:12:58Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"publication_status":"published"},{"abstract":[{"lang":"eng","text":"Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger."}],"arxiv":1,"oa_version":"Published Version","date_created":"2023-11-12T23:00:55Z","title":"Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories","department":[{"_id":"GaTk"}],"publication":"Physical Review X","publisher":"American Physical Society","citation":{"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>","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>.","short":"M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (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.","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.","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>.","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>"},"publication_identifier":{"eissn":["2160-3308"]},"status":"public","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).","oa":1,"external_id":{"arxiv":["2203.03461"]},"article_type":"original","issue":"4","_id":"14515","has_accepted_license":"1","year":"2023","volume":13,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","date_published":"2023-10-26T00:00:00Z","author":[{"last_name":"Reinhardt","first_name":"Manuel","full_name":"Reinhardt, Manuel"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ten Wolde, Pieter Rein","first_name":"Pieter Rein","last_name":"Ten Wolde"}],"date_updated":"2023-11-13T09:03:30Z","doi":"10.1103/PhysRevX.13.041017","article_processing_charge":"Yes","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-11-13T09:00:19Z","article_number":"041017","language":[{"iso":"eng"}],"month":"10","day":"26","ddc":["530"],"intvolume":"        13","publication_status":"published","file":[{"checksum":"32574aeebcca7347a4152c611b66b3d5","file_name":"2023_PhysReviewX_Reinhardt.pdf","file_size":1595223,"date_updated":"2023-11-13T09:00:19Z","file_id":"14522","date_created":"2023-11-13T09:00:19Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}]},{"quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes","alternative_title":["LIPIcs"],"date_updated":"2023-11-13T08:52:01Z","doi":"10.4230/LIPIcs.AFT.2023.7","date_published":"2023-10-01T00:00:00Z","author":[{"full_name":"Beaver, Donald","last_name":"Beaver","first_name":"Donald"},{"first_name":"Mahimna","last_name":"Kelkar","full_name":"Kelkar, Mahimna"},{"full_name":"Lewi, Kevin","first_name":"Kevin","last_name":"Lewi"},{"first_name":"Valeria","last_name":"Nikolaenko","full_name":"Nikolaenko, Valeria"},{"last_name":"Sonnino","first_name":"Alberto","full_name":"Sonnino, Alberto"},{"full_name":"Chalkias, Konstantinos","first_name":"Konstantinos","last_name":"Chalkias"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"first_name":"Ladi De","last_name":"Naurois","full_name":"Naurois, Ladi De"},{"full_name":"Roy, Arnab","last_name":"Roy","first_name":"Arnab"}],"conference":{"end_date":"2023-10-25","name":"AFT: Conference on Advances in Financial Technologies","start_date":"2023-10-23","location":"Princeton, NJ, United States"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"7","file_date_updated":"2023-11-13T08:44:34Z","month":"10","language":[{"iso":"eng"}],"ddc":["000"],"day":"01","file":[{"checksum":"c1f98831cb5149d6c030c41999e6e960","file_name":"2023_LIPIcs_Beaver.pdf","file_size":793495,"date_updated":"2023-11-13T08:44:34Z","file_id":"14521","date_created":"2023-11-13T08:44:34Z","success":1,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":"       282","main_file_link":[{"url":"https://eprint.iacr.org/2021/1643","open_access":"1"}],"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"}],"date_created":"2023-11-12T23:00:55Z","oa_version":"Published Version","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"5th Conference on Advances in Financial Technologies","department":[{"_id":"ElKo"}],"title":"STROBE: Streaming Threshold Random Beacons","publication_identifier":{"isbn":["9783959773034"],"issn":["1868-8969"]},"citation":{"chicago":"Beaver, Donald, Mahimna Kelkar, Kevin Lewi, Valeria Nikolaenko, Alberto Sonnino, Konstantinos Chalkias, Eleftherios Kokoris Kogias, Ladi De Naurois, and Arnab Roy. “STROBE: Streaming Threshold Random Beacons.” In <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>.","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.","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>","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>","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.","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.","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>."},"acknowledgement":"Work done when all the authors were at Novi Research, Meta.","status":"public","oa":1,"has_accepted_license":"1","year":"2023","_id":"14516","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":282},{"intvolume":"        20","main_file_link":[{"url":"https://arxiv.org/abs/2206.14104","open_access":"1"}],"publication_status":"published","day":"20","month":"10","project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"bdb7cfc1-d553-11ed-ba76-d2eaab167738","grant_number":"101080139","name":"Open Superconducting Quantum Computers (OpenSuperQPlus)"}],"language":[{"iso":"eng"}],"article_number":"044054","acknowledged_ssus":[{"_id":"NanoFab"}],"author":[{"last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena"},{"orcid":"0000-0002-3415-4628","last_name":"Peruzzo","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda"},{"orcid":"0000-0001-6937-5773","last_name":"Hassani","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"first_name":"Andrea","last_name":"Trioni","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M"}],"date_published":"2023-10-20T00:00:00Z","article_processing_charge":"No","doi":"10.1103/PhysRevApplied.20.044054","related_material":{"record":[{"status":"public","relation":"research_data","id":"14520"}]},"date_updated":"2024-08-07T07:11:55Z","scopus_import":"1","quality_controlled":"1","volume":20,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14517","year":"2023","oa":1,"status":"public","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105), the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences, and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility.","issue":"4","article_type":"original","external_id":{"arxiv":["2206.14104"]},"citation":{"chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">https://doi.org/10.1103/PhysRevApplied.20.044054</a>.","ieee":"M. Zemlicka <i>et al.