[{"oa_version":"Published Version","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"],"issnl":[" 1745-2473"]},"corr_author":"1","PlanS_conform":"1","OA_place":"publisher","scopus_import":"1","author":[{"first_name":"Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","full_name":"Mishra, Nikhil","last_name":"Mishra","orcid":"0000-0002-6425-5788"},{"last_name":"Li","full_name":"Li, Yuting I","id":"ee7a5ca8-8b71-11ed-b662-b3341c05b7eb","first_name":"Yuting I"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","year":"2026","volume":22,"has_accepted_license":"1","date_updated":"2026-04-28T12:55:30Z","publisher":"Springer Nature","file":[{"file_size":7335694,"creator":"dernst","content_type":"application/pdf","date_updated":"2026-01-21T08:21:11Z","file_id":"21026","success":1,"relation":"main_file","checksum":"0ab7ac2fbcb61a364dba57152db64ed7","access_level":"open_access","date_created":"2026-01-21T08:21:11Z","file_name":"2026_NaturePhysics_Mishra.pdf"}],"oaworkid":1,"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"oaworkid":["W7118187193"]},"department":[{"_id":"EdHa"},{"_id":"CaHe"}],"abstract":[{"text":"Early embryo geometry is one of the most invariant species-specific traits, yet its role in ensuring developmental reproducibility and robustness remains underexplored. Here we show that in zebrafish, the geometry of the fertilized egg—specifically its curvature and volume—serves as a critical initial condition triggering a cascade of events that influence development. The embryo geometry guides patterned asymmetric cell divisions in the blastoderm, generating radial gradients of cell volume and nucleocytoplasmic ratio. These gradients generate mitotic phase waves, with the nucleocytoplasmic ratio determining individual cell cycle periods independently of other cells. We demonstrate that reducing cell autonomy reshapes these waves, emphasizing the instructive role of geometry-derived volume patterns in setting the intrinsic period of the cell cycle oscillator. In addition to organizing cell cycles, early embryo geometry spatially patterns zygotic genome activation at the midblastula transition, a key step in establishing embryonic autonomy. Disrupting the embryo shape alters the zygotic genome activation pattern and causes ectopic germ layer specification, underscoring the developmental significance of geometry. Together, our findings reveal a symmetry-breaking function of early embryo geometry in coordinating cell cycle and transcriptional patterning.","lang":"eng"}],"date_published":"2026-01-05T00:00:00Z","acknowledgement":"We thank N. Petridou (EMBL) for sharing results before publication. N.M. was supported by funding from the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie COFUND Actions ISTplus grant agreement number 754411. Y.I.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. The research was supported by funding to C.-P.H. from the NOMIS Foundation, Project ID 1.844. We would like to thank past and present members of the Heisenberg and Hannezo groups for discussions, particularly S. Shamipour, V. Doddihal, M. Jovic, N. Hino, F. N. Arslan, R. Kobylinska and C. Camelo for feedback on the draft manuscript. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria through resources provided by the Aquatics Facility, Imaging & Optics Facility (IOF), Scientific Computing (SciComp) facility and Lab Support Facility (LSF). Open access funding provided by Institute of Science and Technology (IST Austria).","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41567-025-03122-1","month":"01","citation":{"ista":"Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. 2026. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. Nature Physics. 22, 139–150.","ama":"Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. <i>Nature Physics</i>. 2026;22:139-150. doi:<a href=\"https://doi.org/10.1038/s41567-025-03122-1\">10.1038/s41567-025-03122-1</a>","short":"N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026) 139–150.","chicago":"Mishra, Nikhil, Yuting I Li, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” <i>Nature Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41567-025-03122-1\">https://doi.org/10.1038/s41567-025-03122-1</a>.","apa":"Mishra, N., Li, Y. I., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2026). Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03122-1\">https://doi.org/10.1038/s41567-025-03122-1</a>","mla":"Mishra, Nikhil, et al. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” <i>Nature Physics</i>, vol. 22, Springer Nature, 2026, pp. 139–50, doi:<a href=\"https://doi.org/10.1038/s41567-025-03122-1\">10.1038/s41567-025-03122-1</a>.","ieee":"N. Mishra, Y. I. Li, E. B. Hannezo, and C.-P. J. Heisenberg, “Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo,” <i>Nature Physics</i>, vol. 22. Springer Nature, pp. 139–150, 2026."},"status":"public","OA_type":"hybrid","type":"journal_article","page":"139-150","doi":"10.1038/s41567-025-03122-1","ec_funded":1,"intvolume":"        22","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"title":"Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2026-01-20T10:12:19Z","file_date_updated":"2026-01-21T08:21:11Z","publication":"Nature Physics","_id":"21015","quality_controlled":"1","article_type":"original","day":"05","related_material":{"link":[{"relation":"research_data","url":"https://ista.ac.at/en/news/geometry-shapes-life/","description":"News on ISTA website"}]},"oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"917c023a-16d5-11f0-9cad-eb5cafc52090","name":"Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development"}]},{"oa":1,"day":"24","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"PAT 5044023","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading"},{"name":"Nano-Analytics of Cellular Systems","_id":"252C3B08-B435-11E9-9278-68D0E5697425","grant_number":"W1250-B20","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"_id":"21137","date_created":"2026-02-04T16:38:02Z","file_date_updated":"2026-03-24T07:21:43Z","title":"Data associated with Keratins coordinate tissue spreading ","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","article_processing_charge":"No","doi":"10.15479/AT-ISTA-21137","ec_funded":1,"type":"research_data","month":"3","citation":{"ieee":"S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026.","mla":"Naik, Suyash. <i>Data Associated with Keratins Coordinate Tissue Spreading </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","apa":"Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>","chicago":"Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>.","short":"S. Naik, (2026).","ista":"Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","ama":"Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>"},"status":"public","acknowledgement":"We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H.","fulldoi":"https://doi.org/10.15479/AT-ISTA-21137","department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","date_published":"2026-03-24T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"file":[{"content_type":"application/zip","description":"Python3 library written in C++20 to integrate vertex models. Please read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed instructions for installation and usage of the code in this repository. 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The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives rise to a biochemical cycle and active turnover of DNA methylation. While the ensuing biochemical oscillations have been implicated in the regulation of cell differentiation, their functional role and spatiotemporal dynamics are unknown. In this work, we demonstrate that chromatin-mediated coupling between these local biochemical cycles can lead to the emergence of phase-locked domains, regions of locally synchronized turnover activity, whose coarsening is arrested by genomic heterogeneity. We introduce a minimal model based on stochastic oscillators with constrained long-range and nonreciprocal interactions, shaped by the local chromatin organization. Through a combination of analytical theory and stochastic simulations, we predict both the degree of synchronization and the typical size of emergent phase-locked domains. We qualitatively test these predictions using single-cell sequencing data. Our results show that DNA methylation turnover exhibits surprisingly rich spatiotemporal patterns that may be used by cells to control cell differentiation."}],"fulldoi":"https://doi.org/10.1103/89bj-79g5","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 950349 and the Marie Skłodowska-Curie Grant Agreement No. 101034413. The computations in this paper were run in part on the the FASRC Cannon cluster supported by the FAS Division of Science Research Computing Group at Harvard University and the cluster of the Max Planck Institute for the Physics of Complex Systems.","language":[{"iso":"eng"}],"oa_version":"Published Version","corr_author":"1","PlanS_conform":"1","publication_identifier":{"eissn":["2835-8279"]},"DOAJ_listed":"1","publication_status":"published","OA_place":"publisher","author":[{"full_name":"Olmeda, Fabrizio","last_name":"Olmeda","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","first_name":"Fabrizio"},{"first_name":"Misha","full_name":"Gupta, Misha","last_name":"Gupta"},{"first_name":"Onurcan","full_name":"Bektas, Onurcan","last_name":"Bektas"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"}],"date_updated":"2026-02-24T06:54:32Z","has_accepted_license":"1","publisher":"American Physical Society","year":"2026","volume":4,"title":"Spatiotemporal patterns of active epigenetic turnover","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-02-17T08:17:53Z","file_date_updated":"2026-02-24T06:53:05Z","publication":"PRX Life","_id":"21275","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"day":"09","quality_controlled":"1","article_type":"original","oa":1,"status":"public","month":"02","OA_type":"gold","citation":{"ista":"Olmeda F, Gupta M, Bektas O, Rulands S. 2026. Spatiotemporal patterns of active epigenetic turnover. PRX Life. 4, 013018.","ama":"Olmeda F, Gupta M, Bektas O, Rulands S. Spatiotemporal patterns of active epigenetic turnover. <i>PRX Life</i>. 2026;4. doi:<a href=\"https://doi.org/10.1103/89bj-79g5\">10.1103/89bj-79g5</a>","short":"F. Olmeda, M. Gupta, O. Bektas, S. Rulands, PRX Life 4 (2026).","chicago":"Olmeda, Fabrizio, Misha Gupta, Onurcan Bektas, and Steffen Rulands. “Spatiotemporal Patterns of Active Epigenetic Turnover.” <i>PRX Life</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/89bj-79g5\">https://doi.org/10.1103/89bj-79g5</a>.","apa":"Olmeda, F., Gupta, M., Bektas, O., &#38; Rulands, S. (2026). Spatiotemporal patterns of active epigenetic turnover. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/89bj-79g5\">https://doi.org/10.1103/89bj-79g5</a>","ieee":"F. Olmeda, M. Gupta, O. Bektas, and S. Rulands, “Spatiotemporal patterns of active epigenetic turnover,” <i>PRX Life</i>, vol. 4. American Physical Society, 2026.","mla":"Olmeda, Fabrizio, et al. “Spatiotemporal Patterns of Active Epigenetic Turnover.” <i>PRX Life</i>, vol. 4, 013018, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/89bj-79g5\">10.1103/89bj-79g5</a>."