[{"oa_version":"Preprint","publication_status":"published","day":"14","abstract":[{"lang":"eng","text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles."}],"status":"public","date_updated":"2023-08-02T06:30:46Z","publication":"Physical Review E","external_id":{"arxiv":["2301.01545"],"isi":["001020265000002"]},"title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01545","open_access":"1"}],"issue":"6","scopus_import":"1","arxiv":1,"citation":{"chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>.","ieee":"M. Schörner <i>et al.</i>, “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” <i>Physical Review E</i>, vol. 107, no. 6. American Physical Society, 2023.","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>.","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., &#38; Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>"},"date_published":"2023-06-14T00:00:00Z","author":[{"first_name":"Maximilian","full_name":"Schörner, Maximilian","last_name":"Schörner"},{"orcid":"0000-0002-1838-2129","last_name":"Bethkenhagen","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","first_name":"Mandy","full_name":"Bethkenhagen, Mandy"},{"last_name":"Döppner","first_name":"Tilo","full_name":"Döppner, Tilo"},{"first_name":"Dominik","full_name":"Kraus, Dominik","last_name":"Kraus"},{"last_name":"Fletcher","first_name":"Luke B.","full_name":"Fletcher, Luke B."},{"last_name":"Glenzer","full_name":"Glenzer, Siegfried H.","first_name":"Siegfried H."},{"full_name":"Redmer, Ronald","first_name":"Ronald","last_name":"Redmer"}],"oa":1,"_id":"13231","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.107.065207","publisher":"American Physical Society","year":"2023","isi":1,"volume":107,"article_type":"original","month":"06","quality_controlled":"1","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","intvolume":"       107","article_number":"065207","date_created":"2023-07-16T22:01:10Z","acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","department":[{"_id":"BiCh"}]},{"scopus_import":"1","issue":"1","citation":{"ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” <i>Physical Review E</i>, vol. 107, no. 1. American Physical Society, 2023.","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. 2023;107(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","apa":"Rojas Vega, M. N., De Castro, P., &#38; Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>."},"arxiv":1,"publication":"Physical Review E","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"status":"public","date_updated":"2023-08-01T13:09:45Z","day":"24","oa_version":"Preprint","publication_status":"published","abstract":[{"lang":"eng","text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front."}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       107","date_created":"2023-02-12T23:00:59Z","article_number":"014608","department":[{"_id":"GradSch"}],"acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","isi":1,"article_type":"original","volume":107,"month":"01","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"quality_controlled":"1","type":"journal_article","doi":"10.1103/PhysRevE.107.014608","language":[{"iso":"eng"}],"year":"2023","publisher":"American Physical Society","date_published":"2023-01-24T00:00:00Z","author":[{"first_name":"Mauricio Nicolas","full_name":"Rojas Vega, Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","last_name":"Rojas Vega"},{"last_name":"De Castro","full_name":"De Castro, Pablo","first_name":"Pablo"},{"full_name":"Soto, Rodrigo","first_name":"Rodrigo","last_name":"Soto"}],"_id":"12545","oa":1},{"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"quality_controlled":"1","month":"03","article_type":"original","volume":107,"isi":1,"department":[{"_id":"ScWa"}],"acknowledgement":"This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.","article_number":"034901","date_created":"2023-04-02T22:01:10Z","intvolume":"       107","file_date_updated":"2023-11-27T09:51:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"article_processing_charge":"No","_id":"12789","oa":1,"author":[{"full_name":"Mujica, Nicolás","first_name":"Nicolás","last_name":"Mujica"},{"first_name":"Scott R","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"date_published":"2023-03-01T00:00:00Z","year":"2023","publisher":"American Physical Society","doi":"10.1103/PhysRevE.107.034901","language":[{"iso":"eng"}],"type":"journal_article","title":"Accurate determination of the shapes of granular charge distributions","file":[{"success":1,"date_updated":"2023-11-27T09:51:48Z","date_created":"2023-11-27T09:51:48Z","checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","file_id":"14612","file_size":1428631,"file_name":"PhysRevE.107.034901 (1).pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"swaituka"}],"external_id":{"isi":["000992142700001"]},"publication":"Physical Review E","citation":{"mla":"Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>.","apa":"Mujica, N., &#38; Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>","short":"N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).","ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901.","ama":"Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. 