--- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21982' abstract: - lang: eng text: A floating Leidenfrost droplet exhibits curvature inversion of its underside, due to the balance of vapor pressure and surface tension. Using interferometric imaging, we find different behavior for a levitated hydrogel sphere. Curvature inversion is observed briefly just after deposition, but quickly gives way to a steady state with no inversion. We show the essential role of vaporization in shaping the underbelly of the hydrogel, where changes due to direct mass loss are more significant than the balance of vapor pressure and elastic forces. acknowledged_ssus: - _id: M-Shop - _id: ScienComp acknowledgement: 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 and the Scientific Computing Facility. J.B. acknowledges funding from the European Union's Horizon research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101106500. article_number: L053502 article_processing_charge: Yes (via OA deal) article_type: letter_note arxiv: 1 author: - first_name: Vicente L full_name: Diaz Melian, Vicente L id: b6798902-eea0-11ea-9cbc-a8e14286c631 last_name: Diaz Melian - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Jack full_name: Binysh, Jack last_name: Binysh - first_name: Anton full_name: Souslov, Anton last_name: Souslov - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 2026;113(5). doi:10.1103/m7gr-2t6j apa: Diaz Melian, V. L., Lenton, I. C., Binysh, J., Souslov, A., & Waitukaitis, S. R. (2026). Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. American Physical Society. https://doi.org/10.1103/m7gr-2t6j chicago: Diaz Melian, Vicente L, Isaac C Lenton, Jack Binysh, Anton Souslov, and Scott R Waitukaitis. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” Physical Review E. American Physical Society, 2026. https://doi.org/10.1103/m7gr-2t6j. ieee: V. L. Diaz Melian, I. C. Lenton, J. Binysh, A. Souslov, and S. R. Waitukaitis, “Geometry of the vapor layer under a Leidenfrost hydrogel sphere,” Physical Review E, vol. 113, no. 5. American Physical Society, 2026. ista: Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. 2026. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 113(5), L053502. mla: Diaz Melian, Vicente L., et al. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” Physical Review E, vol. 113, no. 5, L053502, American Physical Society, 2026, doi:10.1103/m7gr-2t6j. short: V.L. Diaz Melian, I.C. Lenton, J. Binysh, A. Souslov, S.R. Waitukaitis, Physical Review E 113 (2026). corr_author: '1' date_created: 2026-06-10T07:36:41Z date_published: 2026-05-14T00:00:00Z date_updated: 2026-06-16T11:24:18Z day: '14' ddc: - '530' department: - _id: ScWa - _id: GradSch doi: 10.1103/m7gr-2t6j external_id: arxiv: - '2507.04982' file: - access_level: open_access checksum: 902cc8d177c8d3ae9cfe07c30375c9a9 content_type: application/pdf creator: dernst date_created: 2026-06-16T11:21:53Z date_updated: 2026-06-16T11:21:53Z file_id: '22014' file_name: 2026_PhysicalReviewE_DiazMelian.pdf file_size: 3173197 relation: main_file success: 1 file_date_updated: 2026-06-16T11:21:53Z has_accepted_license: '1' intvolume: ' 113' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Geometry of the vapor layer under a Leidenfrost hydrogel sphere tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22307' abstract: - lang: eng text: We investigate magnetic active matter in confined geometries using both experiments with magnetic toy robots, Hexbugs, and simulations of elongated magnetic active Brownian particles in circular domains. Standard active particles tend to accumulate at boundaries, forming clusters even at relatively low densities. In the presence of magnetic interactions, we provide evidence for a effect that inhibits clustering and shifts its onset to higher packing fractions. Moreover, magnetic dipolar interactions give rise to collective behaviors such as train-like formations, rotating pairs, and rotating clusters. acknowledgement: "The authors acknowledge discussions with Lorenzo\r\nCaprini. A.G., M.P., and A.P. acknowledge funding from the\r\nItalianMinistero dell’Università e della Ricerca under the program\r\nPRIN 2022 (“Re-ranking of the final lists”), Grants No.\r\n2022KWTEB7 with CUP No. B53C24006470006. L.A. acknowledges\r\nfunding from the ItalianMinistero dell’Università\r\ne della Ricerca under the program PRIN 2020, Grant No.\r\n2020PFCXPE." article_number: '055413' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Marco full_name: Musacchio, Marco last_name: Musacchio - first_name: Markus full_name: Felber, Markus id: c12d7e3a-4e8f-11ef-ad48-ffba54b8aa10 last_name: Felber - first_name: Matteo full_name: Paoluzzi, Matteo last_name: Paoluzzi - first_name: Andrea full_name: Gnoli, Andrea last_name: Gnoli - first_name: Andrea full_name: Puglisi, Andrea last_name: Puglisi - first_name: Luca full_name: Angelani, Luca last_name: Angelani citation: ama: Musacchio M, Felber M, Paoluzzi M, Gnoli A, Puglisi A, Angelani L. Fluidization induced by magnetic interactions in confined active matter. Physical Review E. 2026;113(5). doi:10.1103/hylm-ljlf apa: Musacchio, M., Felber, M., Paoluzzi, M., Gnoli, A., Puglisi, A., & Angelani, L. (2026). Fluidization induced by magnetic interactions in confined active matter. Physical Review E. American Physical