},"type":"journal_article","article_number":"013018","doi":"10.1103/89bj-79g5","ec_funded":1,"intvolume":"         4","ddc":["570"],"article_processing_charge":"Yes"},{"abstract":[{"text":"Analog quantum simulators provide access to many-body dynamics beyond the reach of classical computation. However, extracting physical insights from experimental data is often hindered by measurement noise, limited observables, and incomplete knowledge of the underlying microscopic model. Here, we develop a machine learning approach based on a variational autoencoder (VAE) to analyze interference measurements of tunnel-coupled one-dimensional Bose gases, which realize the sine-Gordon quantum field theory. Trained in an unsupervised manner, the VAE learns a minimal latent representation that strongly correlates with the equilibrium control parameter of the system. Applied to nonequilibrium protocols, the latent space uncovers signatures of frozen-in solitons following rapid cooling, and reveals anomalous postquench dynamics not captured by conventional correlation-based methods. These results demonstrate that generative models can extract physically interpretable variables directly from noisy and sparse experimental data, providing complementary probes of equilibrium and nonequilibrium physics in quantum simulators. More broadly, our work highlights how machine learning can supplement established field-theoretical techniques, paving the way for scalable, data-driven discovery in quantum many-body systems.","lang":"eng"}],"department":[{"_id":"EdHa"}],"date_published":"2026-04-29T00:00:00Z","acknowledgement":"We thank Sebastian Erne and Igor Mazets for helpful discussions and sharing codes for the transfer matrix sampling. This research was funded in part by the European Research Council: ERC Advanced Grant “Emergence in Quantum Physics” (EmQ) under Grant Agreement No. 101097858 and ERC Advanced Grant “Artificial agency and learning in quantum environments” (QuantAI) under Grant Agreement No. 101055129. This work was also supported by the Austrian Science Fund (FWF) (SFB BeyondC F7102, 10.55776/F71). G.F.-F. acknowledges the European Research Council AdG NOQIA; MCIN/AEI [PGC2018-0910.13039/501100011033, CEX2019-000910-S/10.13039/501100011033, Plan National FIDEUA PID2019-106901GB-I00, Plan National STAMEENA PID2022-139099NB, I00, project funded by MCIN/AEI/10.13039/501100011033 and by the “European Union NextGenerationEU/PRTR” (PRTR-C17.I1), FPI]; QUANTERA DYNAMITE PCI2022-132919 under Grant Agreement No. 101017733; Ministry for Digital Transformation and of Civil Service of the Spanish Government through the QUANTUM ENIA project call—Quantum Spain project, and by the European Union through the Recovery, Transformation and Resilience Plan—NextGenerationEU within the framework of the Digital Spain 2026 Agenda; Fundació Cellex; Fundació Mir-Puig; Generalitat de Catalunya (European Social Fund FEDER and CERCA program); Barcelona Supercomputing Center MareNostrum (FI-2023-3-0024); (HORIZON-CL4-2022-QUANTUM-02-SGA PASQuanS2.1, 101113690, EU Horizon 2020 FET-OPEN OPTOlogic, Grant No. 899794, QU-ATTO, 101168628), EU Horizon Europe Program (This project has received funding from the European Union's Horizon Europe research and innovation program under Grant Agreement No. 101080086 NeQST); ICFO Internal “QuantumGaudi” project. This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/COE1] through the Cluster of Excellence quantA (Quantum Science Austria).\r\n\r\nThe views and opinions expressed in this article are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council—neither the European Union nor the granting authority can be held responsible for them.","arxiv":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1103/r7pj-gl7r","file":[{"relation":"main_file","date_created":"2026-05-11T06:56:58Z","checksum":"dbfc58e1e176f7b63e0d274eb0d1bffa","access_level":"open_access","file_name":"2026_PhysicalReviewResearch_Moller.pdf","content_type":"application/pdf","file_id":"21852","success":1,"date_updated":"2026-05-11T06:56:58Z","creator":"dernst","file_size":1829628}],"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2509.13821"]},"author":[{"first_name":"Frederik Skovbo","id":"43cbcc83-0564-11f0-a935-e37325525859","last_name":"Moller","full_name":"Moller, Frederik Skovbo"},{"full_name":"Fernández-Fernández, Gabriel","last_name":"Fernández-Fernández","first_name":"Gabriel"},{"first_name":"Thomas","full_name":"Schweigler, Thomas","last_name":"Schweigler"},{"last_name":"De Schoulepnikoff","full_name":"De Schoulepnikoff, Paulin","first_name":"Paulin"},{"full_name":"Schmiedmayer, Jörg","last_name":"Schmiedmayer","first_name":"Jörg"},{"last_name":"Muñoz-Gil","full_name":"Muñoz-Gil, Gorka","first_name":"Gorka"}],"OA_place":"publisher","scopus_import":"1","publication_status":"published","DOAJ_listed":"1","volume":8,"year":"2026","publisher":"American Physical Society","has_accepted_license":"1","date_updated":"2026-05-11T06:58:56Z","oa_version":"Published Version","publication_identifier":{"eissn":["2643-1564"]},"PlanS_conform":"1","_id":"21847","publication":"Physical Review Research","file_date_updated":"2026-05-11T06:56:58Z","date_created":"2026-05-10T22:02:15Z","oa":1,"day":"29","article_type":"original","quality_controlled":"1","title":"Learning minimal representations of many-body physics from snapshots of a quantum simulator","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/r7pj-gl7r","intvolume":"         8","article_number":"023094","article_processing_charge":"Yes","ddc":["530"],"month":"04","status":"public","OA_type":"gold","citation":{"ista":"Moller FS, Fernández-Fernández G, Schweigler T, De Schoulepnikoff P, Schmiedmayer J, Muñoz-Gil G. 2026. Learning minimal representations of many-body physics from snapshots of a quantum simulator. Physical Review Research. 8(2), 023094.","ama":"Moller FS, Fernández-Fernández G, Schweigler T, De Schoulepnikoff P, Schmiedmayer J, Muñoz-Gil G. Learning minimal representations of many-body physics from snapshots of a quantum simulator. <i>Physical Review Research</i>. 2026;8(2). doi:<a href=\"https://doi.org/10.1103/r7pj-gl7r\">10.1103/r7pj-gl7r</a>","chicago":"Moller, Frederik Skovbo, Gabriel Fernández-Fernández, Thomas Schweigler, Paulin De Schoulepnikoff, Jörg Schmiedmayer, and Gorka Muñoz-Gil. “Learning Minimal Representations of Many-Body Physics from Snapshots of a Quantum Simulator.” <i>Physical Review Research</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/r7pj-gl7r\">https://doi.org/10.1103/r7pj-gl7r</a>.","short":"F.S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff, J. Schmiedmayer, G. Muñoz-Gil, Physical Review Research 8 (2026).","apa":"Moller, F. S., Fernández-Fernández, G., Schweigler, T., De Schoulepnikoff, P., Schmiedmayer, J., &#38; Muñoz-Gil, G. (2026). Learning minimal representations of many-body physics from snapshots of a quantum simulator. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/r7pj-gl7r\">https://doi.org/10.1103/r7pj-gl7r</a>","ieee":"F. S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff, J. Schmiedmayer, and G. Muñoz-Gil, “Learning minimal representations of many-body physics from snapshots of a quantum simulator,” <i>Physical Review Research</i>, vol. 8, no. 2. American Physical Society, 2026.","mla":"Moller, Frederik Skovbo, et al. “Learning Minimal Representations of Many-Body Physics from Snapshots of a Quantum Simulator.” <i>Physical Review Research</i>, vol. 8, no. 2, 023094, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/r7pj-gl7r\">10.1103/r7pj-gl7r</a>."},"issue":"2","type":"journal_article"},{"file":[{"file_name":"2026_PhysicalReviewX_Drozdowski.pdf","checksum":"a90e905968648ac4425c256de901e9c3","access_level":"open_access","date_created":"2026-05-21T06:05:49Z","relation":"main_file","date_updated":"2026-05-21T06:05:49Z","file_id":"21901","success":1,"content_type":"application/pdf","creator":"dernst","file_size":5603164}],"tmp":{"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)","image":"/images/cc_by.png"},"abstract":[{"text":"Cell extrusion is an essential mechanism for controlling cell density in epithelial tissues. Another essential element of epithelia is curvature, which is required to achieve complex shapes, like in the lung or intestine. Here, we introduce a three-dimensional bubbly vertex model to study the interplay between extrusion and curvature. We find a generic cellular bulging instability at topological defects, which is much stronger than for standard vertex models. Analyzing cell shapes in three-dimensional imaging data of spherical mouse colon organoids, we infer that pentagonal cells have an increased basal interfacial tension, suggesting that cells at topological defects react to the different force conditions. Using the bubbly vertex model, we show that such basal tensions stabilize against the predicted instability and result in better cell shape control than tissue-scale mechanisms such as lumen pressure and spontaneous curvature. Our theory suggests that epithelial curvature naturally leads to bulged and extrusionlike cell shapes because the interfacial curvature of individual cells at the defects strongly amplifies buckling effected by tissue-scale topological defects in elastic sheets. Our results highlight the complex interplay of forces across scales in three-dimensional tissue organization.","lang":"eng"}],"department":[{"_id":"EdHa"}],"date_published":"2026-04-30T00:00:00Z","acknowledgement":"O. M. D., M. B., and U.S. S. acknowledge support from the Max Planck School Matter to Life, with funding by the German Federal Ministry of Education and Research (BMBF), the Dieter Schwarz Foundation, and the Max Planck Society. M. B. and U.S. S. acknowledge support from the cluster of excellence 3DMM2O (EXC 2082/1-390761711 and EXC 2082/2-390761711) funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). The authors acknowledge the data storage service SDS@hd supported by the Ministry of Science, Research and the Arts Baden-Württemberg (MWK) and the DFG through Grant No. INST 35/1503-1 FUGG. For the publication fee we acknowledge financial support by Heidelberg University. O. M. D. thanks Edouard Hannezo for valuable discussions. U.S. S. is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg.","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1103/x82g-cq7n","oa_version":"Published Version","publication_identifier":{"issn":["2160-3308"]},"author":[{"id":"cd4ed792-b872-11ef-bb90-b7b3a3f62f75","first_name":"Oliver M","full_name":"Drozdowski, Oliver M","last_name":"Drozdowski"},{"first_name":"Büşra","full_name":"Kocameşe-Tamgac𝚤, Büşra","last_name":"Kocameşe-Tamgac𝚤"},{"full_name":"Boonekamp, Kim E.","last_name":"Boonekamp","first_name":"Kim E."},{"last_name":"Boutros","full_name":"Boutros, Michael","first_name":"Michael"},{"first_name":"Ulrich S.","full_name":"Schwarz, Ulrich S.","last_name":"Schwarz"}],"scopus_import":"1","OA_place":"publisher","publication_status":"published","DOAJ_listed":"1","volume":16,"year":"2026","publisher":"American Physical Society","date_updated":"2026-05-21T06:08:11Z","has_accepted_license":"1","title":"Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Physical Review X","_id":"21899","date_created":"2026-05-20T14:35:57Z","file_date_updated":"2026-05-21T06:05:49Z","oa":1,"quality_controlled":"1","day":"30","article_type":"original","citation":{"ama":"Drozdowski OM, Kocameşe-Tamgac𝚤 B, Boonekamp KE, Boutros M, Schwarz US. Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. <i>Physical Review X</i>. 2026;16(2). doi:<a href=\"https://doi.org/10.1103/x82g-cq7n\">10.1103/x82g-cq7n</a>","ista":"Drozdowski OM, Kocameşe-Tamgac𝚤 B, Boonekamp KE, Boutros M, Schwarz US. 2026. Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. Physical Review X. 16(2), 021023.","short":"O.M. Drozdowski, B. Kocameşe-Tamgac𝚤, K.E. Boonekamp, M. Boutros, U.S. Schwarz, Physical Review X 16 (2026).","chicago":"Drozdowski, Oliver M, Büşra Kocameşe-Tamgac𝚤, Kim E. Boonekamp, Michael Boutros, and Ulrich S. Schwarz. “Cell Bulging and Extrusion in a Three-Dimensional Bubbly Vertex Model for Curved Epithelial Sheets.” <i>Physical Review X</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/x82g-cq7n\">https://doi.org/10.1103/x82g-cq7n</a>.","apa":"Drozdowski, O. M., Kocameşe-Tamgac𝚤, B., Boonekamp, K. E., Boutros, M., &#38; Schwarz, U. S. (2026). Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/x82g-cq7n\">https://doi.org/10.1103/x82g-cq7n</a>","ieee":"O. M. Drozdowski, B. Kocameşe-Tamgac𝚤, K. E. Boonekamp, M. Boutros, and U. S. Schwarz, “Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets,” <i>Physical Review X</i>, vol. 16, no. 2. American Physical Society, 2026.","mla":"Drozdowski, Oliver M., et al. “Cell Bulging and Extrusion in a Three-Dimensional Bubbly Vertex Model for Curved Epithelial Sheets.” <i>Physical Review X</i>, vol. 16, no. 2, 021023, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/x82g-cq7n\">10.1103/x82g-cq7n</a>."