</i>, “Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses,” <i>Physical Review Applied</i>, vol. 20, no. 4. American Physical Society, 2023.","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., &#38; Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">https://doi.org/10.1103/PhysRevApplied.20.044054</a>","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. <i>Physical Review Applied</i>. 2023;20(4). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">10.1103/PhysRevApplied.20.044054</a>","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 20(4), 044054.","mla":"Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” <i>Physical Review Applied</i>, vol. 20, no. 4, 044054, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">10.1103/PhysRevApplied.20.044054</a>.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, Physical Review Applied 20 (2023)."},"publication_identifier":{"eissn":["2331-7019"]},"publication":"Physical Review Applied","title":"Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","ec_funded":1,"date_created":"2023-11-12T23:00:55Z","oa_version":"Preprint","arxiv":1,"abstract":[{"lang":"eng","text":"State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with  100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. "}]},{"date_published":"2023-09-28T00:00:00Z","author":[{"orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"first_name":"Suman","last_name":"Sadhukhan","full_name":"Sadhukhan, Suman"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","first_name":"Dorde"}],"article_processing_charge":"No","doi":"10.3233/FAIA230264","date_updated":"2025-07-14T09:09:57Z","scopus_import":"1","quality_controlled":"1","file_date_updated":"2023-11-13T10:16:10Z","conference":{"name":"ECAI: European Conference on Artificial Intelligence","end_date":"2023-10-04","location":"Krakow, Poland","start_date":"2023-09-30"},"tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"ddc":["000"],"day":"28","month":"09","language":[{"iso":"eng"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","intvolume":"       372","file":[{"date_updated":"2023-11-13T10:16:10Z","file_id":"14529","file_size":501011,"file_name":"2023_FAIA_Avni.pdf","checksum":"1390ca38480fa4cf286b0f1a42e8c12f","relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2023-11-13T10:16:10Z"}],"publication_status":"published","arxiv":1,"abstract":[{"text":"We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets.","lang":"eng"}],"publication":"Frontiers in Artificial Intelligence and Applications","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Reachability poorman discrete-bidding games","publisher":"IOS Press","date_created":"2023-11-12T23:00:56Z","ec_funded":1,"oa_version":"Published Version","oa":1,"status":"public","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.","external_id":{"arxiv":["2307.15218"]},"citation":{"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>","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>.","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>.","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.","short":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.","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>"},"publication_identifier":{"issn":["0922-6389"],"isbn":["9781643684369"]},"volume":372,"page":"141-148","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"14518","has_accepted_license":"1","year":"2023"},{"abstract":[{"lang":"eng","text":"see Readme file"}],"article_processing_charge":"No","related_material":{"record":[{"id":"14514","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.8329143","date_updated":"2023-11-13T09:21:31Z","date_published":"2023-09-08T00:00:00Z","author":[{"last_name":"Binysh","first_name":"Jack","full_name":"Binysh, Jack"},{"full_name":"Chakraborty, Indrajit","last_name":"Chakraborty","first_name":"Indrajit"},{"full_name":"Chubynsky, Mykyta","last_name":"Chubynsky","first_name":"Mykyta"},{"full_name":"Diaz Melian, Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L","last_name":"Diaz Melian"},{"first_name":"Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sprittles, James","first_name":"James","last_name":"Sprittles"},{"full_name":"Souslov, Anton","last_name":"Souslov","first_name":"Anton"}],"date_created":"2023-11-13T09:12:11Z","oa_version":"Published Version","publisher":"Zenodo","department":[{"_id":"ScWa"}],"title":"SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1","month":"09","citation":{"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>","short":"J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023).","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>.","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>.","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>.","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>"},"ddc":["530"],"day":"08","status":"public","oa":1,"year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8329143"}],"_id":"14523","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference"},{"oa":1,"status":"public","publication_identifier":{"issn":["2663 - 337X"]},"citation":{"ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>."},"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"260","year":"2023","has_accepted_license":"1","_id":"14530","supervisor":[{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order.  In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex.  "}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"title":"Synchronization in collectively moving active matter","oa_version":"Updated Version","date_created":"2023-11-15T09:59:03Z","day":"16","ddc":["530","570"],"language":[{"iso":"eng"}],"month":"11","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","creator":"mriedl","content_type":"application/pdf","date_created":"2023-11-15T09:52:54Z","success":1,"date_updated":"2023-11-15T09:52:54Z","file_id":"14536","file_size":36743942,"checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","file_name":"Thesis_Riedl_2023_corr.pdf"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10703"},{"status":"public","relation":"part_of_dissertation","id":"10791"},{"status":"public","relation":"part_of_dissertation","id":"7932"},{"id":"461","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"old_edition","id":"12726"}]},"alternative_title":["ISTA Thesis"],"doi":"10.15479/14530","date_updated":"2023-11-30T10:55:13Z","article_processing_charge":"No","date_published":"2023-11-16T00:00:00Z","author":[{"first_name":"Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"file_date_updated":"2023-11-15T09:52:54Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}]},{"degree_awarded":"PhD","author":[{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde"}],"date_published":"2023-11-15T00:00:00Z","doi":"10.15479/14539","date_updated":"2025-07-14T09:10:10Z","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1194"},{"id":"12000","relation":"part_of_dissertation","status":"public"},{"id":"12511","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14600"},{"status":"public","relation":"part_of_dissertation","id":"14601"},{"id":"9644","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10414"}]},"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"file_date_updated":"2023-11-15T13:44:24Z","language":[{"iso":"eng"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"month":"11","day":"15","ddc":["000"],"publication_status":"published","file":[{"date_updated":"2023-11-15T13:43:28Z","file_id":"14540","file_size":2116426,"file_name":"main.pdf","checksum":"f23e002b0059ca78e1fbb864da52dd7e","relation":"main_file","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-11-15T13:43:28Z"},{"file_name":"thesis_source.zip","checksum":"80ca37618a3c7b59866875f8be9b15ed","file_size":35884057,"file_id":"14541","date_updated":"2023-11-15T13:44:24Z","date_created":"2023-11-15T13:44:24Z","content_type":"application/x-zip-compressed","access_level":"closed","creator":"cchlebak","relation":"source_file"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","abstract":[{"lang":"eng","text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n"}],"oa_version":"Published Version","date_created":"2023-11-15T13:39:10Z","ec_funded":1,"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"title":"Automated verification and control of infinite state stochastic systems","publisher":"Institute of Science and Technology Austria","citation":{"short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","mla":"Zikelic, Dorde. <i>Automated Verification and Control of Infinite State Stochastic Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>.","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>","apa":"Zikelic, D. (2023). <i>Automated verification and control of infinite state stochastic systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>.","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023."},"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-036-7"]},"oa":1,"status":"public","_id":"14539","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"}],"year":"2023","page":"256","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"citation":{"ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. 2023. doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>, 2360005, World Scientific Publishing, 2023, doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>.","short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).","ista":"Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005.","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023.","chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>.","apa":"Henheik, S. J., Lauritsen, A. B., &#38; Roos, B. (2023). Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>"},"publication_identifier":{"eissn":["1793-6659"],"issn":["0129-055X"]},"status":"public","acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges  partial  financial  support  by  the  ERC  Advanced  Grant  “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","oa":1,"article_type":"original","external_id":{"arxiv":["2301.05621"]},"_id":"14542","year":"2023","has_accepted_license":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.","lang":"eng"}],"arxiv":1,"oa_version":"Published Version","date_created":"2023-11-15T23:48:14Z","ec_funded":1,"title":"Universality in low-dimensional BCS theory","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"publication":"Reviews in Mathematical Physics","publisher":"World Scientific Publishing","project":[{"call_identifier":"H2020","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d"},{"grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"language":[{"iso":"eng"}],"month":"10","day":"31","main_file_link":[{"url":"https://doi.org/10.1142/S0129055X2360005X","open_access":"1"}],"publication_status":"epub_ahead","scopus_import":"1","quality_controlled":"1","date_published":"2023-10-31T00:00:00Z","author":[{"last_name":"Henheik","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","full_name":"Henheik, Sven Joscha"},{"full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288"},{"full_name":"Roos, Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","orcid":"0000-0002-9071-5880","last_name":"Roos"}],"doi":"10.1142/s0129055x2360005x","date_updated":"2023-11-20T10:04:38Z","article_processing_charge":"Yes (in subscription journal)","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"2360005 "},{"file_date_updated":"2023-11-22T09:46:06Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"author":[{"first_name":"Duc