[{"OA_place":"publisher","related_material":{"record":[{"id":"19658","status":"public","relation":"research_data"}]},"title":"Token-driven totally asymmetric simple exclusion processes","external_id":{"isi":["001496415600007"]},"article_type":"original","volume":111,"year":"2025","publication":"Physical Review E","acknowledgement":"B.K. thanks Stefano Elefante, Simon Rella, and Michal Hledík for their help with the usage of the cluster. B.K. additionally thanks Călin Guet and his group for help and advice. We thank M. Hennessey-Wesen and Luca Ciandrini for constructive comments on the paper. We thank Ankita Gupta (Indian Institute of Technology) for spotting a typographical error in Eq. (50) in the preprint version of this paper.","date_created":"2025-06-03T09:01:55Z","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"department":[{"_id":"GaTk"}],"has_accepted_license":"1","scopus_import":"1","article_number":"054122","quality_controlled":"1","citation":{"chicago":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Processes.” <i>Physical Review E</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/physreve.111.054122\">https://doi.org/10.1103/physreve.111.054122</a>.","apa":"Kavcic, B., &#38; Tkačik, G. (2025). Token-driven totally asymmetric simple exclusion processes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.111.054122\">https://doi.org/10.1103/physreve.111.054122</a>","short":"B. Kavcic, G. Tkačik, Physical Review E 111 (2025).","ama":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion processes. <i>Physical Review E</i>. 2025;111(5). doi:<a href=\"https://doi.org/10.1103/physreve.111.054122\">10.1103/physreve.111.054122</a>","mla":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Processes.” <i>Physical Review E</i>, vol. 111, no. 5, 054122, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/physreve.111.054122\">10.1103/physreve.111.054122</a>.","ista":"Kavcic B, Tkačik G. 2025. Token-driven totally asymmetric simple exclusion processes. Physical Review E. 111(5), 054122.","ieee":"B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion processes,” <i>Physical Review E</i>, vol. 111, no. 5. American Physical Society, 2025."},"author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"_id":"19785","file_date_updated":"2025-06-03T09:18:20Z","intvolume":"       111","publisher":"American Physical Society","type":"journal_article","isi":1,"abstract":[{"text":"We consider a family of totally asymmetric simple exclusion processes (TASEPs), consisting of particles on a lattice that require binding by a “token” in various physical configurations to advance over the lattice. Using a combination of theory and simulations, we address the following questions: (i) How does token binding kinetics affect the current-density relation on the lattice? (ii) How does this current-density relation depend on the scarcity of tokens? (iii) How do tokens propagate the effects of the locally imposed disorder (such as a slow site) over the entire lattice? (iv) How does a shared pool of tokens couple concurrent TASEPs running on multiple lattices? and (v) How do our results translate to TASEPs with open boundaries that exchange particles with the reservoir? Since real particle motion (including in biological systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations.","lang":"eng"}],"publication_status":"published","ddc":["570"],"date_published":"2025-05-19T00:00:00Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"05","OA_type":"hybrid","doi":"10.1103/physreve.111.054122","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"5","oa_version":"Published Version","date_updated":"2025-09-30T12:44:55Z","language":[{"iso":"eng"}],"oa":1,"day":"19","corr_author":"1","file":[{"checksum":"e8851ccd7cd0525c08c7308710413e74","file_id":"19787","date_created":"2025-06-03T09:18:20Z","file_size":2766143,"file_name":"2025_PhysRevE_Kavcic.pdf","success":1,"access_level":"open_access","creator":"dernst","date_updated":"2025-06-03T09:18:20Z","relation":"main_file","content_type":"application/pdf"}]},{"author":[{"orcid":" 0000-0002-8843-9485 ","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","first_name":"Ivan","full_name":"Palaia, Ivan"},{"full_name":"Asta, Adelchi J.","first_name":"Adelchi J.","last_name":"Asta"},{"full_name":"Dutta, Megh","last_name":"Dutta","first_name":"Megh"},{"full_name":"Warren, Patrick B.","last_name":"Warren","first_name":"Patrick B."},{"full_name":"Rotenberg, Benjamin","last_name":"Rotenberg","first_name":"Benjamin"},{"last_name":"Trizac","first_name":"Emmanuel","full_name":"Trizac, Emmanuel"}],"file_date_updated":"2025-10-23T09:15:56Z","_id":"20483","citation":{"mla":"Palaia, Ivan, et al. “Poisson-Nernst-Planck Charging Dynamics of an Electric Double-Layer Capacitor: Symmetric and Asymmetric Binary Electrolytes.” <i>Physical Review E</i>, vol. 112, no. 3, 035417, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/p4dg-snqf\">10.1103/p4dg-snqf</a>.","ista":"Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. 