},"OA_type":"gold","status":"public","month":"04","type":"journal_article","issue":"2","article_number":"021023","doi":"10.1103/x82g-cq7n","intvolume":"        16","article_processing_charge":"Yes","ddc":["530"]},{"publication_status":"draft","author":[{"last_name":"Hino","full_name":"Hino, Naoya","first_name":"Naoya","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"full_name":"Kapoor, Tushna","last_name":"Kapoor","id":"e3b3eda7-fd4d-11eb-8fd8-c40af7a478b1","first_name":"Tushna"},{"first_name":"Uday R","id":"bb4a0dc4-32c9-11ee-b5ce-a97ceedd5924","last_name":"Gubbala","full_name":"Gubbala, Uday R"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","supplementarymaterial":"yes","publisher":"Institute of Science and Technology Austria","date_updated":"2026-07-14T07:07:41Z","has_accepted_license":"1","year":"2026","das_tickbox":"1","oa_version":"Preprint","researchdata_availability":"yes","corr_author":"1","date_published":"2026-07-14T00:00:00Z","abstract":[{"text":"Tissue tension is a key determinant of tissue shape, and its regulation is essential for both morphogenesis and the maintenance of tissue integrity. During zebrafish embryogenesis, the enveloping layer (EVL) – an epithelial monolayer covering the blastoderm – undergoes extensive spreading that is driven by pulling forces exerted at its margin and more than doubles its surface area. Yet whether and how the EVL actively regulates its tissue tension during this process remains unclear. Here, we show that the EVL maintains constant tissue tension while spreading, and that it achieves this by reducing apical cell contractility in response to the same pulling forces that drive its spreading. We identify a mechanosensitive pathway underlying this response, mediated by the scaffold/adaptor protein Kibra regulating the activity of atypical protein kinase C (aPKC) at the apical domain of EVL cells. Under low mechanical stretch, Kibra forms condensates at the base of actin-based apical projections, where it activates Myosin II to increase apical contractility through aPKC downregulation. As mechanical stretch increases, apical projections disassemble, Kibra condensates dissolve, and aPKC activity rises. Elevated aPKC activity in turn reduces apical contractility by reducing Myosin II activity, thereby maintaining constant tissue tension despite increased mechanical stretch. Together, these findings reveal a mechanosensitive mechanism that enables robust adaptation of tissue tension to changing mechanical stretch, ensuring efficient tissue spreading and morphogenesis.","lang":"eng"}],"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank all members of the Heisenberg group for discussion and feedback on the manuscript, and the Imaging and Optics Facility, the Life Science Support Facility and the Electron Microscopy Facility of the Institute of Science and Technology Austria (ISTA) for their continued support. We are grateful to M. Sonawane (Tata Institute of Fundamental Research, India) for providing the pCS2-HA-aPKC (PKCι)-V260F (DN) and pCS2-HA-aPKC (PKCι)-A122E (CA) plasmids, and to I. Mayer for the discussion. Molecular graphics and analyses were performed with UCSF ChimeraX, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases. This research was funded in whole or in part by the Austrian Science Fund (FWF; grant no. PAT5044023) to C.-P.H., and by a JSPS Overseas Research Fellowship and an EMBO Postdoctoral Fellowship (ALTF 16-2022) to N.H.","file":[{"checksum":"66444afd243dce7d383d52d44e8d34a4","access_level":"open_access","date_created":"2026-07-13T09:16:20Z","relation":"main_file","file_name":"Main_text_and_figures.pdf","content_type":"application/pdf","date_updated":"2026-07-13T09:16:20Z","success":1,"file_id":"22283","creator":"nhino","file_size":12477675},{"file_size":4545901,"creator":"nhino","date_updated":"2026-07-13T09:16:25Z","success":1,"file_id":"22284","content_type":"application/pdf","file_name":"Supplementary_figures.pdf","access_level":"open_access","checksum":"90bceb34de64ec792c5de117f0890d05","date_created":"2026-07-13T09:16:25Z","relation":"main_file"},{"date_created":"2026-07-13T09:16:28Z","access_level":"open_access","checksum":"9d9ab89c372142f2ffb6c8c625334d7f","relation":"main_file","file_name":"Supplementary_Video1.mp4","content_type":"video/mp4","date_updated":"2026-07-13T09:16:28Z","success":1,"file_id":"22285","creator":"nhino","file_size":10349451}],"tmp":{"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)","image":"/images/cc_by.png"},"ddc":["570"],"article_processing_charge":"No","OA_type":"green","citation":{"ieee":"N. Hino, T. Kapoor, U. R. Gubbala, E. B. Hannezo, and C.-P. J. Heisenberg, “Apical domain mechanosensation regulates tissue tension homeostasis.” Institute of Science and Technology Austria.","mla":"Hino, Naoya, et al. <i>Apical Domain Mechanosensation Regulates Tissue Tension Homeostasis</i>. Institute of Science and Technology Austria.","apa":"Hino, N., Kapoor, T., Gubbala, U. R., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (n.d.). Apical domain mechanosensation regulates tissue tension homeostasis. Institute of Science and Technology Austria.","chicago":"Hino, Naoya, Tushna Kapoor, Uday R Gubbala, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Apical Domain Mechanosensation Regulates Tissue Tension Homeostasis.” Institute of Science and Technology Austria, n.d.","short":"N. Hino, T. Kapoor, U.R. Gubbala, E.B. Hannezo, C.-P.J. Heisenberg, (n.d.).","ista":"Hino N, Kapoor T, Gubbala UR, Hannezo EB, Heisenberg C-PJ. Apical domain mechanosensation regulates tissue tension homeostasis.","ama":"Hino N, Kapoor T, Gubbala UR, Hannezo EB, Heisenberg C-PJ. Apical domain mechanosensation regulates tissue tension homeostasis."},"month":"07","status":"public","type":"preprint","_id":"22276","date_created":"2026-07-13T09:03:26Z","file_date_updated":"2026-07-13T09:16:28Z","project":[{"grant_number":"PAT 5044023","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading"},{"grant_number":"LTF 16-2022","name":"Mechanosensitive signaling activation in the crosstalk between mechanical force and tissuefluidity","_id":"34dd7f3b-11ca-11ed-8bc3-856f2c87f5da"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"oa":1,"day":"14","related_material":{"record":[{"relation":"earlier_version","id":"21864","status":"public"}]},"title":"Apical domain mechanosensation regulates tissue tension homeostasis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","dataavailabilitystatement":"The MATLAB code for image analysis, and the full model code, including all parameter values\r\nand condition-specific settings, are available on GitHub at https://github.com/uday2607/EVL-tension-homeostasis.git.","keyword":["Epithelial spreading","tissue tension","mechanosensation","aPKC","Kibra","zebrafish"]},{"article_processing_charge":"Yes (via OA deal)","ddc":["530"],"article_number":"038401","intvolume":"       137","doi":"10.1103/mbjk-v4ym","type":"journal_article","OA_type":"hybrid","citation":{"ama":"Zhang CY, Mateu Hoyos P, Brückner D, Tkačik G. Nonlocal decoding of positional and correlational information during development. <i>Physical Review Letters</i>. 2026;137. doi:<a href=\"https://doi.org/10.1103/mbjk-v4ym\">10.1103/mbjk-v4ym</a>","ista":"Zhang CY, Mateu Hoyos P, Brückner D, Tkačik G. 2026. Nonlocal decoding of positional and correlational information during development. Physical Review Letters. 137, 038401.","chicago":"Zhang, Chen Y, Pablo Mateu Hoyos, David Brückner, and Gašper Tkačik. “Nonlocal Decoding of Positional and Correlational Information during Development.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/mbjk-v4ym\">https://doi.org/10.1103/mbjk-v4ym</a>.","short":"C.Y. Zhang, P. Mateu Hoyos, D. Brückner, G. Tkačik, Physical Review Letters 137 (2026).","apa":"Zhang, C. Y., Mateu Hoyos, P., Brückner, D., &#38; Tkačik, G. (2026). Nonlocal decoding of positional and correlational information during development. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/mbjk-v4ym\">https://doi.org/10.1103/mbjk-v4ym</a>","ieee":"C. Y. Zhang, P. Mateu Hoyos, D. Brückner, and G. Tkačik, “Nonlocal decoding of positional and correlational information during development,” <i>Physical Review Letters</i>, vol. 137. American Physical Society, 2026.","mla":"Zhang, Chen Y., et al. “Nonlocal Decoding of Positional and Correlational Information during Development.” <i>Physical Review Letters</i>, vol. 137, 038401, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/mbjk-v4ym\">10.1103/mbjk-v4ym</a>."},"month":"07","status":"public","oa":1,"day":"15","quality_controlled":"1","article_type":"original","project":[{"grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"publication":"Physical Review Letters","_id":"22326","date_created":"2026-07-14T05:38:28Z","file_date_updated":"2026-07-16T09:54:55Z","dataavailabilitystatement":"Code to evaluate PI, to run algorithmic implementations of ALP and RLP decoding, and to\r\nperform simulations is publicly available at https://github.com/alex-chenyi-zhang/nonlocdec_pici.","title":"Nonlocal decoding of positional and correlational information during development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":137,"das_tickbox":"1","year":"2026","publisher":"American Physical Society","date_updated":"2026-07-16T09:58:04Z","has_accepted_license":"1","author":[{"last_name":"Zhang","full_name":"Zhang, Chen Y","first_name":"Chen Y","id":"81b43fb8-c9d5-11ef-bf68-ade532a1f204"},{"first_name":"Pablo","id":"50b236c7-50c1-11ef-bb9a-a2375694f8b5","last_name":"Mateu Hoyos","full_name":"Mateu Hoyos, Pablo"},{"first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","last_name":"Brückner","orcid":"0000-0001-7205-2975"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","scopus_import":"1","supplementarymaterial":"no","publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":[" 1079-7114"]},"PlanS_conform":"1","corr_author":"1","oa_version":"Published Version","researchdata_availability":"no","acknowledgement":"This work was supported in part\r\nby European Research Council No. ERC-2023-SyG\r\n“DynaTrans” Grant No. 101118866 (G. T.). We thank\r\nPieter Rein ten Wolde and Vahe Galstyan for stimulating\r\ndiscussions.","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1103/mbjk-v4ym","abstract":[{"text":"In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision of this process be improved by nonlocal information, e.g., via cell-cell communication? Using a Bayes-optimal framework, we show that positional inference depends crucially on morphogen spatial correlations and on the \"structural prior\" that encodes the geometry of the cellular lattice performing the readout, thereby determining what a cell can reliably assume about the position of its neighbors when interpreting nonlocal morphogen signals. We derive upper bounds on positional information gain due to nonlocal readout and identify signal processing algorithms that approximate optimal positional inference, as well as simple chemical reaction schemes which implement such algorithms. Our theory suggests that correlational information can be exploited to significantly enhance developmental precision.","lang":"eng"}],"department":[{"_id":"GaTk"},{"_id":"EdHa"},{"_id":"GradSch"}],"date_published":"2026-07-15T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"file":[{"file_name":"2026_PhysicalReviewLetters_Zhang.pdf","date_created":"2026-07-16T09:54:55Z","access_level":"open_access","checksum":"28861d31d0f6cf541aaca04faaed1767","relation":"main_file","success":1,"date_updated":"2026-07-16T09:54:55Z","file_id":"22352","content_type":"application/pdf","creator":"dernst","file_size":2550345}]},{"title":"Lumen charge governs gated ion transport in β-barrel nanopores","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","dataavailabilitystatement":"All data that support the findings of this study are available within the article and its Supplementary Information. Source data are available via Zenodo at https://doi.org/10.5281/zenodo.17200775 (ref. 64). Cryo-EM data for aerolysin can be accessed through the EMDB with the code EMD-51664 for E254A–E258A and EMD-52853 for post-prepore and quasipore. All data processing codes, simulation and modelling codes are available at https://github.com/lukasvandenheuvel/Biomemristors.","publication":"Nature Nanotechnology","_id":"20670","file_date_updated":"2026-07-27T08:22:57Z","date_created":"2025-11-23T23:01:40Z","oa":1,"quality_controlled":"1","article_type":"original","related_material":{"link":[{"relation":"software","url":"https://github.com/lukasvandenheuvel/Biomemristors"}]},"day":"01","citation":{"ieee":"S. Mayer <i>et al.