T","last_name":"Phan","full_name":"Phan, Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-11-16T00:00:00Z","doi":"10.15479/14547","date_updated":"2023-11-30T10:56:04Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10851"},{"status":"public","relation":"part_of_dissertation","id":"13264"}]},"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"degree_awarded":"PhD","publication_status":"published","file":[{"relation":"main_file","creator":"pduc","access_level":"open_access","content_type":"application/pdf","date_created":"2023-11-17T13:36:44Z","date_updated":"2023-11-22T09:46:06Z","file_id":"14548","file_size":34828019,"file_name":"Phan_Thesis_pdfa.pdf","checksum":"db0c37d213bc002125bd59690e9db246"},{"creator":"pduc","access_level":"closed","relation":"source_file","date_created":"2023-11-17T13:44:53Z","content_type":"application/zip","file_id":"14549","date_updated":"2023-11-17T13:47:54Z","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","file_name":"dissertation_src.zip","file_size":279319709}],"day":"16","ddc":["530"],"language":[{"iso":"eng"}],"month":"11","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"title":"Resonant microwave spectroscopy of Al-InAs","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","date_created":"2023-11-17T13:45:26Z","abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}],"page":"80","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"}],"_id":"14547","year":"2023","has_accepted_license":"1","status":"public","oa":1,"citation":{"ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","mla":"Phan, Duc T. <i>Resonant Microwave Spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>.","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>","apa":"Phan, D. T. (2023). <i>Resonant microwave spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>."},"publication_identifier":{"issn":["2663 - 337X"]}},{"file_date_updated":"2023-11-20T11:22:52Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2023-11-15T00:00:00Z","author":[{"last_name":"Briffa","first_name":"Amy","full_name":"Briffa, Amy"},{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth","last_name":"Hollwey","first_name":"Elizabeth"},{"full_name":"Shahzad, Zaigham","first_name":"Zaigham","last_name":"Shahzad"},{"first_name":"Jonathan D.","last_name":"Moore","full_name":"Moore, Jonathan D."},{"full_name":"Lyons, David B.","last_name":"Lyons","first_name":"David B."},{"full_name":"Howard, Martin","first_name":"Martin","last_name":"Howard"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"article_processing_charge":"Yes (via OA deal)","date_updated":"2023-11-20T11:24:34Z","doi":"10.1016/j.cels.2023.10.007","scopus_import":"1","quality_controlled":"1","intvolume":"        14","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2023-11-20T11:22:52Z","file_id":"14580","date_updated":"2023-11-20T11:22:52Z","file_size":5587897,"file_name":"2023_CellSystems_Briffa.pdf","checksum":"101fdac59e6f1102d68ef91f2b5bd51a"}],"publication_status":"published","pmid":1,"ddc":["570"],"day":"15","month":"11","language":[{"iso":"eng"}],"project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020"}],"publication":"Cell Systems","title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","department":[{"_id":"DaZi"}],"publisher":"Elsevier","ec_funded":1,"date_created":"2023-11-19T23:00:54Z","oa_version":"Published Version","abstract":[{"text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.","lang":"eng"}],"volume":14,"page":"953-967","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14551","year":"2023","has_accepted_license":"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.","oa":1,"status":"public","issue":"11","external_id":{"pmid":["37944515"]},"article_type":"original","citation":{"short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.","mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <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>.","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>","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>","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.","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>."},"publication_identifier":{"issn":["2405-4712"],"eissn":["2405-4720"]}},{"oa_version":"None","date_created":"2023-11-19T23:00:54Z","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","department":[{"_id":"NiBa"}],"publication":"Science","publisher":"AAAS","abstract":[{"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.","lang":"eng"}],"_id":"14552","year":"2023","page":"679-683","volume":382,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 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>.","short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683.","ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. <i>Science</i>. 2023;382(6671):679-683. doi:<a href=\"https://doi.org/10.1126/science.adh8830\">10.1126/science.adh8830</a>","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>","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."},"publication_identifier":{"eissn":["1095-9203"]},"status":"public","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.","external_id":{"pmid":["37943897"]},"article_type":"original","issue":"6671","scopus_import":"1","quality_controlled":"1","date_published":"2023-11-09T00:00:00Z","author":[{"first_name":"M. L.","last_name":"Robinson","full_name":"Robinson, M. L."},{"full_name":"Hahn, P. G.","first_name":"P. G.","last_name":"Hahn"},{"full_name":"Inouye, B. D.","first_name":"B. D.","last_name":"Inouye"},{"full_name":"Underwood, N.","first_name":"N.","last_name":"Underwood"},{"full_name":"Whitehead, S. R.","first_name":"S. R.","last_name":"Whitehead"},{"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","first_name":"N. I.","full_name":"Cacho, N. I."},{"last_name":"Dyer","first_name":"L. A.","full_name":"Dyer, L. A."},{"full_name":"Abdala-Roberts, L.","first_name":"L.","last_name":"Abdala-Roberts"},{"first_name":"W. J.","last_name":"Allen","full_name":"Allen, W. J."},{"full_name":"Andrade, J. F.","last_name":"Andrade","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"},{"first_name":"D. N.","last_name":"Anstett","full_name":"Anstett, D. N."},{"full_name":"Bagchi, R.","first_name":"R.","last_name":"Bagchi"},{"full_name":"Bagchi, S.","last_name":"Bagchi","first_name":"S."