2023;107(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>","chicago":"Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>.","ieee":"N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” <i>Physical Review E</i>, vol. 107, no. 3. American Physical Society, 2023."},"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","call_identifier":"H2020"}],"has_accepted_license":"1","scopus_import":"1","issue":"3","abstract":[{"text":"Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.","lang":"eng"}],"ec_funded":1,"day":"01","oa_version":"Published Version","publication_status":"published","date_updated":"2023-11-28T09:22:25Z","status":"public","acknowledged_ssus":[{"_id":"M-Shop"}]},{"arxiv":1,"citation":{"mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. 2023;108(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>.","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” <i>Physical Review E</i>, vol. 108, no. 5. American Physical Society, 2023."},"issue":"5","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.02153"}],"publication":"Physical Review E","related_material":{"record":[{"relation":"research_data","id":"12869","status":"public"}],"link":[{"url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation","relation":"software"}]},"external_id":{"arxiv":["2305.02153"]},"title":"Stochastic cellular automaton model of culture formation","date_updated":"2023-11-13T07:47:30Z","status":"public","publication_status":"published","oa_version":"Preprint","day":"08","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.","lang":"eng"}],"article_number":"054307","date_created":"2023-05-04T08:35:01Z","acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":"       108","month":"11","quality_controlled":"1","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"volume":108,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.108.054307","publisher":"American Physical Society","year":"2023","type":"journal_article","author":[{"last_name":"Klausen","first_name":"Frederik Ravn","full_name":"Klausen, Frederik Ravn"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard"}],"oa":1,"_id":"12890","date_published":"2023-11-08T00:00:00Z"},{"type":"journal_article","doi":"10.1103/physreve.106.034321","language":[{"iso":"eng"}],"year":"2022","publisher":"American Physical Society","date_published":"2022-09-29T00:00:00Z","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Jakub","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"},{"full_name":"Zikelic, Dorde","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic"},{"first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"},{"first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"_id":"12257","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","intvolume":"       106","date_created":"2023-01-16T09:57:57Z","article_number":"034321","acknowledgement":"K.C. acknowledges support from ERC Start Grant No. (279307: Graph Games), ERC Consolidator Grant No. (863818: ForM-SMart), and Austrian Science Fund (FWF)\r\nGrants No. P23499-N23 and No. S11407-N23 (RiSE). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385.","department":[{"_id":"KrCh"}],"isi":1,"article_type":"original","volume":106,"month":"09","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"quality_controlled":"1","status":"public","date_updated":"2025-07-14T09:09:49Z","day":"29","publication_status":"published","oa_version":"Preprint","abstract":[{"text":"Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings.","lang":"eng"}],"ec_funded":1,"scopus_import":"1","issue":"3","arxiv":1,"citation":{"chicago":"Chatterjee, Krishnendu, Jakub Svoboda, Dorde Zikelic, Andreas Pavlogiannis, and Josef Tkadlec. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” <i>Physical Review E</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physreve.106.034321\">https://doi.org/10.1103/physreve.106.034321</a>.","ieee":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, and J. Tkadlec, “Social balance on networks: Local minima and best-edge dynamics,” <i>Physical Review E</i>, vol. 106, no. 3. American Physical Society, 2022.","ista":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. 2022. Social balance on networks: Local minima and best-edge dynamics. Physical Review E. 106(3), 034321.","apa":"Chatterjee, K., Svoboda, J., Zikelic, D., Pavlogiannis, A., &#38; Tkadlec, J. (2022). Social balance on networks: Local minima and best-edge dynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.106.034321\">https://doi.org/10.1103/physreve.106.034321</a>","short":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical Review E 106 (2022).","mla":"Chatterjee, Krishnendu, et al. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” <i>Physical Review E</i>, vol. 106, no. 3, 034321, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physreve.106.034321\">10.1103/physreve.106.034321</a>.","ama":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. Social balance on networks: Local minima and best-edge dynamics. <i>Physical Review E</i>. 