</i>, “Lumen charge governs gated ion transport in β-barrel nanopores,” <i>Nature Nanotechnology</i>, vol. 21. Springer Nature, pp. 116–124, 2026.","mla":"Mayer, Simon, et al. “Lumen Charge Governs Gated Ion Transport in β-Barrel Nanopores.” <i>Nature Nanotechnology</i>, vol. 21, Springer Nature, 2026, pp. 116–24, doi:<a href=\"https://doi.org/10.1038/s41565-025-02052-6\">10.1038/s41565-025-02052-6</a>.","apa":"Mayer, S., Mitsioni, M. F., Robin, P., Van Den Heuvel, L., Ronceray, N., Marcaida, M. J., … Radenovic, A. (2026). Lumen charge governs gated ion transport in β-barrel nanopores. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41565-025-02052-6\">https://doi.org/10.1038/s41565-025-02052-6</a>","chicago":"Mayer, Simon, Marianna Fanouria Mitsioni, Paul Robin, Lukas Van Den Heuvel, Nathan Ronceray, Maria Jose Marcaida, Luciano A. Abriata, et al. “Lumen Charge Governs Gated Ion Transport in β-Barrel Nanopores.” <i>Nature Nanotechnology</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41565-025-02052-6\">https://doi.org/10.1038/s41565-025-02052-6</a>.","short":"S. Mayer, M.F. Mitsioni, P. Robin, L. Van Den Heuvel, N. Ronceray, M.J. Marcaida, L.A. Abriata, L.F. Krapp, J.S. Anton, S. Soussou, J. Jeanneret-Grosjean, A. Fulciniti, A. Möller, S. Vacle, L. Feletti, H. Brinkerhoff, A.H. Laszlo, J.H. Gundlach, T. Emmerich, M. Dal Peraro, A. Radenovic, Nature Nanotechnology 21 (2026) 116–124.","ista":"Mayer S, Mitsioni MF, Robin P, Van Den Heuvel L, Ronceray N, Marcaida MJ, Abriata LA, Krapp LF, Anton JS, Soussou S, Jeanneret-Grosjean J, Fulciniti A, Möller A, Vacle S, Feletti L, Brinkerhoff H, Laszlo AH, Gundlach JH, Emmerich T, Dal Peraro M, Radenovic A. 2026. Lumen charge governs gated ion transport in β-barrel nanopores. Nature Nanotechnology. 21, 116–124.","ama":"Mayer S, Mitsioni MF, Robin P, et al. Lumen charge governs gated ion transport in β-barrel nanopores. <i>Nature Nanotechnology</i>. 2026;21:116-124. doi:<a href=\"https://doi.org/10.1038/s41565-025-02052-6\">10.1038/s41565-025-02052-6</a>"},"month":"01","status":"public","OA_type":"hybrid","type":"journal_article","doi":"10.1038/s41565-025-02052-6","intvolume":"        21","page":"116-124","article_processing_charge":"Yes (in subscription journal)","isi":1,"ddc":["570"],"file":[{"file_id":"22412","success":1,"date_updated":"2026-07-27T08:22:57Z","content_type":"application/pdf","file_name":"2026_NatureNanotech_Mayer.pdf","checksum":"ff9a5eafe60af1d97da545453bd53eca","access_level":"open_access","date_created":"2026-07-27T08:22:57Z","relation":"main_file","file_size":10091503,"creator":"dernst"}],"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"isi":["001611698900001"],"pmid":["41219410"]},"abstract":[{"text":"β-Barrel nanopores are involved in crucial biological processes, from ATP export in mitochondria to bacterial resistance, and represent a promising platform for emerging sequencing technologies. However, in contrast to ion channels, the understanding of the fundamental principles governing ion transport through these nanopores remains largely unexplored. Here we integrate experimental, numerical and theoretical approaches to elucidate ion transport mechanisms in β-barrel nanopores. We identify and characterize two distinct nonlinear phenomena: open-pore rectification and gating. Through extensive mutation analysis of aerolysin nanopores, we demonstrate that open-pore rectification is caused by ionic accumulation driven by the distribution of lumen charges. In addition, we provide converging evidence suggesting that gating is controlled by electric fields dissociating counterions from lumen charges, promoting local structural deformations. Our findings establish a rigorous framework for characterizing and understanding ion transport processes in protein-based nanopores, enabling the design of adaptable nanofluidic biotechnologies. We illustrate this by optimizing an aerolysin mutant for computing applications.","lang":"eng"}],"department":[{"_id":"EdHa"}],"date_published":"2026-01-01T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"acknowledgement":"We are grateful to M. Mayer and G. van der Goot for their insightful discussions and thoughtful feedback. We acknowledge funding from the European Research Council (grants 101020445—2D-LIQUID N.R. and A.R., MSCA number 101034413 P.R.), the Swiss National Science Foundation (grants 205321_192371 and 200021L_212128 to M.D.P., TMPFP2-217134 to T.E., and IZSEZ0_183779 to J.H.G. and A.R.) and the Swiss National Supercomputing Centre (CSCS) for access to the HPC resources used to run MD simulations. We thank the staff members of the Dubochet Center for Imaging in Lausanne, in particular E. Uchikawa and S. Nazarov, for their assistance with cryo-EM sample preparation and data collection. We thank A. Antanasijevic and Y. Duhoo from EPFL Protein Production and Structure Core Facility for their support in cryo-EM data processing.","fulldoi":"https://doi.org/10.1038/s41565-025-02052-6","researchdata_availability":"yes","oa_version":"Published Version","publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"PlanS_conform":"1","author":[{"last_name":"Mayer","full_name":"Mayer, Simon","first_name":"Simon"},{"first_name":"Marianna Fanouria","last_name":"Mitsioni","full_name":"Mitsioni, Marianna Fanouria"},{"orcid":"0000-0002-5728-9189","last_name":"Robin","full_name":"Robin, Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","first_name":"Paul"},{"first_name":"Lukas","full_name":"Van Den Heuvel, Lukas","last_name":"Van Den Heuvel"},{"last_name":"Ronceray","full_name":"Ronceray, Nathan","first_name":"Nathan"},{"full_name":"Marcaida, Maria Jose","last_name":"Marcaida","first_name":"Maria Jose"},{"first_name":"Luciano A.","last_name":"Abriata","full_name":"Abriata, Luciano A."},{"full_name":"Krapp, Lucien F.","last_name":"Krapp","first_name":"Lucien F."},{"first_name":"Jana S.","full_name":"Anton, Jana S.","last_name":"Anton"},{"first_name":"Sarah","last_name":"Soussou","full_name":"Soussou, Sarah"},{"last_name":"Jeanneret-Grosjean","full_name":"Jeanneret-Grosjean, Justin","first_name":"Justin"},{"first_name":"Alessandro","full_name":"Fulciniti, Alessandro","last_name":"Fulciniti"},{"full_name":"Möller, Alexia","last_name":"Möller","first_name":"Alexia"},{"full_name":"Vacle, Sarah","last_name":"Vacle","first_name":"Sarah"},{"first_name":"Lely","full_name":"Feletti, Lely","last_name":"Feletti"},{"first_name":"Henry","full_name":"Brinkerhoff, Henry","last_name":"Brinkerhoff"},{"full_name":"Laszlo, Andrew H.","last_name":"Laszlo","first_name":"Andrew H."},{"full_name":"Gundlach, Jens H.","last_name":"Gundlach","first_name":"Jens H."},{"last_name":"Emmerich","full_name":"Emmerich, Theo","first_name":"Theo"},{"first_name":"Matteo","full_name":"Dal Peraro, Matteo","last_name":"Dal Peraro"},{"full_name":"Radenovic, Aleksandra","last_name":"Radenovic","first_name":"Aleksandra"}],"scopus_import":"1","supplementarymaterial":"yes","OA_place":"publisher","publication_status":"published","volume":21,"year":"2026","das_tickbox":"1","publisher":"Springer Nature","date_updated":"2026-07-27T08:24:20Z","has_accepted_license":"1"},{"date_updated":"2026-07-27T13:56:09Z","has_accepted_license":"1","publisher":"Springer Nature","das_tickbox":"1","year":"2026","volume":22,"publication_status":"published","OA_place":"publisher","supplementarymaterial":"yes","scopus_import":"1","author":[{"first_name":"Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","last_name":"Olmeda","full_name":"Olmeda, Fabrizio"},{"first_name":"Tim","last_name":"Lohoff","full_name":"Lohoff, Tim"},{"full_name":"Kafetzopoulos, Ioannis","last_name":"Kafetzopoulos","first_name":"Ioannis"},{"first_name":"Stephen J.","full_name":"Clark, Stephen J.","last_name":"Clark"},{"last_name":"Benson","full_name":"Benson, Laura","first_name":"Laura"},{"last_name":"Santos","full_name":"Santos, Fatima","first_name":"Fatima"},{"last_name":"Krueger","full_name":"Krueger, Felix","first_name":"Felix"},{"last_name":"Walker","full_name":"Walker, Simon","first_name":"Simon"},{"full_name":"Reik, Wolf","last_name":"Reik","first_name":"Wolf"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"}],"PlanS_conform":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"oa_version":"Published Version","researchdata_availability":"yes","fulldoi":"https://doi.org/10.1038/s41567-026-03263-x","acknowledgement":"We thank all members of the W.R. and S.R. laboratories, F. Piazza, B. D. Simons, and F. Jülicher for helpful discussions. We thank M. Ciarchi for providing annotations for the chromatin compartments. S.R. is a member of the Center for Nano Science (CeNS). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 950349). Research in W.R.’s laboratory was supported by the Biotechnology and Biological Sciences Research Council (BB/K010867/1), Wellcome (095645/Z/11/Z) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (EpiCell lineage 882798). F.O. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. Open access funding provided by Max Planck Society.","language":[{"iso":"eng"}],"pmid":1,"date_published":"2026-06-01T00:00:00Z","department":[{"_id":"EdHa"}],"abstract":[{"text":"The development of complex tissues relies on the precise assignment of cell identity. At the molecular scale, this process depends on the deposition of epigenetic modifications—such as methylation—that are regulated by complex biochemical networks and occur at specific regions on the DNA and chromatin. Here we show that despite the complexity of epigenetic regulation, dynamical scaling and self-similarity of DNA methylation marks emerge in embryonic development. Drawing on single-cell multi-omics experiments, super-resolution microscopy and statistical physics, we demonstrate that these phenomena originate in dynamical feedback between DNA methylation and the formation of nanoscale dynamic chromatin aggregates. These nanoscale processes lead to genome-wide increase in DNA methylation marks following a power law and self-similar correlation functions. Using this framework, we identify methylation patterns that precede gene expression changes in embryonic symmetry breaking. Our work identifies linear sequencing measurements as a laboratory to study mesoscopic biophysical processes in vivo.","lang":"eng"}],"external_id":{"pmid":["42318073"]},"tmp":{"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)","image":"/images/cc_by.png"},"file":[{"creator":"dernst","file_size":7932222,"date_created":"2026-07-27T13:54:58Z","checksum":"58e7734f1ebaf6def642140cb489f08f","access_level":"open_access","relation":"main_file","file_name":"2026_NaturePhysics_Olmeda.pdf","content_type":"application/pdf","date_updated":"2026-07-27T13:54:58Z","file_id":"22591","success":1}],"ddc":["570"],"article_processing_charge":"Yes (via OA deal)","page":"931-940","intvolume":"        22","ec_funded":1,"doi":"10.1038/s41567-026-03263-x","type":"journal_article","status":"public","OA_type":"hybrid","month":"06","citation":{"chicago":"Olmeda, Fabrizio, Tim Lohoff, Ioannis Kafetzopoulos, Stephen J. Clark, Laura Benson, Fatima Santos, Felix Krueger, Simon Walker, Wolf Reik, and Steffen Rulands. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” <i>Nature Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41567-026-03263-x\">https://doi.org/10.1038/s41567-026-03263-x</a>.","short":"F. Olmeda, T. Lohoff, I. Kafetzopoulos, S.J. Clark, L. Benson, F. Santos, F. Krueger, S. Walker, W. Reik, S. Rulands, Nature Physics 22 (2026) 931–940.","ista":"Olmeda F, Lohoff T, Kafetzopoulos I, Clark SJ, Benson L, Santos F, Krueger F, Walker S, Reik W, Rulands S. 2026. Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. 22, 931–940.","ama":"Olmeda F, Lohoff T, Kafetzopoulos I, et al. Scaling and self-similarity in the formation of the embryonic epigenome. <i>Nature Physics</i>. 