},{"first_name":"M.","last_name":"Barbosa","full_name":"Barbosa, M."},{"first_name":"S.","last_name":"Barrett","full_name":"Barrett, S."},{"full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574"},{"full_name":"Ben-Simchon, E.","first_name":"E.","last_name":"Ben-Simchon"},{"first_name":"K. J.","last_name":"Bloodworth","full_name":"Bloodworth, K. J."},{"last_name":"Bronstein","first_name":"J. L.","full_name":"Bronstein, J. L."},{"full_name":"Buckley, Y. M.","last_name":"Buckley","first_name":"Y. M."},{"first_name":"K. T.","last_name":"Burghardt","full_name":"Burghardt, K. T."},{"full_name":"Bustos-Segura, C.","last_name":"Bustos-Segura","first_name":"C."},{"last_name":"Calixto","first_name":"E. S.","full_name":"Calixto, E. S."},{"first_name":"R. L.","last_name":"Carvalho","full_name":"Carvalho, R. L."},{"first_name":"B.","last_name":"Castagneyrol","full_name":"Castagneyrol, B."},{"full_name":"Chiuffo, M. C.","last_name":"Chiuffo","first_name":"M. C."},{"full_name":"Cinoğlu, D.","last_name":"Cinoğlu","first_name":"D."},{"full_name":"Cinto Mejía, E.","first_name":"E.","last_name":"Cinto Mejía"},{"full_name":"Cock, M. C.","last_name":"Cock","first_name":"M. C."},{"full_name":"Cogni, R.","last_name":"Cogni","first_name":"R."},{"full_name":"Cope, O. L.","last_name":"Cope","first_name":"O. L."},{"full_name":"Cornelissen, T.","first_name":"T.","last_name":"Cornelissen"},{"last_name":"Cortez","first_name":"D. R.","full_name":"Cortez, D. R."},{"first_name":"D. W.","last_name":"Crowder","full_name":"Crowder, D. W."},{"first_name":"C.","last_name":"Dallstream","full_name":"Dallstream, C."},{"full_name":"Dáttilo, W.","last_name":"Dáttilo","first_name":"W."},{"full_name":"Davis, J. K.","first_name":"J. K.","last_name":"Davis"},{"full_name":"Dimarco, R. D.","first_name":"R. D.","last_name":"Dimarco"},{"full_name":"Dole, H. E.","first_name":"H. E.","last_name":"Dole"},{"full_name":"Egbon, I. N.","first_name":"I. N.","last_name":"Egbon"},{"first_name":"M.","last_name":"Eisenring","full_name":"Eisenring, M."},{"last_name":"Ejomah","first_name":"A.","full_name":"Ejomah, A."},{"full_name":"Elderd, B. D.","last_name":"Elderd","first_name":"B. D."},{"first_name":"M. J.","last_name":"Endara","full_name":"Endara, M. J."},{"first_name":"M. D.","last_name":"Eubanks","full_name":"Eubanks, M. D."},{"full_name":"Everingham, S. E.","last_name":"Everingham","first_name":"S. E."},{"full_name":"Farah, K. N.","last_name":"Farah","first_name":"K. N."},{"first_name":"R. P.","last_name":"Farias","full_name":"Farias, R. P."},{"full_name":"Fernandes, A. P.","last_name":"Fernandes","first_name":"A. P."},{"last_name":"Fernandes","first_name":"G. W.","full_name":"Fernandes, G. W."},{"last_name":"Ferrante","first_name":"M.","full_name":"Ferrante, M."},{"first_name":"A.","last_name":"Finn","full_name":"Finn, A."},{"full_name":"Florjancic, G. A.","first_name":"G. A.","last_name":"Florjancic"},{"last_name":"Forister","first_name":"M. L.","full_name":"Forister, M. L."},{"full_name":"Fox, Q. N.","last_name":"Fox","first_name":"Q. N."},{"full_name":"Frago, E.","last_name":"Frago","first_name":"E."},{"first_name":"F. M.","last_name":"França","full_name":"França, F. M."},{"full_name":"Getman-Pickering, A. S.","first_name":"A. S.","last_name":"Getman-Pickering"},{"full_name":"Getman-Pickering, Z.","first_name":"Z.","last_name":"Getman-Pickering"},{"full_name":"Gianoli, E.","first_name":"E.","last_name":"Gianoli"},{"first_name":"B.","last_name":"Gooden","full_name":"Gooden, B."},{"full_name":"Gossner, M. M.","first_name":"M. M.","last_name":"Gossner"},{"full_name":"Greig, K. A.","last_name":"Greig","first_name":"K. A."},{"full_name":"Gripenberg, S.","first_name":"S.","last_name":"Gripenberg"},{"full_name":"Groenteman, R.","first_name":"R.","last_name":"Groenteman"},{"full_name":"Grof-Tisza, P.","first_name":"P.","last_name":"Grof-Tisza"},{"full_name":"Haack, N.","last_name":"Haack","first_name":"N."},{"full_name":"Hahn, L.","last_name":"Hahn","first_name":"L."},{"last_name":"Haq","first_name":"S. M.","full_name":"Haq, S. M."},{"last_name":"Helms","first_name":"A. M.","full_name":"Helms, A. M."},{"last_name":"Hennecke","first_name":"J.","full_name":"Hennecke, J."},{"last_name":"Hermann","first_name":"S. L.","full_name":"Hermann, S. L."},{"first_name":"L. M.","last_name":"Holeski","full_name":"Holeski, L. M."},{"full_name":"Holm, S.","last_name":"Holm","first_name":"S."},{"last_name":"Hutchinson","first_name":"M. C.","full_name":"Hutchinson, M. C."},{"last_name":"Jackson","first_name":"E. E.","full_name":"Jackson, E. E."},{"first_name":"S.","last_name":"Kagiya","full_name":"Kagiya, S."},{"last_name":"Kalske","first_name":"A.","full_name":"Kalske, A."},{"last_name":"Kalwajtys","first_name":"M.","full_name":"Kalwajtys, M."},{"first_name":"R.","last_name":"Karban","full_name":"Karban, R."},{"first_name":"R.","last_name":"Kariyat","full_name":"Kariyat, R."},{"full_name":"Keasar, T.","first_name":"T.","last_name":"Keasar"},{"full_name":"Kersch-Becker, M. F.","last_name":"Kersch-Becker","first_name":"M. F."},{"full_name":"Kharouba, H. M.","first_name":"H. M.","last_name":"Kharouba"},{"full_name":"Kim, T. N.","first_name":"T. N.","last_name":"Kim"},{"full_name":"Kimuyu, D. M.","last_name":"Kimuyu","first_name":"D. M."},{"full_name":"Kluse, J.","last_name":"Kluse","first_name":"J."},{"full_name":"Koerner, S. E.","last_name":"Koerner","first_name":"S. E."},{"first_name":"K. J.","last_name":"Komatsu","full_name":"Komatsu, K. J."},{"last_name":"Krishnan","first_name":"S.","full_name":"Krishnan, S."},{"first_name":"M.","last_name":"Laihonen","full_name":"Laihonen, M."},{"first_name":"L.","last_name":"Lamelas-López","full_name":"Lamelas-López, L."},{"last_name":"Lascaleia","first_name":"M. C.","full_name":"Lascaleia, M. C."},{"last_name":"Lecomte","first_name":"N.","full_name":"Lecomte, N."},{"full_name":"Lehn, C. R.","last_name":"Lehn","first_name":"C. R."},{"first_name":"X.","last_name":"Li","full_name":"Li, X."},{"last_name":"Lindroth","first_name":"R. L.","full_name":"Lindroth, R. L."},{"first_name":"E. F.","last_name":"Lopresti","full_name":"Lopresti, E. F."},{"first_name":"M.","last_name":"Losada","full_name":"Losada, M."