2025. Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes. Physical Review E. 112(3), 035417.","ieee":"I. Palaia, A. J. Asta, M. Dutta, P. B. Warren, B. Rotenberg, and E. Trizac, “Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes,” <i>Physical Review E</i>, vol. 112, no. 3. American Physical Society, 2025.","ama":"Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes. <i>Physical Review E</i>. 2025;112(3). doi:<a href=\"https://doi.org/10.1103/p4dg-snqf\">10.1103/p4dg-snqf</a>","short":"I. Palaia, A.J. Asta, M. Dutta, P.B. Warren, B. Rotenberg, E. Trizac, Physical Review E 112 (2025).","apa":"Palaia, I., Asta, A. J., Dutta, M., Warren, P. B., Rotenberg, B., &#38; Trizac, E. (2025). Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/p4dg-snqf\">https://doi.org/10.1103/p4dg-snqf</a>","chicago":"Palaia, Ivan, Adelchi J. Asta, Megh Dutta, Patrick B. Warren, Benjamin Rotenberg, and Emmanuel Trizac. “Poisson-Nernst-Planck Charging Dynamics of an Electric Double-Layer Capacitor: Symmetric and Asymmetric Binary Electrolytes.” <i>Physical Review E</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/p4dg-snqf\">https://doi.org/10.1103/p4dg-snqf</a>."},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"035417","type":"journal_article","isi":1,"publisher":"American Physical Society","PlanS_conform":"1","intvolume":"       112","year":"2025","publication":"Physical Review E","project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"external_id":{"isi":["001586173200001"],"arxiv":["2303.07859"]},"title":"Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes","article_type":"original","volume":112,"OA_place":"publisher","department":[{"_id":"AnSa"}],"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"date_created":"2025-10-16T13:15:16Z","acknowledgement":"This work has received funding from the European Union's Horizon 2020 and Horizon Europe research and innovation programs under the Marie Skłodowska-Curie Grants No. 674979-NANOTRANS (I.P., P.B.W., B.R., and E.T.), No. 101034413 (I.P.), and No. 101119598-FLUXIONIC (M.D., B.R., and E.T.), as well as from the European Research Council under Grant No. 863473 (B.R.). B.R. acknowledges financial support from the French Agence Nationale de la Recherche (ANR) under Grant No. ANR-21-CE29-0021-02 (DIADEM). I.P. thanks Anđela Šarić for further support at ISTA.","article_processing_charge":"Yes (via OA deal)","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"arxiv":1,"issue":"3","date_updated":"2025-12-01T13:06:51Z","oa_version":"Published Version","file":[{"file_name":"2025_PhysReviewE_Palaia.pdf","file_size":1211712,"success":1,"checksum":"658a9b1ce6b2edcf138b54c55a566f0e","file_id":"20521","date_created":"2025-10-23T09:15:56Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2025-10-23T09:15:56Z"}],"corr_author":"1","day":"29","status":"public","date_published":"2025-09-29T00:00:00Z","publication_status":"published","abstract":[{"text":"A parallel plate capacitor containing an electrolytic solution is the simplest model of a supercapacitor or electric double-layer capacitor. Using both analytical and numerical techniques, we solve the Poisson-Nernst-Planck equations for such a system, describing the mean-field charging dynamics of the capacitor, when a constant potential difference is abruptly applied to its plates. Working at constant total number of ions, we focus on the physical processes involved in the relaxation and, whenever possible, give its functional shape and exact time constants. We first review and study the case of a symmetric binary electrolyte, where we assume the two ionic species to have the same charges and diffusivities. We then relax these assumptions and present results for a generic strong (i.e fully dissociated) binary electrolyte. At low electrolyte concentration, the relaxation is simple to understand, as the dynamics of positive and negative ions appear decoupled. At higher electrolyte concentration, we distinguish several regimes. In the linear regime (low voltages), relaxation is multiexponential, it starts by the buildup of the equilibrium charge profile and continues with neutral mass diffusion, and the relevant timescales feature both the average and the Nernst-Hartley diffusion coefficients. In the purely nonlinear regime (intermediate voltages), the initial relaxation is slowed down exponentially due to increased capacitance, while bulk effects become more and more evident. In the fully nonlinear regime (high voltages), the dynamics of charge