2026;22:931-940. doi:<a href=\"https://doi.org/10.1038/s41567-026-03263-x\">10.1038/s41567-026-03263-x</a>","mla":"Olmeda, Fabrizio, et al. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” <i>Nature Physics</i>, vol. 22, Springer Nature, 2026, pp. 931–40, doi:<a href=\"https://doi.org/10.1038/s41567-026-03263-x\">10.1038/s41567-026-03263-x</a>.","ieee":"F. Olmeda <i>et al.</i>, “Scaling and self-similarity in the formation of the embryonic epigenome,” <i>Nature Physics</i>, vol. 22. Springer Nature, pp. 931–940, 2026.","apa":"Olmeda, F., Lohoff, T., Kafetzopoulos, I., Clark, S. J., Benson, L., Santos, F., … Rulands, S. (2026). Scaling and self-similarity in the formation of the embryonic epigenome. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-026-03263-x\">https://doi.org/10.1038/s41567-026-03263-x</a>"},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"article_type":"original","quality_controlled":"1","day":"01","oa":1,"file_date_updated":"2026-07-27T13:54:58Z","date_created":"2026-05-10T22:02:16Z","_id":"21849","publication":"Nature Physics","dataavailabilitystatement":"All sequencing datasets reported in this paper are available on Gene Expression Omnibus (GEO) under accession GSE166226. STORM localization data are available on Zenodo (https://doi.org/10.5281/zenodo.18965309)57. Raw images are available upon request. Code for computing the correlation functions and STORM analysis are available via GitHub at https://github.com/srulands/inference_of_spatio-temporal_processes.","title":"Scaling and self-similarity in the formation of the embryonic epigenome","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"pmid":["42143048"]},"file":[{"file_size":15363936,"creator":"dernst","date_updated":"2026-07-29T10:27:25Z","file_id":"22609","success":1,"content_type":"application/pdf","file_name":"2026_NatureComm_Naik.pdf","access_level":"open_access","date_created":"2026-07-29T10:27:25Z","checksum":"f26d96e180c1d034d9c9c8f57c3c258b","relation":"main_file"}],"pmid":1,"acknowledgement":"We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H.","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41467-026-72366-z","abstract":[{"lang":"eng","text":"For tissues to spread, they must deform while staying intact. How spreading tissues balance flexibility with integrity is not yet well understood. Here, we show that keratin intermediate filaments adapt tissue mechanical resilience to the stresses arising in epithelial tissues during spreading. By analyzing the expansion of the enveloping cell layer (EVL) over the yolk cell in zebrafish embryos in vivo, we find that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, to prevent tissue rupture. Further, keratins are required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the forces pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production and EVL mechanical resilience, ensuring uniform and robust tissue spreading."}],"department":[{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EdHa"}],"date_published":"2026-07-17T00:00:00Z","publication_identifier":{"eissn":["2041-1723"]},"PlanS_conform":"1","corr_author":"1","researchdata_availability":"yes","oa_version":"Published Version","volume":17,"das_tickbox":"1","year":"2026","publisher":"Springer Nature","date_updated":"2026-07-29T10:33:31Z","has_accepted_license":"1","author":[{"full_name":"Naik, Suyash","last_name":"Naik","orcid":"0000-0001-8421-5508","first_name":"Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Keta","full_name":"Keta, Yann-Edwin","first_name":"Yann-Edwin"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Silke","full_name":"Henkes, Silke","last_name":"Henkes"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"OA_place":"publisher","scopus_import":"1","supplementarymaterial":"yes","publication_status":"published","dataavailabilitystatement":"The authors declare that the minimum dataset that is necessary to\r\ninterpret, verify, and extend the research in this article is included in\r\nthe supplementary information, the source data, and the archived data\r\nrepository (https://doi.org/10.15479/AT-ISTA-21137). This is also available\r\non GitHub at https://github.com/Suyash-Naik/2026-\r\nKeratinepithlialspreadingcoordinate-Data. Source data are provided\r\nwith this paper. The framework to develop the vertex models used in this paper are\r\navailable online on GitHub and archived in the source data provided.\r\nCustom scripts used for analysis of imaging and simulation data are\r\nprovided along with data files for all panels in the source data for this\r\nmanuscript on GitHub and in data repo (https://doi.org/10.15479/ATISTA-\r\n21137). Framework for the vertex model is available at https://\r\ngithub.com/yketta/cells. Code for analysis is available on GitHub\r\nhttps://github.com/Suyash-Naik/2026-\r\nKeratinepithlialspreadingcoordinate-Data.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties","oa":1,"quality_controlled":"1","day":"17","article_type":"original","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"20465"}]},"project":[{"grant_number":"PAT 5044023","name":"Keratins in epithelial tissue spreading","_id":"8f060199-16d5-11f0-9cad-f3253b266c46"},{"grant_number":"W1250-B20","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"252C3B08-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"publication":"Nature Communications","_id":"22608","date_created":"2026-07-29T09:10:35Z","file_date_updated":"2026-07-29T10:27:25Z","type":"journal_article","month":"07","citation":{"apa":"Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., &#38; Heisenberg, C.-P. J. (2026). Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-72366-z\">https://doi.org/10.1038/s41467-026-72366-z</a>","ieee":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E. B. Hannezo, S. Henkes, and C.-P. J. Heisenberg, “Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","mla":"Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>Nature Communications</i>, vol. 17, 6499, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-72366-z\">10.1038/s41467-026-72366-z</a>.","ista":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. 2026. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. Nature Communications. 17, 6499.","ama":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-72366-z\">10.1038/s41467-026-72366-z</a>","short":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, Nature Communications 17 (2026).","chicago":"Naik, Suyash, Yann-Edwin Keta, Kornelija Pranjic-Ferscha, Edouard B Hannezo, Silke Henkes, and Carl-Philipp J Heisenberg. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-72366-z\">https://doi.org/10.1038/s41467-026-72366-z</a>."},"OA_type":"gold","status":"public","article_processing_charge":"Yes","ddc":["570"],"doi":"10.1038/s41467-026-72366-z","intvolume":"        17","article_number":"6499"},{"has_accepted_license":"1","date_updated":"2026-09-09T07:24:10Z","contributor":[{"first_name":"Andreas","contributor_type":"data_collector","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","last_name":"Ehrmann","orcid":"0000-0002-0997-5678"}],"publisher":"Institute of Science and Technology Austria","year":"2026","OA_place":"repository","author":[{"last_name":"Ehrmann","full_name":"Ehrmann, Andreas","orcid":"0000-0002-0997-5678","first_name":"Andreas","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2"}],"doi_confirm":"1","corr_author":"1","oa_version":"None","fulldoi":"https://doi.org/10.15479/AT-ISTA-22852","date_published":"2026-09-09T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"CaGo"},{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"This Research Data contains supplemental videos for Chapter 4 \"Designing bistable nanostructures for target behavior\" of my PhD Thesis \"Biological functionality without biochemistry: designing nanomachines for target behavior\".\r\nSupplemental video 1: Video showing the transition pathway of a bistable nanostructure with sphere-based arms, corresponding to the Machine in Scenario 4.\r\nSupplemental video 2: Video showing the transition pathway of the Source in Scenario 1. The arm tips change sides during the transition, demonstrating that the arms pass through each other.\r\nSupplemental video 3: Video showing the transition pathway of a fully polyhedral hinge structure with unconstrained arms. Note that we only show the ends of the arms.\r\nSupplemental video 4: Video showing the transition pathway of the coupled energy-delivery reaction of a Machine (gray) and a Source (blue) nanostructure for the optimized parameters in Scenario 3. Note that we only show the ends of the arms."}],"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"file":[{"file_size":1513964,"creator":"aehrmann","file_id":"22853","success":1,"date_updated":"2026-09-08T11:31:32Z","content_type":"video/mp4","file_name":"Supplemental video 1.mp4","relation":"main_file","access_level":"open_access","checksum":"966417b3eab49523068bb0dfba4ecc07","date_created":"2026-09-08T11:31:32Z"},{"file_name":"Supplemental video 2.mp4","relation":"main_file","access_level":"open_access","checksum":"deddcae30875bff8e59d5dc9ee3c196f","date_created":"2026-09-08T11:31:37Z","file_id":"22854","success":1,"date_updated":"2026-09-08T11:31:37Z","content_type":"video/mp4","creator":"aehrmann","file_size":2634179},{"relation":"main_file","date_created":"2026-09-08T11:31:42Z","checksum":"721446b7595edc670d877185637cf15c","access_level":"open_access","file_name":"Supplemental video 3.mp4","content_type":"video/mp4","file_id":"22855","success":1,"date_updated":"2026-09-08T11:31:42Z","creator":"aehrmann","file_size":2080684},{"date_updated":"2026-09-08T11:31:48Z","success":1,"file_id":"22856","content_type":"video/mp4","file_name":"Supplemental video 4.mp4","relation":"main_file","access_level":"open_access","date_created":"2026-09-08T11:31:48Z","checksum":"da44153821aa4f8f3cbc2860ef6d1bad","file_size":4047831,"creator":"aehrmann"},{"content_type":"text/plain","file_id":"22860","success":1,"date_updated":"2026-09-08T18:36:14Z","relation":"main_file","date_created":"2026-09-08T18:36:14Z","access_level":"open_access","checksum":"1e94cd067809e1a93e21676181b4c102","file_name":"README.txt","file_size":1122,"creator":"aehrmann"}],"article_processing_charge":"No","doi":"10.15479/AT-ISTA-22852","type":"research_data","month":"09","status":"public","citation":{"ista":"Ehrmann A. 2026. Supplemental videos for Designing bistable nanostructures for target behavior, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-22852\">10.15479/AT-ISTA-22852</a>.","ama":"Ehrmann A. Supplemental videos for Designing bistable nanostructures for target behavior. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22852\">10.15479/AT-ISTA-22852</a>","chicago":"Ehrmann, Andreas. “Supplemental Videos for Designing Bistable Nanostructures for Target Behavior.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22852\">https://doi.org/10.15479/AT-ISTA-22852</a>.","short":"A. Ehrmann, (2026).","apa":"Ehrmann, A. (2026). Supplemental videos for Designing bistable nanostructures for target behavior. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22852\">https://doi.org/10.15479/AT-ISTA-22852</a>","mla":"Ehrmann, Andreas. <i>Supplemental Videos for Designing Bistable Nanostructures for Target Behavior</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22852\">10.15479/AT-ISTA-22852</a>.","ieee":"A. Ehrmann, “Supplemental videos for Designing bistable nanostructures for target behavior.” Institute of Science and Technology Austria, 2026."},"acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"name":"Functional bio-inspired nanomachines from sticky colloids","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","grant_number":"PAT 8537123"}],"day":"09","oa":1,"date_created":"2026-09-08T11:32:53Z","file_date_updated":"2026-09-08T18:36:14Z","_id":"22852","keyword":["functional nanostructures","bistability","target behavior","transition pathway"],"title":"Supplemental videos for Designing bistable nanostructures for target behavior","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d"},{"file":[{"date_updated":"2026-09-17T08:59:39Z","file_id":"22901","content_type":"application/pdf","embargo":"2027-01-15","file_name":"2026_Ehrmann_Andreas_Thesis.pdf","access_level":"closed","date_created":"2026-09-11T07:23:57Z","checksum":"a5e3d79e0e5f3f4fb3c414e48116dc9e","embargo_to":"open_access","relation":"main_file","file_size":14782662,"creator":"aehrmann"},{"file_name":"thesis_latex_files.zip","relation":"source_file","access_level":"closed","date_created":"2026-09-11T07:24:14Z","checksum":"0235b9c52fee0c97f402f1c3d4efc1eb","file_id":"22902","date_updated":"2026-09-11T07:24:14Z","content_type":"application/zip","description":"All LaTeX files to compile my PhD Thesis.","creator":"aehrmann","file_size":155228}],"supervisor":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"degree_awarded":"PhD","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"date_published":"2026-09-04T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"CaGo"},{"_id":"EdHa"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22873","language":[{"iso":"eng"}],"acknowledgement":"I acknowledge funding by the Austrian Science Fund (FWF) [10.55776/PAT8537123].","researchdata_availability":"upon request","oa_version":"Published Version","corr_author":"1","doi_confirm":"1","publication_identifier":{"isbn":["978-3-99078-092-3"],"issn":["2663-337X"]},"publication_status":"published","supplementarymaterial":"not applicable","OA_place":"publisher","author":[{"orcid":"0000-0002-0997-5678","full_name":"Ehrmann, Andreas","last_name":"Ehrmann","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","first_name":"Andreas"}],"date_updated":"2026-09-18T11:28:29Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","das_tickbox":"0","year":"2026","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Biological functionality without biochemistry: Designing nanomachines for target behavior","keyword":["PhD Thesis","functional nanomachines","biological functionality","nanotechnology","energy delivery","target behavior","dynamics","design principles","optimization","differentiable statistical physics","machine learning"],"file_date_updated":"2026-09-17T08:59:39Z","date_created":"2026-09-09T12:18:24Z","_id":"22873","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"project":[{"name":"Functional bio-inspired nanomachines from sticky colloids","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","grant_number":"PAT 8537123"}],"day":"04","related_material":{"record":[{"status":"public","id":"22893","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"22892"}]},"status":"public","citation":{"ieee":"A. Ehrmann, “Biological functionality without biochemistry: Designing nanomachines for target behavior,” Institute of Science and Technology Austria, 2026.","mla":"Ehrmann, Andreas. <i>Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22873\">10.15479/AT-ISTA-22873</a>.","apa":"Ehrmann, A. (2026). <i>Biological functionality without biochemistry: Designing nanomachines for target behavior</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22873\">https://doi.org/10.15479/AT-ISTA-22873</a>","short":"A. Ehrmann, Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior, Institute of Science and Technology Austria, 2026.","chicago":"Ehrmann, Andreas. “Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22873\">https://doi.org/10.15479/AT-ISTA-22873</a>.","ista":"Ehrmann A. 2026. Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria.","ama":"Ehrmann A. Biological functionality without biochemistry: Designing nanomachines for target behavior. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22873\">10.15479/AT-ISTA-22873</a>"},"month":"09","type":"dissertation","alternative_title":["ISTA Thesis"],"page":"168","doi":"10.15479/AT-ISTA-22873","ddc":["530","600","621","004","005"],"article_processing_charge":"No"},{"_id":"22893","publication":"arXiv","date_created":"2026-09-09T13:19:13Z","project":[{"_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","name":"Functional bio-inspired nanomachines from sticky colloids","grant_number":"PAT 8537123"}],"oa":1,"related_material":{"record":[{"status":"public","id":"22873","relation":"dissertation_contains"}]},"day":"30","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2606.31620"}],"title":"Designing bistable nanostructures for target behavior","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.48550/arXiv.2606.31620","article_processing_charge":"No","OA_type":"green","citation":{"apa":"Ehrmann, A., Krstić, M., Samadzadeh, S., &#38; Goodrich, C. P. (n.d.). Designing bistable nanostructures for target behavior. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2606.31620\">https://doi.org/10.48550/arXiv.2606.31620</a>","mla":"Ehrmann, Andreas, et al. “Designing Bistable Nanostructures for Target Behavior.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2606.31620\">10.48550/arXiv.2606.31620</a>.","ieee":"A. Ehrmann, M. Krstić, S. Samadzadeh, and C. P. Goodrich, “Designing bistable nanostructures for target behavior,” <i>arXiv</i>. .","ista":"Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2606.31620\">10.48550/arXiv.2606.31620</a>.","ama":"Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2606.31620\">10.48550/arXiv.2606.31620</a>","chicago":"Ehrmann, Andreas, Marija Krstić, Sahar Samadzadeh, and Carl Peter Goodrich. “Designing Bistable Nanostructures for Target Behavior.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2606.31620\">https://doi.org/10.48550/arXiv.2606.31620</a>.","short":"A. Ehrmann, M. Krstić, S. Samadzadeh, C.P. Goodrich, ArXiv (n.d.)."},"status":"public","month":"06","type":"preprint","date_published":"2026-06-30T00:00:00Z","abstract":[{"lang":"eng","text":"Many biological machines function through controlled conformational transitions, yet designing synthetic nanostructures with prescribed dynamical behavior remains a major challenge. Here, we develop a modular inverse-design framework for bistable nanostructures whose function is controlled by an energy profile along a geometric reaction coordinate. Inspired by proteins with rigid domains connected by flexible hinges, we introduce a hinge-arm paradigm in which a small bistable hinge controls the energetics of a conformational transition, while rigid arms map this transition onto the separation between external binding sites. Specifically, we ask which features of a target energy profile can be programmed under different design constraints. We find that the energy barriers and the binding-site separations in the two metastable states can be readily designed, while controlling the location of the transition state or the full shape of the energy profile requires additional design freedom. Using a differentiable design framework, we find that some optimized solutions are numerically inexact but still display the functional behavior for which the target profile was selected, emphasizing the importance of function-based evaluation criteria. These results establish a practical hierarchy of designability for bistable nanostructures and provide a route toward synthetic nanomachines that couple conformational transitions to target behavior."}],"department":[{"_id":"CaGo"},{"_id":"EdHa"},{"_id":"AnSa"}],"fulldoi":"https://doi.org/10.48550/arXiv.2606.31620","arxiv":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank Maitane Muñoz-Basagoiti for stimulating\r\ndiscussions. This research was funded in part by the\r\nAustrian Science Fund (FWF) [10.55776/PAT8537123].\r\n","external_id":{"arxiv":["2606.31620"]},"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publication_status":"draft","author":[{"id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","first_name":"Andreas","orcid":"0000-0002-0997-5678","full_name":"Ehrmann, Andreas","last_name":"Ehrmann"},{"last_name":"Krstić","full_name":"Krstić, Marija","id":"a8f6d1c6-3200-11ee-973b-dab948eace26","first_name":"Marija"},{"id":"0099896b-5fb8-11ef-8420-b30b14627e93","first_name":"Sahar","full_name":"Samadzadeh, Sahar","last_name":"Samadzadeh"},{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"OA_place":"repository","date_updated":"2026-09-18T11:28:28Z","year":"2026","oa_version":"Preprint","corr_author":"1"},{"oa_version":"Preprint","corr_author":"1","publication_status":"draft","OA_place":"repository","author":[{"last_name":"Ehrmann","full_name":"Ehrmann, Andreas","orcid":"0000-0002-0997-5678","first_name":"Andreas","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2"},{"orcid":"0000-0002-1307-5074","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"}],"date_updated":"2026-09-18T11:28:29Z","year":"2026","external_id":{"arxiv":["2506.14266"]},"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2026-06-07T00:00:00Z","department":[{"_id":"CaGo"},{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"Countless biological processes are fueled by energy-rich molecules like ATP and GTP that supply energy with extreme efficiency. However, designing similar energy-delivery schemes from the bottom up, essential for the development of powered nanostructures and other \\emph{de novo} machinery, presents a significant challenge: how can an energy-rich structure be stable in solution yet still deliver this energy at precisely the right time? In this paper, we present a purely physical mechanism that solves this challenge, facilitating energy transfer akin to ATP hydrolysis, yet occurring between synthetic nanostructures without any biochemical interactions. This targeted energy delivery is achieved by exploiting a differentiable state-based model to balance the energy profiles that govern the structural transitions in the two nanostructures, creating a coupled relaxation pathway with minimal barriers that facilitates energy delivery. We verify the effectiveness and robustness of this mechanism through Langevin Dynamics simulations, demonstrating that a bath of the high-energy structures can systematically and repeatedly drive the target structure out of equilibrium, enabling it to perform tasks. As the mechanism operates only through explicit physical forces without any biochemistry or internal state variables, our results present generic and far-reaching design principles, setting the stage for the next generation of synthetic nanomachines."}],"fulldoi":"https://doi.org/10.48550/arXiv.2506.14266","acknowledgement":"We thank Edouard Hannezo, Ella King, Maximilian Lechner, and Jérémie Palacci for stimulating discussions, and Edouard Hannezo, Maximilian Hübl, and\r\nMaitane Muñoz-Basagoiti for helpful comments on the manuscript. This research was funded in part by the\r\nAustrian Science Fund (FWF) [10.55776/PAT8537123].","arxiv":1,"language":[{"iso":"eng"}],"status":"public","month":"06","citation":{"chicago":"Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery with Bistable Nanostructures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2506.14266\">https://doi.org/10.48550/arXiv.2506.14266</a>.","short":"A. Ehrmann, C.P. Goodrich, ArXiv (n.d.).","ista":"Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2506.14266\">10.48550/arXiv.2506.14266</a>.","ama":"Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2506.14266\">10.48550/arXiv.2506.14266</a>","ieee":"A. Ehrmann and C. P. Goodrich, “Controlling energy delivery with bistable nanostructures,” <i>arXiv</i>. .","mla":"Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery with Bistable Nanostructures.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2506.14266\">10.48550/arXiv.2506.14266</a>.","apa":"Ehrmann, A., &#38; Goodrich, C. P. (n.d.). Controlling energy delivery with bistable nanostructures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2506.14266\">https://doi.org/10.48550/arXiv.2506.14266</a>"},"type":"preprint","doi":"10.48550/arXiv.2506.14266","article_processing_charge":"No","title":"Controlling energy delivery with bistable nanostructures","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2506.14266"}],"date_created":"2026-09-09T13:16:54Z","_id":"22892","publication":"arXiv","project":[{"grant_number":"PAT 8537123","name":"Functional bio-inspired nanomachines from sticky colloids","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d"}],"day":"07","related_material":{"record":[{"relation":"dissertation_contains","id":"22873","status":"public"}]},"oa":1},{"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"degree_awarded":"PhD","supervisor":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"file":[{"date_updated":"2026-09-11T22:30:02Z","file_id":"21446","content_type":"application/pdf","file_name":"2026_Dunajova_Zuzana_Thesis_pdfA.pdf","embargo":"2026-09-11","relation":"main_file","date_created":"2026-03-12T20:38:52Z","access_level":"open_access","checksum":"47ce6a48a0c63f28eca6e64c9ffd2c84","file_size":14662770,"creator":"zdunajov"},{"creator":"zdunajov","file_size":32961408,"relation":"source_file","embargo_to":"open_access","access_level":"closed","checksum":"5dec5afdffd47c2b0b162d0fe1bed925","date_created":"2026-03-12T20:40:18Z","file_name":"Thesis-Dunajova_source_file.