Society. https://doi.org/10.1103/hylm-ljlf chicago: Musacchio, Marco, Markus Felber, Matteo Paoluzzi, Andrea Gnoli, Andrea Puglisi, and Luca Angelani. “Fluidization Induced by Magnetic Interactions in Confined Active Matter.” Physical Review E. American Physical Society, 2026. https://doi.org/10.1103/hylm-ljlf. ieee: M. Musacchio, M. Felber, M. Paoluzzi, A. Gnoli, A. Puglisi, and L. Angelani, “Fluidization induced by magnetic interactions in confined active matter,” Physical Review E, vol. 113, no. 5. American Physical Society, 2026. ista: Musacchio M, Felber M, Paoluzzi M, Gnoli A, Puglisi A, Angelani L. 2026. Fluidization induced by magnetic interactions in confined active matter. Physical Review E. 113(5), 055413. mla: Musacchio, Marco, et al. “Fluidization Induced by Magnetic Interactions in Confined Active Matter.” Physical Review E, vol. 113, no. 5, 055413, American Physical Society, 2026, doi:10.1103/hylm-ljlf. short: M. Musacchio, M. Felber, M. Paoluzzi, A. Gnoli, A. Puglisi, L. Angelani, Physical Review E 113 (2026). dataavailabilitystatement: "The data that support the findings of this article are not\r\npublicly available upon publication because it is not technically\r\nfeasible and/or the cost of preparing, depositing, and\r\nhosting the data would be prohibitive within the terms of this\r\nresearch project. The data are available from the authors upon\r\nreasonable request." date_created: 2026-07-13T10:53:06Z date_published: 2026-05-18T00:00:00Z date_updated: 2026-07-14T07:00:17Z day: '18' ddc: - '530' department: - _id: ScWa - _id: GradSch doi: 10.1103/hylm-ljlf external_id: arxiv: - '2511.21472' file: - access_level: open_access checksum: f029efcf6dd51e10e3bc7623b5365da6 content_type: application/pdf creator: dernst date_created: 2026-07-14T06:58:35Z date_updated: 2026-07-14T06:58:35Z file_id: '22332' file_name: 2026_PhysicalReviewE_Musacchio.pdf file_size: 1836050 relation: main_file success: 1 file_date_updated: 2026-07-14T06:58:35Z has_accepted_license: '1' intvolume: ' 113' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Fluidization induced by magnetic interactions in confined active matter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20847' abstract: - lang: eng 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 (|\U0001D469|=0) leads to circular trajectories interspersed with short spontaneous runs. Intermediate fields (|\U0001D469|≲20mT) linearize the motion along the axis perpendicular to \U0001D469. At high magnetic fields, we observe the surprising emergence of a second, distinct linearization along the axis parallel to \U0001D469. With numerical simulations, we show that this behavior can be explained by anisotropic magnetic susceptibility." acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: ScienComp - _id: LifeSc 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. " article_number: '065418' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Eavan full_name: Fitzgerald, Eavan id: 2df8ab8f-080d-11ed-979a-bfe651ca3afa last_name: Fitzgerald - first_name: Cécile full_name: Clavaud, Cécile id: 5f654c5d-04a1-11eb-ab36-ba9ffec58bd8 last_name: Clavaud orcid: 0000-0002-1843-3803 - first_name: Debasish full_name: Das, Debasish last_name: Das - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: 'Fitzgerald E, Clavaud C, Das D, Lenton IC, Waitukaitis SR. Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter. Physical Review E. 2025;112(6). doi:10.1103/1ss8-31rb' apa: 'Fitzgerald, E., Clavaud, C., Das, D., Lenton, I. C., & Waitukaitis, S. R. (2025). Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter. Physical Review E. American Physical Society. https://doi.org/10.1103/1ss8-31rb' 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.” Physical Review E. American Physical Society, 2025. https://doi.org/10.1103/1ss8-31rb.' 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,” Physical Review E, vol. 112, no. 6. American Physical Society, 2025.' 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.' mla: 'Fitzgerald, Eavan, et al. “Rolling at Right Angles: Magnetic Anisotropy Enables Dual-Anisotropic Active Matter.” Physical Review E, vol. 112, no. 6, 065418, American Physical Society, 2025, doi:10.1103/1ss8-31rb.' short: E. Fitzgerald, C. Clavaud, D. Das, I.C. Lenton, S.R. Waitukaitis, Physical Review E 112 (2025). corr_author: '1' date_created: 2025-12-21T23:01:34Z date_published: 2025-12-01T00:00:00Z date_updated: 2025-12-29T11:19:34Z day: '01' ddc: - '530' department: - _id: ScWa doi: 10.1103/1ss8-31rb ec_funded: 1 external_id: arxiv: - '2508.05643' file: - access_level: open_access checksum: d593e933f976c3f3cde37ad66539d57d content_type: application/pdf creator: dernst date_created: 2025-12-29T11:15:42Z date_updated: 2025-12-29T11:15:42Z file_id: '20862' file_name: 2025_PhysReviewE_Fitzgerald.pdf file_size: 2131491 relation: main_file success: 1 file_date_updated: 2025-12-29T11:15:42Z has_accepted_license: '1' intvolume: ' 112' issue: '6' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: bd8eede5-d553-11ed-ba76-eaded0d13485 grant_number: E 298 name: 'MixQUIckR: Mixing with QUIncke Rollers' - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Rolling at right angles: Magnetic anisotropy enables dual-anisotropic active matter' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20483' abstract: - lang: eng 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. 