2022;106(3). doi:<a href=\"https://doi.org/10.1103/physreve.106.034321\">10.1103/physreve.106.034321</a>"},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"publication":"Physical Review E","title":"Social balance on networks: Local minima and best-edge dynamics","external_id":{"isi":["000870243100001"],"arxiv":["2210.02394"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.02394"}]},{"status":"public","date_updated":"2021-11-26T11:21:16Z","abstract":[{"lang":"eng","text":"In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events."}],"day":"28","publication_status":"published","oa_version":"Preprint","scopus_import":"1","issue":"2","citation":{"apa":"Davis, L. K., Ford, I. J., Šarić, A., &#38; Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.101.022420\">https://doi.org/10.1103/physreve.101.022420</a>","short":"L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).","mla":"Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” <i>Physical Review E</i>, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physreve.101.022420\">10.1103/physreve.101.022420</a>.","ista":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 101(2), 022420.","ama":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. <i>Physical Review E</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/physreve.101.022420\">10.1103/physreve.101.022420</a>","chicago":"Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” <i>Physical Review E</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physreve.101.022420\">https://doi.org/10.1103/physreve.101.022420</a>.","ieee":"L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” <i>Physical Review E</i>, vol. 101, no. 2. American Physical Society, 2020."},"title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","external_id":{"pmid":["32168597"]},"publication":"Physical Review E","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/571687"}],"type":"journal_article","year":"2020","publisher":"American Physical Society","doi":"10.1103/physreve.101.022420","language":[{"iso":"eng"}],"date_published":"2020-02-28T00:00:00Z","_id":"10352","oa":1,"author":[{"last_name":"Davis","first_name":"Luke K.","full_name":"Davis, Luke K."},{"full_name":"Ford, Ian J.","first_name":"Ian J.","last_name":"Ford"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"last_name":"Hoogenboom","first_name":"Bart W.","full_name":"Hoogenboom, Bart W."}],"intvolume":"       101","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","acknowledgement":"We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos (Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto) for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering and Physical Sciences Research Council (EP/L504889/1, B.W.H.).","pmid":1,"article_number":"022420","date_created":"2021-11-26T09:41:04Z","volume":101,"article_type":"original","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"quality_controlled":"1","month":"02"},{"article_type":"original","volume":100,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"month":"07","intvolume":"       100","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["532"],"article_processing_charge":"No","department":[{"_id":"BjHo"}],"date_created":"2019-08-09T09:40:41Z","article_number":"013112","date_published":"2019-07-25T00:00:00Z","oa":1,"_id":"6779","author":[{"first_name":"Balachandra","full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri"},{"full_name":"Pallantla, Ravi Kumar","first_name":"Ravi Kumar","last_name":"Pallantla"},{"first_name":"Michael F.","full_name":"Schatz, Michael F.","last_name":"Schatz"},{"last_name":"Grigoriev","full_name":"Grigoriev, Roman O.","first_name":"Roman O."}],"type":"journal_article","publisher":"American Physical Society","year":"2019","language":[{"iso":"eng"}],"doi":"10.1103/physreve.100.013112","external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","publication":"Physical Review E","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.05860"}],"issue":"1","scopus_import":"1","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"citation":{"short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., &#38; Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.100.013112\">https://doi.org/10.1103/physreve.100.013112</a>","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” <i>Physical Review E</i>, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physreve.100.013112\">10.1103/physreve.100.013112</a>.","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. <i>Physical Review E</i>. 2019;100(1). doi:<a href=\"https://doi.org/10.1103/physreve.100.013112\">10.1103/physreve.100.013112</a>","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” <i>Physical Review E</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physreve.100.013112\">https://doi.org/10.1103/physreve.100.013112</a>.","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” <i>Physical Review E</i>, vol. 100, no. 1. American Physical Society, 2019."},"arxiv":1,"ec_funded":1,"abstract":[{"lang":"eng","text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace."}],"oa_version":"Preprint","publication_status":"published","day":"25","status":"public","date_updated":"2024-02-28T13:13:00Z"},{"day":"10","oa_version":"Submitted Version","publication_status":"published","abstract":[{"text":"We present a numerical study of wavy supercritical cylindrical Couette flow between counter-rotating cylinders in which the wavy pattern propagates either prograde with the inner cylinder or retrograde opposite the rotation of the inner cylinder. The wave propagation reversals from prograde to retrograde and vice versa occur at distinct values of the inner cylinder Reynolds number when the associated frequency of the wavy instability vanishes. The reversal occurs for both twofold and threefold symmetric wavy vortices. Moreover, the wave propagation reversal only occurs for sufficiently strong counter-rotation. The flow pattern reversal appears to be intrinsic in the system as either periodic boundary conditions or fixed end wall boundary conditions for different system sizes always result in the wave propagation reversal. We present a detailed bifurcation sequence and parameter space diagram with respect to retrograde behavior of wavy flows. The retrograde propagation of the instability occurs when the inner Reynolds number is about two times the outer Reynolds number. The mechanism for the retrograde propagation is associated with the inviscidly unstable region near the inner cylinder and the direction of the global average azimuthal velocity. Flow dynamics, spatio-temporal behavior, global mean angular velocity, and torque of the flow with the wavy pattern are explored.","lang":"eng"}],"status":"public","date_updated":"2023-10-10T13:30:03Z","publication":"Physical Review E","title":"Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow","main_file_link":[{"url":"https://arxiv.org/pdf/physics/0505164.pdf","open_access":"1"}],"scopus_import":"1","issue":"5","citation":{"apa":"Altmeyer, S., &#38; Lueptow, R. (2017). Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">https://doi.org/10.1103/PhysRevE.95.053103</a>","short":"S. Altmeyer, R. Lueptow, Physical Review E 95 (2017).","mla":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” <i>Physical Review E</i>, vol. 95, no. 5, 053103, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">10.1103/PhysRevE.95.053103</a>.","ista":"Altmeyer S, Lueptow R. 2017. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 95(5), 053103.","ama":"Altmeyer S, Lueptow R. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. <i>Physical Review E</i>. 2017;95(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">10.1103/PhysRevE.95.053103</a>","chicago":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">https://doi.org/10.1103/PhysRevE.95.053103</a>.","ieee":"S. Altmeyer and R. Lueptow, “Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow,” <i>Physical Review E</i>, vol. 95, no. 5. American Physical Society, 2017."},"date_published":"2017-05-10T00:00:00Z","author":[{"full_name":"Altmeyer, Sebastian","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","last_name":"Altmeyer","orcid":"0000-0001-5964-0203"},{"first_name":"Richard","full_name":"Lueptow, Richard","last_name":"Lueptow"}],"_id":"673","oa":1,"type":"journal_article","doi":"10.1103/PhysRevE.95.053103","language":[{"iso":"eng"}],"year":"2017","publisher":"American Physical Society","volume":95,"month":"05","publication_identifier":{"issn":["2470-0045"]},"publist_id":"7049","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        95","date_created":"2018-12-11T11:47:50Z","article_number":"053103","department":[{"_id":"BjHo"}]},{"day":"21","publication_status":"published","oa_version":"Submitted Version","abstract":[{"text":"In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region.","lang":"eng"}],"ec_funded":1,"status":"public","date_updated":"2023-10-10T13:29:38Z","publication":"Physical Review E","title":"Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1707.00320"}],"scopus_import":"1","issue":"6","alternative_title":["Rapid Communications"],"citation":{"ieee":"D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” <i>Physical Review E</i>, vol. 96, no. 6. American Physical Society, 2017.","chicago":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>.","ama":"De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. 2017;96(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>","ista":"De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.","mla":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>.","apa":"De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>","short":"D. De Martino, Physical Review E 96 (2017)."},"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"date_published":"2017-12-21T00:00:00Z","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","first_name":"Daniele"}],"_id":"548","oa":1,"type":"journal_article","doi":"10.1103/PhysRevE.96.060401","language":[{"iso":"eng"}],"year":"2017","publisher":"American Physical Society","volume":96,"month":"12","publist_id":"7266","publication_identifier":{"issn":["2470-0045"]},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":"        96","article_number":"060401","date_created":"2018-12-11T11:47:06Z","department":[{"_id":"GaTk"}]}]