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-09-11T22:30:02Z","file_id":"21447"}],"acknowledgement":"Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360.","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-21423","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"date_published":"2026-03-11T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-076-3"]},"corr_author":"1","oa_version":"Published Version","year":"2026","has_accepted_license":"1","date_updated":"2026-09-11T22:30:04Z","publisher":"Institute of Science and Technology Austria","OA_place":"repository","author":[{"last_name":"Dunajova","full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"}],"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Geometry-driven self-organization of migrating cells and chiral filaments","related_material":{"record":[{"status":"public","id":"13314","relation":"part_of_dissertation"},{"relation":"research_data","status":"public","id":"13116"},{"relation":"research_data","id":"21439","status":"public"},{"relation":"part_of_dissertation","id":"21427","status":"public"}]},"day":"11","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments"}],"file_date_updated":"2026-09-11T22:30:02Z","date_created":"2026-03-11T08:30:49Z","_id":"21423","type":"dissertation","alternative_title":["ISTA Thesis"],"status":"public","citation":{"mla":"Dunajova, Zuzana. <i>Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21423\">10.15479/AT-ISTA-21423</a>.","ieee":"Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026.","apa":"Dunajova, Z. (2026). <i>Geometry-driven self-organization of migrating cells and chiral filaments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21423\">https://doi.org/10.15479/AT-ISTA-21423</a>","short":"Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026.","chicago":"Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21423\">https://doi.org/10.15479/AT-ISTA-21423</a>.","ista":"Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria.","ama":"Dunajova Z. Geometry-driven self-organization of migrating cells and chiral filaments. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21423\">10.15479/AT-ISTA-21423</a>"},"month":"03","article_processing_charge":"No","ddc":["539","570"],"page":"110","doi":"10.15479/AT-ISTA-21423"},{"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","title":"Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"project":[{"grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments"}],"day":"12","related_material":{"record":[{"status":"public","id":"13314","relation":"used_in_publication"},{"relation":"used_in_publication","id":"21427","status":"public"},{"relation":"used_in_publication","id":"21423","status":"public"}]},"oa":1,"file_date_updated":"2026-03-11T20:52:39Z","date_created":"2026-03-11T21:05:20Z","_id":"21439","type":"research_data","status":"public","OA_type":"free access","month":"03","citation":{"ama":"Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>","ista":"Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>.","short":"Z. Dunajova, (2026).","chicago":"Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">https://doi.org/10.15479/AT-ISTA-21439</a>.","apa":"Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">https://doi.org/10.15479/AT-ISTA-21439</a>","mla":"Dunajova, Zuzana. <i>Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>.","ieee":"Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization of migrating cells and chiral filaments.’” Institute of Science and Technology Austria, 2026."},"ddc":["570"],"article_processing_charge":"No","doi":"10.15479/AT-ISTA-21439","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"file":[{"file_id":"21440","date_updated":"2026-03-11T20:41:28Z","success":1,"content_type":"application/zip","file_name":"Supplementary_movies_Thesis_Dunajova.zip","access_level":"open_access","checksum":"47809a9a31b748b16e21e92d11ddc87f","date_created":"2026-03-11T20:41:28Z","relation":"main_file","file_size":154465214,"creator":"zdunajov"},{"content_type":"text/plain","success":1,"file_id":"21441","date_updated":"2026-03-11T20:52:39Z","access_level":"open_access","date_created":"2026-03-11T20:52:39Z","checksum":"a64a174bc6abf0a5e77631e4fd121f1f","relation":"main_file","file_name":"readme.txt","file_size":2289,"creator":"zdunajov"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-21439","date_published":"2026-03-12T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"abstract":[{"text":"These files contain supplementary movies accompanying the PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” by Zuzana Dunajova (2026). The videos provide additional visual material supporting the experiments and results described in the thesis.","lang":"eng"}],"corr_author":"1","oa_version":"Published Version","has_accepted_license":"1","contributor":[{"last_name":"Tasciyan","orcid":"0000-0003-1671-393X","first_name":"Saren","contributor_type":"researcher","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler"}],"date_updated":"2026-09-19T22:30:08Z","publisher":"Institute of Science and Technology Austria","year":"2026","OA_place":"repository","author":[{"first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova","full_name":"Dunajova, Zuzana"}]},{"oa_version":"Published Version","publication_identifier":{"eissn":["2835-8279"]},"PlanS_conform":"1","corr_author":"1","author":[{"orcid":"0000-0002-9645-6576","last_name":"Sorichetti","full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","first_name":"Valerio"},{"orcid":"0000-0002-5728-9189","full_name":"Robin, Paul","last_name":"Robin","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","first_name":"Paul"},{"last_name":"Palaia","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"first_name":"Alberto","full_name":"Hernandez-Armendariz, Alberto","last_name":"Hernandez-Armendariz"},{"first_name":"Sara","full_name":"Cuylen-Haering, Sara","last_name":"Cuylen-Haering"},{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"OA_place":"publisher","publication_status":"published","DOAJ_listed":"1","volume":3,"year":"2025","publisher":"American Physical Society","date_updated":"2026-02-17T11:16:26Z","has_accepted_license":"1","file":[{"creator":"dernst","file_size":3732843,"relation":"main_file","checksum":"1702b9bdbfd902a7c08aa4f1479b390d","access_level":"open_access","date_created":"2026-02-17T11:12:30Z","file_name":"2025_PRXLife_Sorichetti.pdf","content_type":"application/pdf","file_id":"21287","success":1,"date_updated":"2026-02-17T11:12:30Z"}],"tmp":{"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)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"The condensation of charged polymers is an important driver for the formation of biomolecular condensates. Recent experiments suggest that this mechanism also controls the clustering of eukaryotic chromosomes during the late stages of cell division. In this process, interchromosome attraction is driven by the condensation of cytoplasmic RNA and Ki-67, a charged intrinsically disordered protein that coats the chromosomes as a brush. Attraction between chromosomes has been shown to be specifically promoted by a localized charged patch on Ki-67, although the physical mechanism remains unclear. To elucidate this process, we combine coarse-grained simulations and analytical theory to study the RNA-mediated interaction between charged polymer brushes on the chromosome surfaces. We show that the charged patch on Ki-67 leads to interchromosome attraction via RNA bridging between the two brushes, whereby the RNA preferentially interacts with the charged patches, leading to stable, long-range forces. By contrast, if the brush is uniformly charged, bridging is basically absent due to complete adsorption of RNA onto the brush. Moreover, the RNA dynamics becomes caged in presence of the charged patch while remaining diffusive with uniform charge. Our work sheds light on the physical origin of chromosome clustering, while also suggesting a general mechanism for cells to tune work production by biomolecular condensates via different charge distributions."}],"department":[{"_id":"AnSa"},{"_id":"EdHa"}],"date_published":"2025-08-11T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation programme (A.Š. and V.S., ERC grant Agreement No. 802960 to A.Š., I.P. and P.R.,\r\nMarie Skłodowska-Curie Grant Agreement No. 101034413), the German Research Foundation (S.C-H. and A.H.-A., DFG Project No. 402723784 to S.C-H.), the Vallee Scholarship\r\n(A.Š. and V.S.), the EMBO Young Investigator Programme (A.Š.), and a Ph.D. fellowship from the Boehringer Ingelheim Fonds (A.H.-A.).","fulldoi":"https://doi.org/10.1103/41fd-r847","citation":{"chicago":"Sorichetti, Valerio, Paul Robin, Ivan Palaia, Alberto Hernandez-Armendariz, Sara Cuylen-Haering, and Anđela Šarić. “Charge Distribution of the Coating Brush Drives Interchromosome Attraction.” <i>PRX Life</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/41fd-r847\">https://doi.org/10.1103/41fd-r847</a>.","short":"V. Sorichetti, P. Robin, I. Palaia, A. Hernandez-Armendariz, S. Cuylen-Haering, A. Šarić, PRX Life 3 (2025).","ama":"Sorichetti V, Robin P, Palaia I, Hernandez-Armendariz A, Cuylen-Haering S, Šarić A. Charge distribution of the coating brush drives interchromosome attraction. <i>PRX Life</i>. 2025;3(3). doi:<a href=\"https://doi.org/10.1103/41fd-r847\">10.1103/41fd-r847</a>","ista":"Sorichetti V, Robin P, Palaia I, Hernandez-Armendariz A, Cuylen-Haering S, Šarić A. 2025. Charge distribution of the coating brush drives interchromosome attraction. PRX Life. 3(3), 033010.","ieee":"V. Sorichetti, P. Robin, I. Palaia, A. Hernandez-Armendariz, S. Cuylen-Haering, and A. Šarić, “Charge distribution of the coating brush drives interchromosome attraction,” <i>PRX Life</i>, vol. 3, no. 3. American Physical Society, 2025.","mla":"Sorichetti, Valerio, et al. “Charge Distribution of the Coating Brush Drives Interchromosome Attraction.” <i>PRX Life</i>, vol. 3, no. 3, 033010, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/41fd-r847\">10.1103/41fd-r847</a>.","apa":"Sorichetti, V., Robin, P., Palaia, I., Hernandez-Armendariz, A., Cuylen-Haering, S., &#38; Šarić, A. (2025). Charge distribution of the coating brush drives interchromosome attraction. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/41fd-r847\">https://doi.org/10.1103/41fd-r847</a>"},"OA_type":"gold","month":"08","status":"public","type":"journal_article","issue":"3","doi":"10.1103/41fd-r847","intvolume":"         3","ec_funded":1,"article_number":"033010","article_processing_charge":"Yes","ddc":["570"],"title":"Charge distribution of the coating brush drives interchromosome attraction","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"PRX Life","_id":"21235","date_created":"2026-02-16T14:50:32Z","file_date_updated":"2026-02-17T11:12:30Z","oa":1,"day":"11","article_type":"original","quality_controlled":"1","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020"},{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"name":"EMBO Young Investigator Program - Andela Saric","_id":"349b6ff1-11ca-11ed-8bc3-f006047c2eeb"}]},{"DOAJ_listed":"1","publication_status":"published","OA_place":"publisher","author":[{"first_name":"Tom","full_name":"Brandstätter, Tom","last_name":"Brandstätter"},{"first_name":"Emily","full_name":"Brieger, Emily","last_name":"Brieger"},{"last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"first_name":"Georg","last_name":"Ladurner","full_name":"Ladurner, Georg"},{"full_name":"Rädler, Joachim O.","last_name":"Rädler","first_name":"Joachim O."