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_number: '035417' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Ivan full_name: Palaia, Ivan id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa last_name: Palaia orcid: ' 0000-0002-8843-9485 ' - first_name: Adelchi J. full_name: Asta, Adelchi J. last_name: Asta - first_name: Megh full_name: Dutta, Megh last_name: Dutta - first_name: Patrick B. full_name: Warren, Patrick B. last_name: Warren - first_name: Benjamin full_name: Rotenberg, Benjamin last_name: Rotenberg - first_name: Emmanuel full_name: Trizac, Emmanuel last_name: Trizac citation: 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. Physical Review E. 2025;112(3). doi:10.1103/p4dg-snqf' apa: 'Palaia, I., Asta, A. J., Dutta, M., Warren, P. B., Rotenberg, B., & Trizac, E. (2025). Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes. Physical Review E. American Physical Society. https://doi.org/10.1103/p4dg-snqf' 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.” Physical Review E. American Physical Society, 2025. https://doi.org/10.1103/p4dg-snqf.' 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,” Physical Review E, vol. 112, no. 3. American Physical Society, 2025.' 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.' mla: 'Palaia, Ivan, et al. “Poisson-Nernst-Planck Charging Dynamics of an Electric Double-Layer Capacitor: Symmetric and Asymmetric Binary Electrolytes.” Physical Review E, vol. 112, no. 3, 035417, American Physical Society, 2025, doi:10.1103/p4dg-snqf.' short: I. Palaia, A.J. Asta, M. Dutta, P.B. Warren, B. Rotenberg, E. Trizac, Physical Review E 112 (2025). corr_author: '1' date_created: 2025-10-16T13:15:16Z date_published: 2025-09-29T00:00:00Z date_updated: 2025-12-01T13:06:51Z day: '29' ddc: - '530' department: - _id: AnSa doi: 10.1103/p4dg-snqf ec_funded: 1 external_id: arxiv: - '2303.07859' isi: - '001586173200001' file: - access_level: open_access checksum: 658a9b1ce6b2edcf138b54c55a566f0e content_type: application/pdf creator: dernst date_created: 2025-10-23T09:15:56Z date_updated: 2025-10-23T09:15:56Z file_id: '20521' file_name: 2025_PhysReviewE_Palaia.pdf file_size: 1211712 relation: main_file success: 1 file_date_updated: 2025-10-23T09:15:56Z has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19785' abstract: - lang: eng 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.' 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. article_number: '054122' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion processes. Physical Review E. 2025;111(5). doi:10.1103/physreve.111.054122 apa: Kavcic, B., & Tkačik, G. (2025). Token-driven totally asymmetric simple exclusion processes. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.111.054122 chicago: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Processes.” Physical Review E. American Physical Society, 2025. https://doi.org/10.1103/physreve.111.054122. ieee: B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion processes,” Physical Review E, vol. 111, no. 5. American Physical Society, 2025. ista: Kavcic B, Tkačik G. 2025. Token-driven totally asymmetric simple exclusion processes. Physical Review E. 111(5), 054122. mla: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Processes.” Physical Review E, vol. 111, no. 5, 054122, American Physical Society, 2025, doi:10.1103/physreve.111.054122. short: B. Kavcic, G. Tkačik, Physical Review E 111 (2025). corr_author: '1' date_created: 2025-06-03T09:01:55Z date_published: 2025-05-19T00:00:00Z date_updated: 2026-08-04T08:34:22Z day: '19' ddc: - '570' department: - _id: GaTk doi: 10.1103/physreve.111.054122 external_id: isi: - '001496415600007' file: - access_level: open_access checksum: e8851ccd7cd0525c08c7308710413e74 content_type: application/pdf creator: dernst date_created: 2025-06-03T09:18:20Z date_updated: 2025-06-03T09:18:20Z file_id: '19787' file_name: 2025_PhysRevE_Kavcic.pdf file_size: 2766143 relation: main_file success: 1 file_date_updated: 2025-06-03T09:18:20Z has_accepted_license: '1' intvolume: ' 111' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '19658' relation: research_data status: public - id: '10579' relation: earlier_version status: public scopus_import: '1' status: public title: Token-driven totally asymmetric simple exclusion processes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 111 year: '2025' ... --- OA_place: repository OA_type: green _id: '18704' 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. 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. article_number: '064403' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey orcid: 0000-0001-8501-6017 - first_name: Ulrich S. full_name: Schwarz, Ulrich S. last_name: Schwarz citation: ama: Frey FF, Schwarz US. Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. 2024;110(6). doi:10.1103/PhysRevE.110.064403 apa: Frey, F. F., & Schwarz, U. S. (2024). Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.064403 chicago: Frey, Felix F, and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.064403. ieee: F. F. Frey and U. S. Schwarz, “Coat stiffening can explain invagination of clathrin-coated membranes,” Physical Review E, 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. mla: Frey, Felix F., and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” Physical Review E, vol. 110, no. 6, 064403, American Physical Society, 2024, doi:10.1103/PhysRevE.110.064403. short: F.F. Frey, U.S. Schwarz, Physical Review E 110 (2024). date_created: 2024-12-22T23:01:48Z date_published: 2024-12-10T00:00:00Z date_updated: 2025-09-09T11:56:34Z day: '10' department: - _id: AnSa doi: 10.1103/PhysRevE.110.064403 external_id: arxiv: - '2405.02820' isi: - '001379135100004' pmid: - '39916158' intvolume: ' 110' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.02820 month: '12' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Coat stiffening can explain invagination of clathrin-coated membranes type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 110 year: '2024' ... --- _id: '17892' 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 −\U0001D6FE. 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−\U0001D6FE) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −\U0001D6FE on short distances and −(2/3)⁢(2−\U0001D6FE) 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." 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. article_number: '024404' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Fabrizio full_name: Olmeda, Fabrizio id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689 last_name: Olmeda - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands citation: ama: Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404 apa: Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404 chicago: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404. ieee: F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024. 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.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404. short: F. Olmeda, S. Rulands, Physical Review E 110 (2024). corr_author: '1' date_created: 2024-09-08T22:01:12Z date_published: 2024-08-01T00:00:00Z date_updated: 2025-09-08T09:17:18Z day: '01' ddc: - '530' department: - _id: EdHa doi: 10.1103/PhysRevE.110.024404 ec_funded: 1 external_id: isi: - '001299670100004' pmid: - '39294986' file: - access_level: open_access checksum: 67fc2cc8eee3155e5c3b7380307d8284 content_type: application/pdf creator: dernst date_created: 2024-09-11T05:59:36Z date_updated: 2024-09-11T05:59:36Z file_id: '18053' file_name: 2024_PhysReviewE_Olmeda.pdf file_size: 445696 relation: main_file success: 1 file_date_updated: 2024-09-11T05:59:36Z has_accepted_license: '1' intvolume: ' 110' isi: 1 issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Field theory of enzyme-substrate systems with restricted long-range interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 110 year: '2024' ... --- _id: '15322' abstract: - lang: eng 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. article_number: L032108 article_processing_charge: No article_type: letter_note author: - first_name: Juan Carlos A full_name: Sobarzo Ponce, Juan Carlos A id: 4B807D68-AE37-11E9-AC72-31CAE5697425 last_name: Sobarzo Ponce - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Sobarzo Ponce JCA, Waitukaitis SR. Multiple charge carrier species as a possible cause for triboelectric cycles. Physical Review E. 2024;109(3). doi:10.1103/PhysRevE.109.L032108 apa: Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2024). Multiple charge carrier species as a possible cause for triboelectric cycles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.109.L032108 chicago: Sobarzo Ponce, Juan Carlos A, and Scott R Waitukaitis. “Multiple Charge Carrier Species as a Possible Cause for Triboelectric Cycles.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.109.L032108. ieee: J. C. A. Sobarzo Ponce and S. R. Waitukaitis, “Multiple charge carrier species as a possible cause for triboelectric cycles,” Physical Review E, 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. mla: Sobarzo Ponce, Juan Carlos A., and Scott R. Waitukaitis. “Multiple Charge Carrier Species as a Possible Cause for Triboelectric Cycles.” Physical Review E, vol. 109, no. 3, L032108, American Physical Society, 2024, doi:10.1103/PhysRevE.109.L032108. short: J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review E 109 (2024). corr_author: '1' date_created: 2024-04-14T22:01:03Z date_published: 2024-03-29T00:00:00Z date_updated: 2026-07-29T13:11:24Z day: '29' department: - _id: ScWa doi: 10.1103/PhysRevE.109.L032108 external_id: isi: - '001199745200004' pmid: - '38632754' intvolume: ' 109' isi: 1 issue: '3' language: - iso: eng month: '03' oa_version: None pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '20203' relation: dissertation_contains status: public scopus_import: '1' status: public title: Multiple charge carrier species as a possible cause for triboelectric cycles type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 109 year: '2024' ... --- _id: '12545' 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. 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.' article_number: '014608' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Mauricio Nicolas full_name: Rojas Vega, Mauricio Nicolas id: 441e7207-f91f-11ec-b67c-9e6fe3d8fd6d last_name: Rojas Vega - first_name: Pablo full_name: De Castro, Pablo last_name: De Castro - first_name: Rodrigo full_name: Soto, Rodrigo last_name: Soto citation: ama: Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608 apa: Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608 chicago: Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608. ieee: M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, 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.