and mass are completely entangled and, asymptotically, the relaxation is linear in time. We finally discuss nonideal behavior in real capacitors and provide conditions for which mean-field is expected to hold.","lang":"eng"}],"ddc":["530"],"doi":"10.1103/p4dg-snqf","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"hybrid","month":"09"},{"oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"arxiv":1,"oa_version":"Published Version","date_updated":"2025-12-29T11:19:34Z","issue":"6","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2025-12-29T11:15:42Z","file_name":"2025_PhysReviewE_Fitzgerald.pdf","file_size":2131491,"success":1,"checksum":"d593e933f976c3f3cde37ad66539d57d","file_id":"20862","date_created":"2025-12-29T11:15:42Z"}],"corr_author":"1","day":"01","status":"public","date_published":"2025-12-01T00:00:00Z","ddc":["530"],"abstract":[{"text":"We report on an experimental active matter system with motion restricted to four cardinal directions. Our particles are magnetite-doped colloidal spheres driven by the Quincke electrorotational instability. The absence of a magnetic field (|𝑩|=0) leads to circular trajectories interspersed with short spontaneous runs. Intermediate fields (|𝑩|≲20mT) linearize the motion along the axis perpendicular to 𝑩. At high magnetic fields, we observe the surprising emergence of a second, distinct linearization along the axis parallel to 𝑩. With numerical simulations, we show that this behavior can be explained by anisotropic magnetic susceptibility.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/1ss8-31rb","month":"12","OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","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":"2025-12-29T11:15:42Z","_id":"20847","author":[{"last_name":"Fitzgerald","id":"2df8ab8f-080d-11ed-979a-bfe651ca3afa","first_name":"Eavan","full_name":"Fitzgerald, Eavan"},{"first_name":"Cécile","last_name":"Clavaud","id":"5f654c5d-04a1-11eb-ab36-ba9ffec58bd8","orcid":"0000-0002-1843-3803","full_name":"Clavaud, Cécile"},{"first_name":"Debasish","last_name":"Das","full_name":"Das, Debasish"},{"first_name":"Isaac C","orcid":"0000-0002-5010-6984","last_name":"Lenton","id":"a550210f-223c-11ec-8182-e2d45e817efb","full_name":"Lenton, Isaac C"},{"full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176"}],"citation":{"ista":"Fitzgerald E, Clavaud C, Das D, Lenton IC, Waitukaitis SR. 2025. Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter. Physical Review E. 112(6), 065418.","ieee":"E. Fitzgerald, C. Clavaud, D. Das, I. C. Lenton, and S. R. Waitukaitis, “Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter,” <i>Physical Review E</i>, vol. 112, no. 6. American Physical Society, 2025.","mla":"Fitzgerald, Eavan, et al. “Rolling at Right Angles: Magnetic Anisotropy Enables Dual-Anisotropic Active Matter.” <i>Physical Review E</i>, vol. 112, no. 6, 065418, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/1ss8-31rb\">10.1103/1ss8-31rb</a>.","ama":"Fitzgerald E, Clavaud C, Das D, Lenton IC, Waitukaitis SR. Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter. <i>Physical Review E</i>. 2025;112(6). doi:<a href=\"https://doi.org/10.1103/1ss8-31rb\">10.1103/1ss8-31rb</a>","apa":"Fitzgerald, E., Clavaud, C., Das, D., Lenton, I. C., &#38; Waitukaitis, S. R. (2025). Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/1ss8-31rb\">https://doi.org/10.1103/1ss8-31rb</a>","short":"E. Fitzgerald, C. Clavaud, D. Das, I.C. Lenton, S.R. Waitukaitis, Physical Review E 112 (2025).","chicago":"Fitzgerald, Eavan, Cécile Clavaud, Debasish Das, Isaac C Lenton, and Scott R Waitukaitis. “Rolling at Right Angles: Magnetic Anisotropy Enables Dual-Anisotropic Active Matter.” <i>Physical Review E</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/1ss8-31rb\">https://doi.org/10.1103/1ss8-31rb</a>."},"article_number":"065418","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","type":"journal_article","PlanS_conform":"1","publisher":"American Physical Society","intvolume":"       112","publication":"Physical Review E","project":[{"_id":"bd8eede5-d553-11ed-ba76-eaded0d13485","name":"MixQUIckR: Mixing with QUIncke Rollers","grant_number":"E 298"},{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120"}],"year":"2025","volume":112,"external_id":{"arxiv":["2508.05643"]},"article_type":"original","title":"Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter","OA_place":"publisher","department":[{"_id":"ScWa"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) [Grant DOI: 10.55776/ESP298]. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nAgreement 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, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. We wish to acknowledge the crucial contributions of Alexandre Morin in getting the project off the ground, and Jack Merrin for creating the SU-8 deposition protocol used in the construction of our\r\ncells. We also wish to thank Kimberley Modic and Hamza Nasir for their work on single-particle characterization. ","date_created":"2025-12-21T23:01:34Z"},{"issue":"2","date_updated":"2025-09-08T09:17:18Z","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"day":"01","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2024-09-11T05:59:36Z","content_type":"application/pdf","relation":"main_file","checksum":"67fc2cc8eee3155e5c3b7380307d8284","date_created":"2024-09-11T05:59:36Z","file_id":"18053","success":1,"file_name":"2024_PhysReviewE_Olmeda.pdf","file_size":445696}],"corr_author":"1","abstract":[{"lang":"eng","text":"Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)⁢(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate."}],"publication_status":"published","ddc":["530"],"status":"public","date_published":"2024-08-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"08","doi":"10.1103/PhysRevE.110.024404","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. <i>Physical Review E</i>. 2024;110(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.024404\">10.1103/PhysRevE.110.024404</a>","ista":"Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404.","mla":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” <i>Physical Review E</i>, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.024404\">10.1103/PhysRevE.110.024404</a>.","ieee":"F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” <i>Physical Review E</i>, vol. 110, no. 2. American Physical Society, 2024.","chicago":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” <i>Physical Review E</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevE.110.024404\">https://doi.org/10.1103/PhysRevE.110.024404</a>.","short":"F. Olmeda, S. Rulands, Physical Review E 110 (2024).","apa":"Olmeda, F., &#38; Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.110.024404\">https://doi.org/10.1103/PhysRevE.110.024404</a>"},"has_accepted_license":"1","article_number":"024404","scopus_import":"1","quality_controlled":"1","author":[{"last_name":"Olmeda","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","first_name":"Fabrizio","full_name":"Olmeda, Fabrizio"},{"first_name":"Steffen","last_name":"Rulands","full_name":"Rulands, Steffen"}],"_id":"17892","file_date_updated":"2024-09-11T05:59:36Z","publisher":"American Physical Society","intvolume":"       110","type":"journal_article","isi":1,"year":"2024","publication":"Physical Review E","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_type":"original","external_id":{"pmid":["39294986"],"isi":["001299670100004"]},"title":"Field theory of enzyme-substrate systems with restricted long-range interactions","volume":110,"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"acknowledgement":"We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413.","date_created":"2024-09-08T22:01:12Z","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"EdHa"}]},{"status":"public","date_published":"2024-12-10T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells to take up extracellular material, but the dominant physical mechanisms driving this process are still elusive. Recently, several high-resolution imaging techniques have been used on different cell lines to measure the geometrical properties of clathrin-coated pits over their whole lifetime. Here, we first show that the combination of all datasets with the recently introduced cooperative curvature model defines a consensus pathway, which is characterized by a flat-to-curved transition at finite area, followed by linear growth and subsequent saturation of curvature. We then apply an energetic model for the composite of the plasma membrane and clathrin coat to this consensus pathway to show that the dominant mechanism for invagination could be coat stiffening, which might originate from cooperative interactions between the different clathrin molecules and progressively drives the system toward its intrinsic curvature. Our theory predicts that two length scales determine the invagination pathway, namely the patch size at which the flat-to-curved transition occurs and the final pit radius."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"doi":"10.1103/PhysRevE.110.064403","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.02820","open_access":"1"}],"month":"12","OA_type":"green","language":[{"iso":"eng"}],"oa":1,"arxiv":1,"oa_version":"Preprint","date_updated":"2025-09-09T11:56:34Z","issue":"6","day":"10","publication":"Physical Review E","year":"2024","volume":110,"title":"Coat stiffening can explain invagination of clathrin-coated membranes","external_id":{"isi":["001379135100004"],"pmid":["39916158"],"arxiv":["2405.02820"]},"article_type":"original","OA_place":"repository","department":[{"_id":"AnSa"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"article_processing_charge":"No","acknowledgement":"We thank Markus Mund, Aline Tschanz, and Jonas Ries for helpful discussions and a critical reading of the manuscript. We also kindly acknowledge Simon Scheuring for providing the HS-AFM data for the analysis of clathrin coat invagination. We thank the reviewers of previous versions of this manuscript for useful feedback that helped us to improve this work. F.F. acknowledges financial support by the NOMIS foundation. U.S.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Project No. 240245660 (SFB 1129). Moreover, he is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg and of the Max Planck School Matter to Life supported by the German Federal Ministry of Education and Research (BMBF) in collaboration with the Max Planck Society.","date_created":"2024-12-22T23:01:48Z","_id":"18704","author":[{"full_name":"Frey, Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017","first_name":"Felix F"},{"first_name":"Ulrich S.","last_name":"Schwarz","full_name":"Schwarz, Ulrich S."}],"citation":{"apa":"Frey, F. F., &#38; Schwarz, U. S. (2024). Coat stiffening can explain invagination of clathrin-coated membranes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">https://doi.org/10.1103/PhysRevE.110.064403</a>","short":"F.F. Frey, U.S. Schwarz, Physical Review E 110 (2024).","chicago":"Frey, Felix F, and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” <i>Physical Review E</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">https://doi.org/10.1103/PhysRevE.110.064403</a>.","mla":"Frey, Felix F., and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” <i>Physical Review E</i>, vol. 110, no. 6, 064403, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">10.1103/PhysRevE.110.064403</a>.","ieee":"F. F. Frey and U. S. Schwarz, “Coat stiffening can explain invagination of clathrin-coated membranes,” <i>Physical Review E</i>, vol. 110, no. 6. American Physical Society, 2024.","ista":"Frey FF, Schwarz US. 2024. Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. 110(6), 064403.","ama":"Frey FF, Schwarz US. Coat stiffening can explain invagination of clathrin-coated membranes. <i>Physical Review E</i>. 2024;110(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">10.1103/PhysRevE.110.064403</a>"},"article_number":"064403","scopus_import":"1","quality_controlled":"1","isi":1,"type":"journal_article","publisher":"American Physical Society","intvolume":"       110"},{"isi":1,"type":"journal_article","intvolume":"       109","publisher":"American Physical Society","_id":"15322","author":[{"full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A"},{"last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","full_name":"Waitukaitis, Scott R"}],"quality_controlled":"1","article_number":"L032108","scopus_import":"1","citation":{"ama":"Sobarzo Ponce JCA, Waitukaitis SR. Multiple charge carrier species as a possible cause for triboelectric cycles. <i>Physical Review E</i>. 2024;109(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">10.1103/PhysRevE.109.L032108</a>","mla":"Sobarzo Ponce, Juan Carlos A., and Scott R. Waitukaitis. “Multiple Charge Carrier Species as a Possible Cause for Triboelectric Cycles.” <i>Physical Review E</i>, vol. 109, no. 3, L032108, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">10.1103/PhysRevE.109.L032108</a>.","ieee":"J. C. A. Sobarzo Ponce and S. R. Waitukaitis, “Multiple charge carrier species as a possible cause for triboelectric cycles,” <i>Physical Review E</i>, vol. 109, no. 3. American Physical Society, 2024.","ista":"Sobarzo Ponce JCA, Waitukaitis SR. 2024. Multiple charge carrier species as a possible cause for triboelectric cycles. Physical Review E. 109(3), L032108.","chicago":"Sobarzo Ponce, Juan Carlos A, and Scott R Waitukaitis. “Multiple Charge Carrier Species as a Possible Cause for Triboelectric Cycles.” <i>Physical Review E</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">https://doi.org/10.1103/PhysRevE.109.L032108</a>.","apa":"Sobarzo Ponce, J. C. A., &#38; Waitukaitis, S. R. (2024). Multiple charge carrier species as a possible cause for triboelectric cycles. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">https://doi.org/10.1103/PhysRevE.109.L032108</a>","short":"J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review E 109 (2024)."},"department":[{"_id":"ScWa"}],"article_processing_charge":"No","date_created":"2024-04-14T22:01:03Z","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"volume":109,"article_type":"letter_note","external_id":{"isi":["001199745200004"],"pmid":["38632754"]},"title":"Multiple charge carrier species as a possible cause for triboelectric cycles","publication":"Physical Review E","year":"2024","related_material":{"record":[{"id":"20203","status":"public","relation":"dissertation_contains"}]},"corr_author":"1","day":"29","language":[{"iso":"eng"}],"date_updated":"2026-04-07T11:50:54Z","oa_version":"None","issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"doi":"10.1103/PhysRevE.109.L032108","month":"03","date_published":"2024-03-29T00:00:00Z","status":"public","abstract":[{"text":"The tendency of materials to order in triboelectric series has prompted suggestions that contact electrification might have a single, unified underlying description. However, the possibility of “triboelectric cycles,” i.e., series that loop back onto themselves, is seemingly at odds with such a coherent description. In this work, we propose that if multiple charge carrying species are at play, both triboelectric series and cycles are possible. We show how series arise naturally if only a single charge carrier species is involved and if the driving mechanism is approach toward thermodynamic equilibrium, and simultaneously, that cycles are forbidden under such conditions. Suspecting multiple carriers might relax the situation, we affirm this is the case by explicit construction of a cycle involving two carriers, and then extend this to show how more complex cycles emerge. Our work highlights the importance of series and cycles towards determining the underlying mechanism(s) and carrier(s) in contact electrification.","lang":"eng"}],"publication_status":"published"},{"intvolume":"       107","publisher":"American Physical Society","isi":1,"type":"journal_article","article_number":"014608","quality_controlled":"1","scopus_import":"1","citation":{"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>","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>.","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.","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.","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>.","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>"},"_id":"12545","author":[{"id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","last_name":"Rojas Vega","first_name":"Mauricio Nicolas","full_name":"Rojas Vega, Mauricio Nicolas"},{"first_name":"Pablo","last_name":"De Castro","full_name":"De Castro, Pablo"},{"last_name":"Soto","first_name":"Rodrigo","full_name":"Soto, Rodrigo"}],"article_processing_charge":"No","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.","date_created":"2023-02-12T23:00:59Z","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"department":[{"_id":"GradSch"}],"volume":107,"title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","article_type":"original","external_id":{"arxiv":["2301.01856"],"pmid":["36797971"],"isi":["000963909800006"]},"publication":"Physical Review E","year":"2023","day":"24","oa_version":"Preprint","date_updated":"2025-03-06T14:01:47Z","issue":"1","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"month":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01856","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevE.107.014608","pmid":1,"abstract":[{"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.","lang":"eng"}],"publication_status":"published","date_published":"2023-01-24T00:00:00Z","status":"public"},{"external_id":{"pmid":["37072968"],"isi":["000992142700001"]},"title":"Accurate determination of the shapes of granular charge distributions","article_type":"original","volume":107,"year":"2023","publication":"Physical Review E","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","grant_number":"949120"}],"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.","date_created":"2023-04-02T22:01:10Z","article_processing_charge":"No","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"department":[{"_id":"ScWa"}],"has_accepted_license":"1","article_number":"034901","quality_controlled":"1","scopus_import":"1","citation":{"ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901.","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.","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>.","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>","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).","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>."},"author":[{"first_name":"Nicolás","last_name":"Mujica","full_name":"Mujica, Nicolás"},{"full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176"}],"file_date_updated":"2023-11-27T09:51:48Z","_id":"12789","intvolume":"       107","publisher":"American Physical Society","type":"journal_article","isi":1,"abstract":[{"lang":"eng","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."