},{"first_name":"A. M.","last_name":"Louthan","full_name":"Louthan, A. M."},{"full_name":"Luizzi, V. J.","first_name":"V. J.","last_name":"Luizzi"},{"first_name":"S. C.","last_name":"Lynch","full_name":"Lynch, S. C."},{"full_name":"Lynn, J. S.","last_name":"Lynn","first_name":"J. S."},{"full_name":"Lyon, N. J.","first_name":"N. J.","last_name":"Lyon"},{"full_name":"Maia, L. F.","first_name":"L. F.","last_name":"Maia"},{"full_name":"Maia, R. A.","first_name":"R. A.","last_name":"Maia"},{"last_name":"Mannall","first_name":"T. L.","full_name":"Mannall, T. L."},{"first_name":"B. S.","last_name":"Martin","full_name":"Martin, B. S."},{"full_name":"Massad, T. J.","last_name":"Massad","first_name":"T. J."},{"last_name":"Mccall","first_name":"A. C.","full_name":"Mccall, A. C."},{"full_name":"Mcgurrin, K.","last_name":"Mcgurrin","first_name":"K."},{"last_name":"Merwin","first_name":"A. C.","full_name":"Merwin, A. C."},{"full_name":"Mijango-Ramos, Z.","first_name":"Z.","last_name":"Mijango-Ramos"},{"full_name":"Mills, C. H.","first_name":"C. H.","last_name":"Mills"},{"first_name":"A. T.","last_name":"Moles","full_name":"Moles, A. T."},{"last_name":"Moore","first_name":"C. M.","full_name":"Moore, C. M."},{"last_name":"Moreira","first_name":"X.","full_name":"Moreira, X."},{"last_name":"Morrison","first_name":"C. R.","full_name":"Morrison, C. R."},{"first_name":"M. C.","last_name":"Moshobane","full_name":"Moshobane, M. C."},{"last_name":"Muola","first_name":"A.","full_name":"Muola, A."},{"last_name":"Nakadai","first_name":"R.","full_name":"Nakadai, R."},{"last_name":"Nakajima","first_name":"K.","full_name":"Nakajima, K."},{"full_name":"Novais, S.","last_name":"Novais","first_name":"S."},{"first_name":"C. O.","last_name":"Ogbebor","full_name":"Ogbebor, C. O."},{"full_name":"Ohsaki, H.","first_name":"H.","last_name":"Ohsaki"},{"last_name":"Pan","first_name":"V. S.","full_name":"Pan, V. S."},{"last_name":"Pardikes","first_name":"N. A.","full_name":"Pardikes, N. A."},{"full_name":"Pareja, M.","last_name":"Pareja","first_name":"M."},{"full_name":"Parthasarathy, N.","first_name":"N.","last_name":"Parthasarathy"},{"first_name":"R. R.","last_name":"Pawar","full_name":"Pawar, R. R."},{"full_name":"Paynter, Q.","first_name":"Q.","last_name":"Paynter"},{"full_name":"Pearse, I. S.","first_name":"I. S.","last_name":"Pearse"},{"first_name":"R. M.","last_name":"Penczykowski","full_name":"Penczykowski, R. M."},{"full_name":"Pepi, A. A.","first_name":"A. A.","last_name":"Pepi"},{"last_name":"Pereira","first_name":"C. C.","full_name":"Pereira, C. C."},{"last_name":"Phartyal","first_name":"S. S.","full_name":"Phartyal, S. S."},{"full_name":"Piper, F. I.","first_name":"F. I.","last_name":"Piper"},{"first_name":"K.","last_name":"Poveda","full_name":"Poveda, K."},{"last_name":"Pringle","first_name":"E. G.","full_name":"Pringle, E. G."},{"last_name":"Puy","first_name":"J.","full_name":"Puy, J."},{"first_name":"T.","last_name":"Quijano","full_name":"Quijano, T."},{"full_name":"Quintero, C.","first_name":"C.","last_name":"Quintero"},{"full_name":"Rasmann, S.","last_name":"Rasmann","first_name":"S."},{"first_name":"C.","last_name":"Rosche","full_name":"Rosche, C."},{"full_name":"Rosenheim, L. Y.","first_name":"L. Y.","last_name":"Rosenheim"},{"full_name":"Rosenheim, J. A.","last_name":"Rosenheim","first_name":"J. A."},{"last_name":"Runyon","first_name":"J. B.","full_name":"Runyon, J. B."},{"first_name":"A.","last_name":"Sadeh","full_name":"Sadeh, A."},{"last_name":"Sakata","first_name":"Y.","full_name":"Sakata, Y."},{"last_name":"Salcido","first_name":"D. M.","full_name":"Salcido, D. M."},{"full_name":"Salgado-Luarte, C.","first_name":"C.","last_name":"Salgado-Luarte"},{"first_name":"B. A.","last_name":"Santos","full_name":"Santos, B. A."},{"full_name":"Sapir, Y.","first_name":"Y.","last_name":"Sapir"},{"last_name":"Sasal","first_name":"Y.","full_name":"Sasal, Y."},{"first_name":"Y.","last_name":"Sato","full_name":"Sato, Y."},{"last_name":"Sawant","first_name":"M.","full_name":"Sawant, M."},{"full_name":"Schroeder, H.","first_name":"H.","last_name":"Schroeder"},{"first_name":"I.","last_name":"Schumann","full_name":"Schumann, I."},{"full_name":"Segoli, M.","last_name":"Segoli","first_name":"M."},{"first_name":"H.","last_name":"Segre","full_name":"Segre, H."},{"last_name":"Shelef","first_name":"O.","full_name":"Shelef, O."},{"first_name":"N.","last_name":"Shinohara","full_name":"Shinohara, N."},{"full_name":"Singh, R. P.","first_name":"R. P.","last_name":"Singh"},{"full_name":"Smith, D. S.","first_name":"D. S.","last_name":"Smith"},{"last_name":"Sobral","first_name":"M.","full_name":"Sobral, M."},{"last_name":"Stotz","first_name":"G. C.","full_name":"Stotz, G. C."},{"full_name":"Tack, A. J.M.","last_name":"Tack","first_name":"A. J.M."},{"full_name":"Tayal, M.","last_name":"Tayal","first_name":"M."},{"first_name":"J. F.","last_name":"Tooker","full_name":"Tooker, J. F."},{"first_name":"D.","last_name":"Torrico-Bazoberry","full_name":"Torrico-Bazoberry, D."},{"full_name":"Tougeron, K.","last_name":"Tougeron","first_name":"K."},{"last_name":"Trowbridge","first_name":"A. M.","full_name":"Trowbridge, A. M."},{"full_name":"Utsumi, S.","first_name":"S.","last_name":"Utsumi"},{"full_name":"Uyi, O.","first_name":"O.","last_name":"Uyi"},{"full_name":"Vaca-Uribe, J. L.","last_name":"Vaca-Uribe","first_name":"J. L."},{"first_name":"A.","last_name":"Valtonen","full_name":"Valtonen, A."},{"full_name":"Van Dijk, L. J.A.","first_name":"L. J.A.","last_name":"Van Dijk"},{"full_name":"Vandvik, V.","last_name":"Vandvik","first_name":"V."},{"full_name":"Villellas, J.","last_name":"Villellas","first_name":"J."},{"full_name":"Waller, L. P.","first_name":"L. P.","last_name":"Waller"},{"last_name":"Weber","first_name":"M. G.","full_name":"Weber, M. G."},{"full_name":"Yamawo, A.","last_name":"Yamawo","first_name":"A."},{"last_name":"Yim","first_name":"S.","full_name":"Yim, S."},{"last_name":"Zarnetske","first_name":"P. L.","full_name":"Zarnetske, P. L."},{"last_name":"Zehr","first_name":"L. N.","full_name":"Zehr, L. N."},{"full_name":"Zhong, Z.","first_name":"Z.","last_name":"Zhong"},{"full_name":"Wetzel, W. C.","first_name":"W. C.","last_name":"Wetzel"}],"doi":"10.1126/science.adh8830","date_updated":"2023-11-20T11:17:34Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"14579"}]},"article_processing_charge":"No","intvolume":"       382","publication_status":"published","language":[{"iso":"eng"}],"month":"11","pmid":1,"day":"09"},{"volume":108,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14553","year":"2023","status":"public","oa":1,"issue":"4","article_type":"original","external_id":{"arxiv":["2212.07406"]},"citation":{"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>.","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.","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>","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>.","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.","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023)."},"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"publication":"Physical Review A","department":[{"_id":"JoFi"}],"title":"Continuous-variable quantum tomography of high-amplitude states","publisher":"American Physical Society","date_created":"2023-11-19T23:00:54Z","oa_version":"Preprint","arxiv":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"}],"intvolume":"       108","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.07406","open_access":"1"}],"publication_status":"published","day":"30","month":"10","language":[{"iso":"eng"}],"article_number":"042430","author":[{"first_name":"Ekaterina","last_name":"Fedotova","orcid":"0000-0001-7242-015X","full_name":"Fedotova, Ekaterina","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab"},{"last_name":"Kuznetsov","first_name":"Nikolai","full_name":"Kuznetsov, Nikolai"},{"full_name":"Tiunov, Egor","last_name":"Tiunov","first_name":"Egor"},{"full_name":"Ulanov, A. E.","last_name":"Ulanov","first_name":"A. E."},{"last_name":"Lvovsky","first_name":"A. I.","full_name":"Lvovsky, A. I."}],"date_published":"2023-10-30T00:00:00Z","article_processing_charge":"No","date_updated":"2023-11-20T10:26:51Z","doi":"10.1103/PhysRevA.108.042430","scopus_import":"1","quality_controlled":"1"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3061-3090","volume":57,"has_accepted_license":"1","year":"2023","_id":"14554","article_type":"original","issue":"5","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).","oa":1,"status":"public","publication_identifier":{"issn":["2822-7840"],"eissn":["2804-7214"]},"citation":{"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.","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>","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>","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>.","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."},"publisher":"EDP Sciences","department":[{"_id":"JuFi"}],"title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime","publication":"ESAIM: Mathematical Modelling and Numerical Analysis","oa_version":"Published Version","date_created":"2023-11-19T23:00:55Z","ec_funded":1,"abstract":[{"lang":"eng","text":"The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format."}],"publication_status":"published","file":[{"checksum":"3aef1475b1882c8dec112df9a5167c39","file_name":"2023_ESAIM_Cornalba.pdf","file_size":1508534,"date_updated":"2023-11-20T08:34:57Z","file_id":"14560","date_created":"2023-11-20T08:34:57Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"intvolume":"        57","day":"01","ddc":["510"],"language":[{"iso":"eng"}],"project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"09","file_date_updated":"2023-11-20T08:34:57Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1051/m2an/2023077","date_updated":"2023-11-20T08:38:47Z","related_material":{"link":[{"relation":"software","url":"https://github.com/tonyshardlow/RIDK-FD"}]},"article_processing_charge":"Yes (in subscription journal)","date_published":"2023-09-01T00:00:00Z","author":[{"id":"2CEB641C-A400-11E9-A717-D712E6697425","full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149","last_name":"Cornalba","first_name":"Federico"},{"full_name":"Shardlow, Tony","first_name":"Tony","last_name":"Shardlow"}],"quality_controlled":"1","scopus_import":"1"},{"publisher":"Frontiers","department":[{"_id":"MiSi"}],"title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","publication":"Frontiers in Cell and Developmental Biology","oa_version":"Published Version","date_created":"2023-11-19T23:00:55Z","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."}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":11,"has_accepted_license":"1","year":"2023","_id":"14555","article_type":"original","oa":1,"status":"public","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"]},"citation":{"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>.","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.","short":"M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).","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>","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>.","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."},"article_number":"1287420","file_date_updated":"2023-11-20T08:41:15Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3389/fcell.2023.1287420","date_updated":"2023-11-20T08:44:17Z","article_processing_charge":"Yes","date_published":"2023-10-31T00:00:00Z","author":[{"last_name":"Riedl","orcid":"0000-0003-4844-6311","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"quality_controlled":"1","scopus_import":"1","publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2023-11-20T08:41:15Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":2047622,"file_name":"2023_FrontiersCellDevBio_Riedl.pdf","checksum":"61857fc3ebf019354932e7ee684658ce","date_updated":"2023-11-20T08:41:15Z","file_id":"14561"}],"intvolume":"        11","day":"31","ddc":["570"],"language":[{"iso":"eng"}],"month":"10"},{"language":[{"iso":"eng"}],"month":"11","day":"08","ddc":["570"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.14242"}],"publication_status":"epub_ahead","scopus_import":"1","quality_controlled":"1","date_published":"2023-11-08T00:00:00Z","author":[{"first_name":"Emma L.","last_name":"Berdan","full_name":"Berdan, Emma L."},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Fragata, Inês","last_name":"Fragata","first_name":"Inês"},{"full_name":"Gilbert, Kimberly J.","first_name":"Kimberly J.","last_name":"Gilbert"},{"full_name":"Jay, Paul","first_name":"Paul","last_name":"Jay"},{"full_name":"Kapun, Martin","first_name":"Martin","last_name":"Kapun"},{"last_name":"Lotterhos","first_name":"Katie E.","full_name":"Lotterhos, Katie E."},{"first_name":"Claire","last_name":"Mérot","full_name":"Mérot, Claire"},{"full_name":"Durmaz Mitchell, Esra","last_name":"Durmaz Mitchell","first_name":"Esra"},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"},{"first_name":"Catherine L.","last_name":"Peichel","full_name":"Peichel, Catherine L."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Schaeffer","first_name":"Stephen W.","full_name":"Schaeffer, Stephen W."},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Flatt, Thomas","last_name":"Flatt","first_name":"Thomas"}],"date_updated":"2023-11-20T08:51:09Z","doi":"10.1111/jeb.14242","article_processing_charge":"No","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_number":"14242","citation":{"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>","ieee":"E. L. Berdan <i>et al.</i>, “How chromosomal inversions reorient the evolutionary process,” <i>Journal of Evolutionary Biology</i>. Wiley, 2023.","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>.","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242.","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” <i>Journal of Evolutionary Biology</i>, 14242, Wiley, 2023, doi:<a href=\"https://doi.org/10.1111/jeb.14242\">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 (2023).","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. <i>Journal of Evolutionary Biology</i>. 2023. doi:<a href=\"https://doi.org/10.1111/jeb.14242\">10.1111/jeb.14242</a>"},"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"oa":1,"status":"public","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.","article_type":"review","_id":"14556","has_accepted_license":"1","year":"2023","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-11-19T23:00:55Z","title":"How chromosomal inversions reorient the evolutionary process","department":[{"_id":"NiBa"}],"publication":"Journal of Evolutionary Biology","publisher":"Wiley"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"191-221","volume":46,"year":"2023","_id":"14557","article_type":"original","issue":"S1","status":"public","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"]},"citation":{"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.","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>.","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>","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>","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>.","ista":"Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.","short":"D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023) 191–221."},"publisher":"Taylor & Francis","title":"Epimorphisms and closure operators of categories of semilattices","department":[{"_id":"HeEd"}],"publication":"Quaestiones Mathematicae","oa_version":"None","date_created":"2023-11-19T23:00:55Z","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"}],"publication_status":"published","intvolume":"        46","day":"01","project":[{"call_identifier":"FWF","grant_number":"I04245","name":"Algebraic Footprints of Geometric Features in Homology","_id":"26AD5D90-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"11","date_updated":"2023-11-20T09:24:48Z","doi":"10.2989/16073606.2023.2247731","article_processing_charge":"No","author":[{"full_name":"Dikranjan, D.","first_name":"D.","last_name":"Dikranjan"},{"last_name":"Giordano Bruno","first_name":"A.","full_name":"Giordano Bruno, A."},{"full_name":"Zava, Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","first_name":"Nicolò","last_name":"Zava","orcid":"0000-0001-8686-1888"}],"date_published":"2023-11-01T00:00:00Z","quality_controlled":"1","scopus_import":"1"},{"article_processing_charge":"No","doi":"10.1137/21M1428649","date_updated":"2025-07-15T12:51:52Z","author":[{"last_name":"Bhattacharya","first_name":"Sayan","full_name":"Bhattacharya, Sayan"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"},{"first_name":"Xiaowei","last_name":"Wu","full_name":"Wu, Xiaowei"}],"date_published":"2023-10-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","day":"01","month":"10","language":[{"iso":"eng"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"},{"name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"}],"publication_status":"published","intvolume":"        52","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"}],"publisher":"Society for Industrial and Applied Mathematics","publication":"SIAM Journal on Computing","department":[{"_id":"MoHe"}],"title":"Deterministic near-optimal approximation algorithms for dynamic set cover","ec_funded":1,"date_created":"2023-11-19T23:00:56Z","oa_version":"None","issue":"5","article_type":"original","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).","status":"public","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"citation":{"ama":"Bhattacharya S, Henzinger MH, 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>","short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing 52 (2023) 1132–1192.","ista":"Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. 2023. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5), 1132–1192.","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>.","ieee":"S. Bhattacharya, M. H. 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.","chicago":"Bhattacharya, Sayan, Monika H 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>.","apa":"Bhattacharya, S., Henzinger, M. H., 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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":52,"page":"1132-1192","year":"2023","_id":"14558"}]