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608. short: M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023). date_created: 2023-02-12T23:00:59Z date_published: 2023-01-24T00:00:00Z date_updated: 2025-03-06T14:01:47Z day: '24' department: - _id: GradSch doi: 10.1103/PhysRevE.107.014608 external_id: arxiv: - '2301.01856' isi: - '000963909800006' pmid: - '36797971' intvolume: ' 107' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.01856 month: '01' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Wetting dynamics by mixtures of fast and slow self-propelled particles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2023' ... --- _id: '12789' 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. acknowledged_ssus: - _id: M-Shop 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' article_processing_charge: No article_type: original author: - first_name: Nicolás full_name: Mujica, Nicolás last_name: Mujica - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901 apa: Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.034901 chicago: Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901. ieee: N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” Physical Review E, vol. 107, no. 3. American Physical Society, 2023. ista: Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901. mla: Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901. short: N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023). corr_author: '1' date_created: 2023-04-02T22:01:10Z date_published: 2023-03-01T00:00:00Z date_updated: 2025-04-14T07:54:10Z day: '01' ddc: - '530' department: - _id: ScWa doi: 10.1103/PhysRevE.107.034901 ec_funded: 1 external_id: isi: - '000992142700001' pmid: - '37072968' file: - access_level: open_access checksum: 48f5dfe4e5f1c46c3c86805cd8f84bea content_type: application/pdf creator: swaituka date_created: 2023-11-27T09:51:48Z date_updated: 2023-11-27T09:51:48Z file_id: '14612' file_name: PhysRevE.107.034901 (1).pdf file_size: 1428631 relation: main_file success: 1 file_date_updated: 2023-11-27T09:51:48Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Accurate determination of the shapes of granular charge distributions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2023' ... --- _id: '12890' abstract: - lang: eng 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. 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. article_number: '054307' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Frederik Ravn full_name: Klausen, Frederik Ravn last_name: Klausen - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307 apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.108.054307 chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307. ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” Physical Review E, vol. 108, no. 5. American Physical Society, 2023. ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307. mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307. short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023). corr_author: '1' date_created: 2023-05-04T08:35:01Z date_published: 2023-11-08T00:00:00Z date_updated: 2025-09-09T12:26:01Z day: '08' department: - _id: GradSch - _id: RoSe doi: 10.1103/PhysRevE.108.054307 external_id: arxiv: - '2305.02153' isi: - '001106396300005' pmid: - '38115445' intvolume: ' 108' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2305.02153 month: '11' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/FrederikRavnKlausen/model-for-culture-formation record: - id: '12869' relation: research_data status: public scopus_import: '1' status: public title: Stochastic cellular automaton model of culture formation type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 108 year: '2023' ... --- OA_place: repository OA_type: green _id: '22212' abstract: - lang: eng text: "Anisotropic colloidal particles exhibit complex dynamics which play a crucial role in their functionality,\r\ntransport, and phase behavior. In this Letter, we investigate the two-dimensional diffusion of smoothly curved\r\ncolloidal rods—also known as colloidal bananas—as a function of their opening angle α. We measure the\r\ntranslational and rotational diffusion coefficients of the particles with opening angles ranging from 0◦ (straight\r\nrods) to nearly 360◦(closed rings). In particular, we find that the anisotropic diffusion of the particles varies\r\nnonmonotonically with their opening angle and that the axis of fastest diffusion switches from the long to the\r\nshort axis of the particles when α> 180◦. We also find that the rotational diffusion coefficient of nearly closed\r\nrings is approximately an order of magnitude higher than that of straight rods of the same length. Finally, we\r\nshow that the experimental results are consistent with slender body theory, indicating that the dynamical behavior\r\nof the particles arises primarily from their local drag anisotropy. These results highlight the impact of curvature\r\non the Brownian motion of elongated colloidal particles, which must be taken into account when seeking to\r\nunderstand