},{"last_name":"Broedersz","full_name":"Broedersz, Chase P.","first_name":"Chase P."}],"date_updated":"2026-02-17T11:20:20Z","has_accepted_license":"1","publisher":"American Physical Society","year":"2025","volume":3,"oa_version":"Published Version","PlanS_conform":"1","publication_identifier":{"eissn":["2835-8279"]},"date_published":"2025-08-26T00:00:00Z","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"The migration behavior of colliding cells is critically determined by transient contact interactions. During these interactions, the motility machinery, including the front-rear polarization of the cell, dynamically responds to surface protein-mediated transmission of forces and biochemical signals between cells. While biomolecular details of such contact interactions are increasingly well understood, it remains unclear what biophysical interaction mechanisms govern the cell-level dynamics of colliding cells and how these mechanisms vary across cell types. Here we develop a phenomenological theory based on 14 candidate contact-interaction mechanisms coupling cell position, protrusion, and polarity. Using high-throughput micropattern experiments, we detect which of these phenomenological contact interactions captures the interaction behaviors of cells. We find that various cell types—ranging from mesenchymal to epithelial cells—are accurately captured by a single model with only two interaction mechanisms: polarity-protrusion coupling and polarity-polarity coupling. Remarkably, the qualitatively different interaction behaviors of distinct cells, as well as cells subject to molecular perturbations of surface protein-mediated signaling, can all be quantitatively captured by varying the strength and sign of the polarity-polarity coupling mechanism. Altogether, our data-driven phenomenological theory of cell-cell interactions reveals polarity-polarity coupling as a versatile and general contact-interaction mechanism, which may underlie diverse collective migration behaviors of motile cells."}],"fulldoi":"https://doi.org/10.1103/3hhj-rt1n","acknowledgement":"We thank Johannes Flommersfeld, Bram Hoogland, and Ricard Alert for helpful discussions. We thank Gerlinde Schwake for producing the E-cadherin mRNA. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Project-ID 201269156 - SFB 1032 (Project B01 and B12).","arxiv":1,"language":[{"iso":"eng"}],"file":[{"file_size":9366716,"creator":"dernst","file_id":"21288","success":1,"date_updated":"2026-02-17T11:18:18Z","content_type":"application/pdf","file_name":"2025_PRXLife_Brandstaetter.pdf","relation":"main_file","date_created":"2026-02-17T11:18:18Z","access_level":"open_access","checksum":"70c067ceef3a8262d9c430e85e3ba9ec"}],"external_id":{"arxiv":["2407.17268"]},"tmp":{"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)","image":"/images/cc_by.png"},"doi":"10.1103/3hhj-rt1n","article_number":"033015","intvolume":"         3","ddc":["570"],"article_processing_charge":"Yes","month":"08","citation":{"chicago":"Brandstätter, Tom, Emily Brieger, David Brückner, Georg Ladurner, Joachim O. Rädler, and Chase P. Broedersz. “Data-Driven Theory Reveals Protrusion and Polarity Interactions Governing Collision Behavior of Distinct Motile Cells.” <i>PRX Life</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/3hhj-rt1n\">https://doi.org/10.1103/3hhj-rt1n</a>.","short":"T. Brandstätter, E. Brieger, D. Brückner, G. Ladurner, J.O. Rädler, C.P. Broedersz, PRX Life 3 (2025).","ista":"Brandstätter T, Brieger E, Brückner D, Ladurner G, Rädler JO, Broedersz CP. 2025. Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. PRX Life. 3(3), 033015.","ama":"Brandstätter T, Brieger E, Brückner D, Ladurner G, Rädler JO, Broedersz CP. Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. <i>PRX Life</i>. 2025;3(3). doi:<a href=\"https://doi.org/10.1103/3hhj-rt1n\">10.1103/3hhj-rt1n</a>","ieee":"T. Brandstätter, E. Brieger, D. Brückner, G. Ladurner, J. O. Rädler, and C. P. Broedersz, “Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells,” <i>PRX Life</i>, vol. 3, no. 3. American Physical Society, 2025.","mla":"Brandstätter, Tom, et al. “Data-Driven Theory Reveals Protrusion and Polarity Interactions Governing Collision Behavior of Distinct Motile Cells.” <i>PRX Life</i>, vol. 3, no. 3, 033015, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/3hhj-rt1n\">10.1103/3hhj-rt1n</a>.","apa":"Brandstätter, T., Brieger, E., Brückner, D., Ladurner, G., Rädler, J. O., &#38; Broedersz, C. P. (2025). Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/3hhj-rt1n\">https://doi.org/10.1103/3hhj-rt1n</a>"},"OA_type":"gold","status":"public","issue":"3","type":"journal_article","file_date_updated":"2026-02-17T11:18:18Z","date_created":"2026-02-16T14:52:02Z","_id":"21236","publication":"PRX Life","day":"26","article_type":"original","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells"},{"isi":1,"article_processing_charge":"No","doi":"10.1101/cshperspect.a041653","ec_funded":1,"article_number":"a041653","intvolume":"        17","type":"journal_article","issue":"4","citation":{"short":"D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17 (2025).","chicago":"Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2025. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>.","ista":"Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 17(4), a041653.","ama":"Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. 2025;17(4). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>","ieee":"D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics and signaling into dynamical models,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.","mla":"Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press, 2025, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>.","apa":"Brückner, D., &#38; Hannezo, E. B. (2025). Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>"},"status":"public","OA_type":"closed access","month":"04","quality_controlled":"1","article_type":"original","day":"01","project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"}],"date_created":"2025-01-29T13:33:47Z","publication":"Cold Spring Harbor Perspectives in Biology","_id":"18960","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tissue active matter: Integrating mechanics and signaling into dynamical models","year":"2025","volume":17,"date_updated":"2025-12-30T07:08:34Z","publisher":"Cold Spring Harbor Laboratory Press","scopus_import":"1","author":[{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","last_name":"Brückner"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"publication_status":"published","publication_identifier":{"issn":["1943-0264"]},"corr_author":"1","oa_version":"None","acknowledgement":"We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg for a critical reading of the manuscript and Claudia Flandoli for the artwork in the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from the European Research Council (ERC) under the European Union\\u2019s Horizon 2020 Research and Innovation Programme Grant Agreement no. 851288.","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1101/cshperspect.a041653","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter."}],"date_published":"2025-04-01T00:00:00Z","external_id":{"isi":["001456660400001"],"pmid":["38951023"]}},{"citation":{"apa":"Toquer, D., Bocquet, L., &#38; Robin, P. (2025). Ionic association and Wien effect in 2D confined electrolytes. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0241949\">https://doi.org/10.1063/5.0241949</a>","mla":"Toquer, Damien, et al. “Ionic Association and Wien Effect in 2D Confined Electrolytes.” <i>Journal of Chemical Physics</i>, vol. 162, no. 6, 064703, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0241949\">10.1063/5.0241949</a>.","ieee":"D. Toquer, L. Bocquet, and P. Robin, “Ionic association and Wien effect in 2D confined electrolytes,” <i>Journal of Chemical Physics</i>, vol. 162, no. 6. AIP Publishing, 2025.","ama":"Toquer D, Bocquet L, Robin P. Ionic association and Wien effect in 2D confined electrolytes. <i>Journal of Chemical Physics</i>. 2025;162(6). doi:<a href=\"https://doi.org/10.1063/5.0241949\">10.1063/5.0241949</a>","ista":"Toquer D, Bocquet L, Robin P. 2025. Ionic association and Wien effect in 2D confined electrolytes. Journal of Chemical Physics. 162(6), 064703.","chicago":"Toquer, Damien, Lydéric Bocquet, and Paul Robin. “Ionic Association and Wien Effect in 2D Confined Electrolytes.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0241949\">https://doi.org/10.1063/5.0241949</a>.","short":"D. Toquer, L. Bocquet, P. Robin, Journal of Chemical Physics 162 (2025)."},"status":"public","month":"02","OA_type":"hybrid","type":"journal_article","issue":"6","doi":"10.1063/5.0241949","article_number":"064703","ec_funded":1,"intvolume":"       162","ddc":["540"],"article_processing_charge":"Yes (in subscription journal)","isi":1,"title":"Ionic association and Wien effect in 2D confined electrolytes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"19279","publication":"Journal of Chemical Physics","date_created":"2025-03-02T23:01:52Z","file_date_updated":"2025-03-04T10:29:36Z","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"oa":1,"article_type":"original","quality_controlled":"1","day":"14","oa_version":"Published Version","corr_author":"1","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"publication_status":"published","author":[{"full_name":"Toquer, Damien","last_name":"Toquer","first_name":"Damien"},{"full_name":"Bocquet, Lydéric","last_name":"Bocquet","first_name":"Lydéric"},{"id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","first_name":"Paul","orcid":"0000-0002-5728-9189","last_name":"Robin","full_name":"Robin, Paul"}],"scopus_import":"1","OA_place":"publisher","publisher":"AIP Publishing","date_updated":"2025-09-30T10:44:48Z","has_accepted_license":"1","volume":162,"year":"2025","file":[{"file_name":"2025_JourChemicalPhysics_Toquer.pdf","relation":"main_file","access_level":"open_access","checksum":"c9008c2c50c917673aa588f75acbcb40","date_created":"2025-03-04T10:29:36Z","date_updated":"2025-03-04T10:29:36Z","file_id":"19290","success":1,"content_type":"application/pdf","creator":"dernst","file_size":5807062}],"external_id":{"pmid":["39932241"],"isi":["001421300300001"],"arxiv":["2410.03316"]},"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2025-02-14T00:00:00Z","abstract":[{"lang":"eng","text":"Recent experimental advances in nanofluidics have allowed to explore ion transport across molecular-scale pores, in particular, for iontronic applications. Two-dimensional nanochannels—in which a single molecular layer of electrolyte is confined between solid walls—constitute a unique platform to investigate fluid and ion transport in extreme confinement, highlighting unconventional transport properties. In this work, we study ionic association in 2D nanochannels, and its consequences on non-linear ionic transport, using both molecular dynamics simulations and analytical theory. We show that under sufficient confinement, ions assemble into pairs or larger clusters in a process analogous to a Kosterlitz–Thouless transition, here modified by the dielectric confinement. We further show that the breaking of pairs results in an electric-field dependent conduction, a mechanism usually known as the second Wien effect. However the 2D nature of the system results in non-universal, temperature-dependent, scaling of the conductivity with electric field, leading to ionic coulomb blockade in some regimes. A 2D generalization of the Onsager theory fully accounts for the non-linear transport. These results suggest ways to exploit electrostatic interactions between ions to build new nanofluidic devices."}],"department":[{"_id":"EdHa"}],"fulldoi":"https://doi.org/10.1063/5.0241949","pmid":1,"language":[{"iso":"eng"}],"arxiv":1,"acknowledgement":"The authors thank B. Coquinot and G. Monet for fruitful discussions. L.B. acknowledges support from ERC-Synergy Grant Agreement No. 101071937, n-AQUA. P.R. acknowledges support from the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska-Curie Grant Agreement No. 101034413."}]