}],"publication_status":"published","ddc":["530"],"date_published":"2023-03-01T00:00:00Z","status":"public","month":"03","doi":"10.1103/PhysRevE.107.034901","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","oa_version":"Published Version","date_updated":"2025-04-14T07:54:10Z","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"day":"01","corr_author":"1","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"swaituka","date_updated":"2023-11-27T09:51:48Z","file_size":1428631,"file_name":"PhysRevE.107.034901 (1).pdf","success":1,"checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","file_id":"14612","date_created":"2023-11-27T09:51:48Z"}]},{"publication_status":"published","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"}],"status":"public","date_published":"2023-11-08T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"1"}],"month":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1103/PhysRevE.108.054307","pmid":1,"arxiv":1,"oa_version":"Preprint","date_updated":"2025-09-09T12:26:01Z","issue":"5","oa":1,"language":[{"iso":"eng"}],"day":"08","corr_author":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"12869"}],"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}]},"publication":"Physical Review E","year":"2023","volume":108,"article_type":"original","external_id":{"arxiv":["2305.02153"],"pmid":["38115445"],"isi":["001106396300005"]},"title":"Stochastic cellular automaton model of culture formation","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"article_processing_charge":"No","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.","date_created":"2023-05-04T08:35:01Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"citation":{"ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","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.","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>.","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>","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","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>","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>."},"scopus_import":"1","quality_controlled":"1","article_number":"054307","_id":"12890","author":[{"full_name":"Klausen, Frederik Ravn","first_name":"Frederik Ravn","last_name":"Klausen"},{"last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard"}],"publisher":"American Physical Society","intvolume":"       108","isi":1,"type":"journal_article"},{"citation":{"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>","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>.","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.","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>.","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>","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023)."},"quality_controlled":"1","article_number":"065207","scopus_import":"1","author":[{"first_name":"Maximilian","last_name":"Schörner","full_name":"Schörner, Maximilian"},{"first_name":"Mandy","orcid":"0000-0002-1838-2129","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy"},{"last_name":"Döppner","first_name":"Tilo","full_name":"Döppner, Tilo"},{"last_name":"Kraus","first_name":"Dominik","full_name":"Kraus, Dominik"},{"full_name":"Fletcher, Luke B.","last_name":"Fletcher","first_name":"Luke B."},{"first_name":"Siegfried H.","last_name":"Glenzer","full_name":"Glenzer, Siegfried H."},{"full_name":"Redmer, Ronald","last_name":"Redmer","first_name":"Ronald"}],"_id":"13231","publisher":"American Physical Society","intvolume":"       107","type":"journal_article","isi":1,"year":"2023","publication":"Physical Review E","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","external_id":{"arxiv":["2301.01545"],"isi":["001020265000002"],"pmid":["37464593"]},"article_type":"original","volume":107,"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"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.","article_processing_charge":"No","department":[{"_id":"BiCh"}],"arxiv":1,"issue":"6","date_updated":"2025-03-06T14:02:33Z","oa_version":"Preprint","language":[{"iso":"eng"}],"oa":1,"day":"14","publication_status":"published","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_published":"2023-06-14T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01545"}],"month":"06","pmid":1,"doi":"10.1103/PhysRevE.107.065207","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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"}],"publication_status":"published","status":"public","date_published":"2022-09-29T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.02394","open_access":"1"}],"month":"09","doi":"10.1103/physreve.106.034321","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"issue":"3","oa_version":"Preprint","date_updated":"2026-04-07T11:49:11Z","oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"day":"29","related_material":{"record":[{"id":"20138","status":"public","relation":"dissertation_contains"}]},"year":"2022","publication":"Physical Review E","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"external_id":{"arxiv":["2210.02394"],"isi":["000870243100001"]},"title":"Social balance on networks: Local minima and best-edge dynamics","article_type":"original","volume":106,"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"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.","date_created":"2023-01-16T09:57:57Z","article_processing_charge":"No","department":[{"_id":"KrCh"}],"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>.","short":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical Review E 106 (2022).","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>","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>","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.","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>.","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."},"scopus_import":"1","article_number":"034321","quality_controlled":"1","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"orcid":"0000-0002-1419-3267","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","full_name":"Svoboda, Jakub"},{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"}],"_id":"12257","publisher":"American Physical Society","intvolume":"       106","type":"journal_article","isi":1},{"citation":{"short":"L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).","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>","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.","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.","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>.","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>"},"article_number":"022420","scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Davis, Luke K.","first_name":"Luke K.","last_name":"Davis"},{"first_name":"Ian J.","last_name":"Ford","full_name":"Ford, Ian J."},{"full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"full_name":"Hoogenboom, Bart W.","last_name":"Hoogenboom","first_name":"Bart W."}],"_id":"10352","publisher":"American Physical Society","intvolume":"       101","type":"journal_article","year":"2020","publication":"Physical Review E","title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","external_id":{"pmid":["32168597"]},"article_type":"original","volume":101,"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"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.).","date_created":"2021-11-26T09:41:04Z","article_processing_charge":"No","issue":"2","date_updated":"2021-11-26T11:21:16Z","oa_version":"Preprint","language":[{"iso":"eng"}],"oa":1,"day":"28","abstract":[{"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.","lang":"eng"}],"publication_status":"published","extern":"1","status":"public","date_published":"2020-02-28T00:00:00Z","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/571687","open_access":"1"}],"month":"02","pmid":1,"doi":"10.1103/physreve.101.022420","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"day":"25","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-04-15T06:50:28Z","oa_version":"Preprint","issue":"1","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/physreve.100.013112","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1907.05860","open_access":"1"}],"date_published":"2019-07-25T00:00:00Z","status":"public","ddc":["532"],"publication_status":"published","abstract":[{"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.","lang":"eng"}],"isi":1,"type":"journal_article","intvolume":"       100","publisher":"American Physical Society","_id":"6779","author":[{"full_name":"Suri, Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra"},{"full_name":"Pallantla, Ravi Kumar","first_name":"Ravi Kumar","last_name":"Pallantla"},{"full_name":"Schatz, Michael F.","first_name":"Michael F.","last_name":"Schatz"},{"last_name":"Grigoriev","first_name":"Roman O.","full_name":"Grigoriev, Roman O."}],"article_number":"013112","quality_controlled":"1","scopus_import":"1","citation":{"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.","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>","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>","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","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>."},"department":[{"_id":"BjHo"}],"article_processing_charge":"No","date_created":"2019-08-09T09:40:41Z","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"volume":100,"article_type":"original","external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"publication":"Physical Review E","year":"2019"}]