the behavior of curved colloidal particles." article_number: L042602 article_processing_charge: No article_type: letter_note arxiv: 1 author: - first_name: Justin-Aurel full_name: Ulbrich, Justin-Aurel last_name: Ulbrich - first_name: Carla full_name: Fernández-Rico, Carla id: 492def71-6250-11f0-b278-d41dbd241b62 last_name: Fernández-Rico - first_name: Brian full_name: Rost, Brian last_name: Rost - first_name: Jacopo full_name: Vialetto, Jacopo last_name: Vialetto - first_name: Lucio full_name: Isa, Lucio last_name: Isa - first_name: Jeffrey S. full_name: Urbach, Jeffrey S. last_name: Urbach - first_name: Roel P. A. full_name: Dullens, Roel P. A. last_name: Dullens citation: ama: Ulbrich J-A, Fernández-Rico C, Rost B, et al. Effect of curvature on the diffusion of colloidal bananas. Physical Review E. 2023;107(4). doi:10.1103/physreve.107.l042602 apa: Ulbrich, J.-A., Fernández-Rico, C., Rost, B., Vialetto, J., Isa, L., Urbach, J. S., & Dullens, R. P. A. (2023). Effect of curvature on the diffusion of colloidal bananas. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.107.l042602 chicago: Ulbrich, Justin-Aurel, Carla Fernández-Rico, Brian Rost, Jacopo Vialetto, Lucio Isa, Jeffrey S. Urbach, and Roel P. A. Dullens. “Effect of Curvature on the Diffusion of Colloidal Bananas.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/physreve.107.l042602. ieee: J.-A. Ulbrich et al., “Effect of curvature on the diffusion of colloidal bananas,” Physical Review E, vol. 107, no. 4. American Physical Society, 2023. ista: Ulbrich J-A, Fernández-Rico C, Rost B, Vialetto J, Isa L, Urbach JS, Dullens RPA. 2023. Effect of curvature on the diffusion of colloidal bananas. Physical Review E. 107(4), L042602. mla: Ulbrich, Justin-Aurel, et al. “Effect of Curvature on the Diffusion of Colloidal Bananas.” Physical Review E, vol. 107, no. 4, L042602, American Physical Society, 2023, doi:10.1103/physreve.107.l042602. short: J.-A. Ulbrich, C. Fernández-Rico, B. Rost, J. Vialetto, L. Isa, J.S. Urbach, R.P.A. Dullens, Physical Review E 107 (2023). date_created: 2026-06-30T06:32:12Z date_published: 2023-04-21T00:00:00Z date_updated: 2026-07-15T07:09:52Z day: '21' ddc: - '530' doi: 10.1103/physreve.107.l042602 extern: '1' external_id: arxiv: - '2211.07274' has_accepted_license: '1' intvolume: ' 107' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2211.07274 month: '04' oa: 1 oa_version: Preprint publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Effect of curvature on the diffusion of colloidal bananas type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2023' ... --- _id: '13231' 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. 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_number: '065207' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Maximilian full_name: Schörner, Maximilian last_name: Schörner - first_name: Mandy full_name: Bethkenhagen, Mandy id: 201939f4-803f-11ed-ab7e-d8da4bd1517f last_name: Bethkenhagen orcid: 0000-0002-1838-2129 - first_name: Tilo full_name: Döppner, Tilo last_name: Döppner - first_name: Dominik full_name: Kraus, Dominik last_name: Kraus - first_name: Luke B. full_name: Fletcher, Luke B. last_name: Fletcher - first_name: Siegfried H. full_name: Glenzer, Siegfried H. last_name: Glenzer - first_name: Ronald full_name: Redmer, Ronald last_name: Redmer 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. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207 apa: Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207 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.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.065207. ieee: M. Schörner et al., “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” Physical Review E, 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. mla: Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:10.1103/PhysRevE.107.065207. short: M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023). das_tickbox: '0' date_created: 2023-07-16T22:01:10Z date_published: 2023-06-14T00:00:00Z date_updated: 2026-08-07T10:59:03Z day: '14' department: - _id: BiCh doi: 10.1103/PhysRevE.107.065207 external_id: arxiv: - '2301.01545' isi: - '001020265000002' pmid: - '37464593' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.01545 month: '06' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 107 year: '2023' ... --- _id: '12257' abstract: - lang: eng 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. 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." article_number: '034321' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 - 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 id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 citation: ama: 'Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. Social balance on networks: Local minima and best-edge dynamics. Physical Review E. 2022;106(3). doi:10.1103/physreve.106.034321' apa: 'Chatterjee, K., Svoboda, J., Zikelic, D., Pavlogiannis, A., & Tkadlec, J. (2022). Social balance on networks: Local minima and best-edge dynamics. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.106.034321' chicago: 'Chatterjee, Krishnendu, Jakub Svoboda, Dorde Zikelic, Andreas Pavlogiannis, and Josef Tkadlec. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” Physical Review E. American Physical Society, 2022. https://doi.org/10.1103/physreve.106.034321.' ieee: 'K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, and J. Tkadlec, “Social balance on networks: Local minima and best-edge dynamics,” Physical Review E, 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.' mla: 'Chatterjee, Krishnendu, et al. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” Physical Review E, vol. 106, no. 3, 034321, American Physical Society, 2022, doi:10.1103/physreve.106.034321.' short: K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical Review E 106 (2022). date_created: 2023-01-16T09:57:57Z date_published: 2022-09-29T00:00:00Z date_updated: 2026-07-27T12:52:03Z day: '29' department: - _id: KrCh doi: 10.1103/physreve.106.034321 ec_funded: 1 external_id: arxiv: - '2210.02394' isi: - '000870243100001' intvolume: ' 106' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2210.02394 month: '09' oa: 1 oa_version: Preprint project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '20138' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Social balance on networks: Local minima and best-edge dynamics' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 106 year: '2022' ... --- _id: '10352' 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. 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.). article_number: '022420' article_processing_charge: No article_type: original author: - first_name: Luke K. full_name: Davis, Luke K. last_name: Davis - first_name: Ian J. full_name: Ford, Ian J. last_name: Ford - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Bart W. full_name: Hoogenboom, Bart W. last_name: Hoogenboom citation: ama: Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 2020;101(2). doi:10.1103/physreve.101.022420 apa: Davis, L. K., Ford, I. J., Šarić, A., & Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.101.022420 chicago: Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E. American Physical Society, 2020. https://doi.org/10.1103/physreve.101.022420. ieee: L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” Physical Review E, 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.” Physical Review E, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:10.1103/physreve.101.022420. short: L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020). date_created: 2021-11-26T09:41:04Z date_published: 2020-02-28T00:00:00Z date_updated: 2021-11-26T11:21:16Z day: '28' doi: 10.1103/physreve.101.022420 extern: '1' external_id: pmid: - '32168597' intvolume: ' 101' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/571687 month: '02' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 101 year: '2020' ... --- _id: '6779' 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." article_number: '013112' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Balachandra full_name: Suri, Balachandra id: 47A5E706-F248-11E8-B48F-1D18A9856A87 last_name: Suri - first_name: Ravi Kumar full_name: Pallantla, Ravi Kumar last_name: Pallantla - first_name: Michael F. full_name: Schatz, Michael F. last_name: Schatz - first_name: Roman O. full_name: Grigoriev, Roman O. last_name: Grigoriev citation: ama: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112 apa: Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112 chicago: Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112. ieee: B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, 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.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112. short: B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019). date_created: 2019-08-09T09:40:41Z date_published: 2019-07-25T00:00:00Z date_updated: 2025-04-15T06:50:28Z day: '25' ddc: - '532' department: - _id: BjHo doi: 10.1103/physreve.100.013112 ec_funded: 1 external_id: arxiv: - '1907.05860' isi: - '000477911800012' intvolume: ' 100' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.05860 month: '07' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Heteroclinic and homoclinic connections in a Kolmogorov-like flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2019' ... --- _id: '31' abstract: - lang: eng text: Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus. acknowledgement: This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013). article_number: '042410' article_processing_charge: No article_type: original author: - first_name: Ulisse full_name: Ferrari, Ulisse last_name: Ferrari - first_name: Stephane full_name: Deny, Stephane last_name: Deny - first_name: Matthew J full_name: Chalk, Matthew J last_name: Chalk - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Thierry full_name: Mora, Thierry last_name: Mora citation: ama: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410 apa: Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410 chicago: Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410. ieee: U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018. ista: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410. mla: Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410. short: U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018). date_created: 2018-12-11T11:44:15Z date_published: 2018-10-17T00:00:00Z date_updated: 2025-05-05T13:48:04Z day: '17' department: - _id: GaTk doi: 10.1103/PhysRevE.98.042410 ec_funded: 1 external_id: isi: - '000447486100004' intvolume: ' 98' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/243816v2.full month: '10' oa: 1 oa_version: Preprint project: - _id: 26436750-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '785907' name: Human Brain Project Specific Grant Agreement 2 publication: Physical Review E publication_identifier: issn: - 2470-0045 publication_status: published publisher: American Physical Society publist_id: '8024' quality_controlled: '1' scopus_import: '1' status: public title: Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 98 year: '2018' ... --- _id: '548' abstract: - lang: eng 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. alternative_title: - Rapid Communications article_number: '060401' article_processing_charge: No arxiv: 1 author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 2017;96(6). doi:10.1103/PhysRevE.96.060401 apa: De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.96.060401 chicago: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401. ieee: D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6. American Physical Society, 2017. 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.” Physical Review E, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.060401. short: D. De Martino, Physical Review E 96 (2017). corr_author: '1' date_created: 2018-12-11T11:47:06Z date_published: 2017-12-21T00:00:00Z date_updated: 2025-09-18T09:41:11Z day: '21' department: - _id: GaTk doi: 10.1103/PhysRevE.96.060401 ec_funded: 1 external_id: arxiv: - '1707.00320' isi: - '000418574400001' intvolume: ' 96' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1707.00320 month: '12' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review E publication_identifier: issn: - 2470-0045 publication_status: published publisher: American Physical Society publist_id: '7266' quality_controlled: '1' scopus_import: '1' status: public title: Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 96 year: '2017' ... --- OA_type: closed access _id: '673' abstract: - lang: eng 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. article_number: '053103' article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Altmeyer, 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 citation: ama: Altmeyer S, Lueptow R. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 2017;95(5). doi:10.1103/PhysRevE.95.053103 apa: Altmeyer, S., & Lueptow, R. (2017). Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.95.053103 chicago: Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.95.053103. ieee: S. Altmeyer and R. Lueptow, “Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow,” Physical Review E, vol. 95, no. 5. American Physical Society, 2017. 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. mla: Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical Review E, vol. 95, no. 5, 053103, American Physical Society, 2017, doi:10.1103/PhysRevE.95.053103. short: S. Altmeyer, R. Lueptow, Physical Review E 95 (2017). corr_author: '1' date_created: 2018-12-11T11:47:50Z date_published: 2017-05-10T00:00:00Z date_updated: 2025-09-10T14:26:12Z day: '10' department: - _id: BjHo doi: 10.1103/PhysRevE.95.053103 external_id: isi: - '000401233900007' pmid: - '28618504' intvolume: ' 95' isi: 1 issue: '5' language: - iso: eng month: '05' oa_version: None pmid: 1 publication: Physical Review E publication_identifier: issn: - 2470-0045 publication_status: published publisher: American Physical Society publist_id: '7049' quality_controlled: '1' scopus_import: '1' status: public title: Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 95 year: '2017' ... --- _id: '947' abstract: - lang: eng text: Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence. article_number: '010401' article_processing_charge: No arxiv: 1 author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Fabrizio full_name: Capuani, Fabrizio last_name: Capuani - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino citation: ama: De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. Physical Review E. 2017;96(1). doi:10.1103/PhysRevE.96.010401 apa: De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.96.010401 chicago: De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.010401. ieee: D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” Physical Review E, vol. 96, no. 1. American Physical Society, 2017. ista: De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E. 96(1), 010401. mla: De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E, vol. 96, no. 1, 010401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.010401. short: D. De Martino, F. Capuani, A. De Martino, Physical Review E 96 (2017). das_tickbox: '1' date_created: 2018-12-11T11:49:21Z date_published: 2017-07-10T00:00:00Z date_updated: 2026-08-12T14:29:46Z day: '10' department: - _id: GaTk doi: 10.1103/PhysRevE.96.010401 ec_funded: 1 external_id: arxiv: - '1703.00219' isi: - '000405194200002' intvolume: ' 96' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.00219 month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review E publication_identifier: issn: - 2470-0045 publication_status: published publisher: American Physical Society publist_id: '6470' quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the entropic cost of cellular growth control type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ...