[{"OA_place":"publisher","fulldoi":"https://doi.org/10.1038/s41567-025-03122-1","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"OA_type":"hybrid","has_accepted_license":"1","date_published":"2026-01-05T00:00:00Z","PlanS_conform":"1","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"}],"file_date_updated":"2026-01-21T08:21:11Z","ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-28T12:55:30Z","file":[{"date_created":"2026-01-21T08:21:11Z","file_size":7335694,"file_name":"2026_NaturePhysics_Mishra.pdf","file_id":"21026","success":1,"creator":"dernst","content_type":"application/pdf","date_updated":"2026-01-21T08:21:11Z","relation":"main_file","access_level":"open_access","checksum":"0ab7ac2fbcb61a364dba57152db64ed7"}],"intvolume":"        22","external_id":{"oaworkid":["W7118187193"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"citation":{"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.","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>","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.","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>.","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>."},"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).","year":"2026","publisher":"Springer Nature","day":"05","oa_version":"Published Version","_id":"21015","status":"public","doi":"10.1038/s41567-025-03122-1","type":"journal_article","publication_identifier":{"eissn":["1745-2481"],"issnl":[" 1745-2473"],"issn":["1745-2473"]},"oa":1,"title":"Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo","author":[{"first_name":"Nikhil","orcid":"0000-0002-6425-5788","full_name":"Mishra, Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","last_name":"Mishra"},{"last_name":"Li","id":"ee7a5ca8-8b71-11ed-b662-b3341c05b7eb","full_name":"Li, Yuting I","first_name":"Yuting I"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"publication":"Nature Physics","scopus_import":"1","corr_author":"1","quality_controlled":"1","related_material":{"link":[{"url":"https://ista.ac.at/en/news/geometry-shapes-life/","description":"News on ISTA website","relation":"research_data"}]},"oaworkid":1,"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"},{"_id":"917c023a-16d5-11f0-9cad-eb5cafc52090","name":"Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development"}],"date_created":"2026-01-20T10:12:19Z","article_processing_charge":"Yes (via OA deal)","month":"01","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"language":[{"iso":"eng"}],"volume":22,"publication_status":"published","page":"139-150"},{"department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"month":"3","date_created":"2026-02-04T16:38:02Z","article_processing_charge":"No","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"PAT 5044023","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading"},{"grant_number":"W1250-B20","_id":"252C3B08-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"}],"corr_author":"1","author":[{"full_name":"Naik, Suyash","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","first_name":"Suyash"}],"doi":"10.15479/AT-ISTA-21137","type":"research_data","title":"Data associated with Keratins coordinate tissue spreading ","oa":1,"contributor":[{"last_name":"Keta","contributor_type":"researcher","first_name":"Yann-Edwin"},{"contributor_type":"supervisor","first_name":"Silke ","last_name":"Henkes"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","contributor_type":"supervisor","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"supervisor","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","_id":"21137","status":"public","year":"2026","citation":{"short":"S. Naik, (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>.","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>.","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>","ieee":"S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026.","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>","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>."},"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.","publisher":"Institute of Science and Technology Austria","day":"24","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"file":[{"relation":"main_file","checksum":"5d1fda7e410f24c311fcf6bcf725698f","access_level":"open_access","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. ","content_type":"application/zip","date_updated":"2026-03-16T11:51:10Z","creator":"snaik","file_id":"21461","file_name":"cells-main.zip","title":"Cell git repository","file_size":725916,"date_created":"2026-03-16T11:51:10Z"},{"relation":"main_file","checksum":"ee350c8eaed99f3ca348c47c8b190d3c","access_level":"open_access","creator":"snaik","content_type":"application/x-zip-compressed","date_updated":"2026-03-18T14:52:02Z","file_id":"21464","success":1,"date_created":"2026-03-18T14:52:02Z","file_size":282168895,"file_name":"DevBranchDataRepo.zip"},{"creator":"snaik","content_type":"text/markdown","date_updated":"2026-03-18T15:01:32Z","access_level":"open_access","checksum":"1ecaf2c1a2ce8ff9c75a128cc02d0b8f","relation":"main_file","file_size":2231,"date_created":"2026-03-18T15:01:32Z","file_name":"ReadMe.md","success":1,"file_id":"21466"},{"file_size":1951210,"date_created":"2026-03-18T15:12:57Z","file_name":"PaperSchematics.svg","success":1,"file_id":"21467","creator":"snaik","date_updated":"2026-03-18T15:12:57Z","content_type":"image/svg+xml","access_level":"open_access","checksum":"da9a4687e5144b61a64ca341f922046a","relation":"main_file"},{"file_size":1897,"date_created":"2026-03-21T03:37:43Z","file_name":"maxwell_sketch.tex","file_id":"21468","success":1,"creator":"snaik","date_updated":"2026-03-21T03:37:43Z","content_type":"application/octet-stream","relation":"main_file","checksum":"9ac1054b16c212c6f34d402dce2c80e0","access_level":"open_access"},{"file_size":749368723,"date_created":"2026-03-24T07:21:43Z","file_name":"DataRepo.zip","success":1,"file_id":"21495","creator":"snaik","content_type":"application/x-zip-compressed","date_updated":"2026-03-24T07:21:43Z","access_level":"open_access","checksum":"7c9ecf78e2593b3830d96fa94baa08df","relation":"main_file"}],"date_updated":"2026-06-10T09:44:10Z","file_date_updated":"2026-03-24T07:21:43Z","ec_funded":1,"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","fulldoi":"https://doi.org/10.15479/AT-ISTA-21137","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"date_published":"2026-03-24T00:00:00Z","has_accepted_license":"1","OA_place":"repository"},{"article_type":"original","fulldoi":"https://doi.org/10.1103/89bj-79g5","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"PlanS_conform":"1","date_published":"2026-02-09T00:00:00Z","has_accepted_license":"1","OA_type":"gold","OA_place":"publisher","DOAJ_listed":"1","date_updated":"2026-02-24T06:54:32Z","file_date_updated":"2026-02-24T06:53:05Z","ec_funded":1,"abstract":[{"text":"DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. 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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"21351","success":1,"date_created":"2026-02-24T06:53:05Z","file_size":5857833,"file_name":"2026_PRXLife_Olmeda.pdf","relation":"main_file","checksum":"df9776422862d1d02c66d98e2d620849","access_level":"open_access","creator":"dernst","date_updated":"2026-02-24T06:53:05Z","content_type":"application/pdf"}],"intvolume":"         4","oa_version":"Published Version","_id":"21275","status":"public","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.","year":"2026","citation":{"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>.","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>.","short":"F. Olmeda, M. Gupta, O. Bektas, S. Rulands, PRX Life 4 (2026).","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>","ista":"Olmeda F, Gupta M, Bektas O, Rulands S. 2026. Spatiotemporal patterns of active epigenetic turnover. PRX Life. 4, 013018.","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."},"publisher":"American Physical Society","day":"09","doi":"10.1103/89bj-79g5","type":"journal_article","publication_identifier":{"eissn":["2835-8279"]},"title":"Spatiotemporal patterns of active epigenetic turnover","oa":1,"article_number":"013018","corr_author":"1","author":[{"first_name":"Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","last_name":"Olmeda","full_name":"Olmeda, Fabrizio"},{"first_name":"Misha","last_name":"Gupta","full_name":"Gupta, Misha"},{"first_name":"Onurcan","full_name":"Bektas, Onurcan","last_name":"Bektas"},{"first_name":"Steffen","full_name":"Rulands, Steffen","last_name":"Rulands"}],"publication":"PRX Life","date_created":"2026-02-17T08:17:53Z","article_processing_charge":"Yes","quality_controlled":"1","project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"volume":4,"department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"02"},{"publication":"Physical Review Research","author":[{"first_name":"Frederik Skovbo","last_name":"Moller","id":"43cbcc83-0564-11f0-a935-e37325525859","full_name":"Moller, Frederik Skovbo"},{"first_name":"Gabriel","full_name":"Fernández-Fernández, Gabriel","last_name":"Fernández-Fernández"},{"first_name":"Thomas","full_name":"Schweigler, Thomas","last_name":"Schweigler"},{"first_name":"Paulin","last_name":"De Schoulepnikoff","full_name":"De Schoulepnikoff, Paulin"},{"full_name":"Schmiedmayer, Jörg","last_name":"Schmiedmayer","first_name":"Jörg"},{"last_name":"Muñoz-Gil","full_name":"Muñoz-Gil, Gorka","first_name":"Gorka"}],"scopus_import":"1","article_number":"023094","publication_identifier":{"eissn":["2643-1564"]},"title":"Learning minimal representations of many-body physics from snapshots of a quantum simulator","oa":1,"doi":"10.1103/r7pj-gl7r","type":"journal_article","month":"04","department":[{"_id":"EdHa"}],"volume":8,"language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","date_created":"2026-05-10T22:02:15Z","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-05-11T06:56:58Z","abstract":[{"lang":"eng","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."}],"date_updated":"2026-05-11T06:58:56Z","OA_place":"publisher","DOAJ_listed":"1","ddc":["530"],"date_published":"2026-04-29T00:00:00Z","OA_type":"gold","PlanS_conform":"1","has_accepted_license":"1","article_type":"original","fulldoi":"https://doi.org/10.1103/r7pj-gl7r","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"arxiv":1,"day":"29","year":"2026","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.","citation":{"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.","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>","short":"F.S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff, J. Schmiedmayer, G. Muñoz-Gil, Physical Review Research 8 (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>.","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>."},"publisher":"American Physical Society","_id":"21847","status":"public","oa_version":"Published Version","external_id":{"arxiv":["2509.13821"]},"issue":"2","file":[{"success":1,"file_id":"21852","file_name":"2026_PhysicalReviewResearch_Moller.pdf","file_size":1829628,"date_created":"2026-05-11T06:56:58Z","checksum":"dbfc58e1e176f7b63e0d274eb0d1bffa","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2026-05-11T06:56:58Z","creator":"dernst"}],"intvolume":"         8"},{"type":"journal_article","doi":"10.1103/x82g-cq7n","oa":1,"title":"Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets","publication_identifier":{"issn":["2160-3308"]},"article_number":"021023","scopus_import":"1","author":[{"last_name":"Drozdowski","id":"cd4ed792-b872-11ef-bb90-b7b3a3f62f75","full_name":"Drozdowski, Oliver M","first_name":"Oliver M"},{"first_name":"Büşra","full_name":"Kocameşe-Tamgac𝚤, Büşra","last_name":"Kocameşe-Tamgac𝚤"},{"first_name":"Kim E.","full_name":"Boonekamp, Kim E.","last_name":"Boonekamp"},{"first_name":"Michael","last_name":"Boutros","full_name":"Boutros, Michael"},{"last_name":"Schwarz","full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S."}],"publication":"Physical Review X","article_processing_charge":"Yes","date_created":"2026-05-20T14:35:57Z","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"volume":16,"department":[{"_id":"EdHa"}],"month":"04","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1103/x82g-cq7n","article_type":"original","date_published":"2026-04-30T00:00:00Z","has_accepted_license":"1","OA_type":"gold","ddc":["530"],"DOAJ_listed":"1","OA_place":"publisher","date_updated":"2026-05-21T06:08:11Z","file_date_updated":"2026-05-21T06:05:49Z","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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        16","file":[{"content_type":"application/pdf","date_updated":"2026-05-21T06:05:49Z","creator":"dernst","relation":"main_file","checksum":"a90e905968648ac4425c256de901e9c3","access_level":"open_access","file_name":"2026_PhysicalReviewX_Drozdowski.pdf","file_size":5603164,"date_created":"2026-05-21T06:05:49Z","file_id":"21901","success":1}],"issue":"2","oa_version":"Published Version","status":"public","_id":"21899","publisher":"American Physical Society","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.","citation":{"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>.","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.","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.","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>"},"year":"2026","day":"30"},{"file":[{"creator":"nhino","content_type":"application/pdf","date_updated":"2026-07-13T09:16:20Z","relation":"main_file","access_level":"open_access","checksum":"66444afd243dce7d383d52d44e8d34a4","date_created":"2026-07-13T09:16:20Z","file_size":12477675,"file_name":"Main_text_and_figures.pdf","file_id":"22283","success":1},{"success":1,"file_id":"22284","file_name":"Supplementary_figures.pdf","file_size":4545901,"date_created":"2026-07-13T09:16:25Z","checksum":"90bceb34de64ec792c5de117f0890d05","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2026-07-13T09:16:25Z","creator":"nhino"},{"relation":"main_file","access_level":"open_access","checksum":"9d9ab89c372142f2ffb6c8c625334d7f","date_updated":"2026-07-13T09:16:28Z","content_type":"video/mp4","creator":"nhino","file_id":"22285","success":1,"file_name":"Supplementary_Video1.mp4","date_created":"2026-07-13T09:16:28Z","file_size":10349451}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"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.","day":"14","das_tickbox":"1","citation":{"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.","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.","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.","mla":"Hino, Naoya, et al. <i>Apical Domain Mechanosensation Regulates Tissue Tension Homeostasis</i>. Institute of Science and Technology Austria.","short":"N. Hino, T. Kapoor, U.R. Gubbala, E.B. Hannezo, C.-P.J. Heisenberg, (n.d.).","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."},"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.","year":"2026","publisher":"Institute of Science and Technology Austria","researchdata_availability":"yes","_id":"22276","status":"public","oa_version":"Preprint","OA_place":"publisher","ddc":["570"],"has_accepted_license":"1","date_published":"2026-07-14T00:00:00Z","OA_type":"green","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Epithelial spreading","tissue tension","mechanosensation","aPKC","Kibra","zebrafish"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"file_date_updated":"2026-07-13T09:16:28Z","date_updated":"2026-07-14T07:07:41Z","project":[{"grant_number":"PAT 5044023","name":"Keratins in epithelial tissue spreading","_id":"8f060199-16d5-11f0-9cad-f3253b266c46"},{"_id":"34dd7f3b-11ca-11ed-8bc3-856f2c87f5da","name":"Mechanosensitive signaling activation in the crosstalk between mechanical force and tissuefluidity","grant_number":"LTF 16-2022"}],"related_material":{"record":[{"id":"21864","relation":"earlier_version","status":"public"}]},"date_created":"2026-07-13T09:03:26Z","supplementarymaterial":"yes","article_processing_charge":"No","month":"07","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"GradSch"}],"publication_status":"draft","oa":1,"title":"Apical domain mechanosensation regulates tissue tension homeostasis","type":"preprint","author":[{"first_name":"Naoya","full_name":"Hino, Naoya","last_name":"Hino","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"first_name":"Tushna","id":"e3b3eda7-fd4d-11eb-8fd8-c40af7a478b1","last_name":"Kapoor","full_name":"Kapoor, Tushna"},{"first_name":"Uday R","id":"bb4a0dc4-32c9-11ee-b5ce-a97ceedd5924","last_name":"Gubbala","full_name":"Gubbala, Uday R"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"corr_author":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-07-16T09:54:55Z","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"}],"date_updated":"2026-07-16T09:58:04Z","OA_place":"publisher","ddc":["530"],"OA_type":"hybrid","PlanS_conform":"1","has_accepted_license":"1","date_published":"2026-07-15T00:00:00Z","fulldoi":"https://doi.org/10.1103/mbjk-v4ym","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"das_tickbox":"1","day":"15","citation":{"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.","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>","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.","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>","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).","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>."},"year":"2026","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.","publisher":"American Physical Society","researchdata_availability":"no","_id":"22326","status":"public","oa_version":"Published Version","file":[{"success":1,"file_id":"22352","file_size":2550345,"date_created":"2026-07-16T09:54:55Z","file_name":"2026_PhysicalReviewLetters_Zhang.pdf","checksum":"28861d31d0f6cf541aaca04faaed1767","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2026-07-16T09:54:55Z"}],"intvolume":"       137","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.","publication":"Physical Review Letters","author":[{"first_name":"Chen Y","id":"81b43fb8-c9d5-11ef-bf68-ade532a1f204","last_name":"Zhang","full_name":"Zhang, Chen Y"},{"first_name":"Pablo","last_name":"Mateu Hoyos","id":"50b236c7-50c1-11ef-bb9a-a2375694f8b5","full_name":"Mateu Hoyos, Pablo"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","full_name":"Brückner, David","first_name":"David","orcid":"0000-0001-7205-2975"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"corr_author":"1","scopus_import":"1","article_number":"038401","publication_identifier":{"eissn":[" 1079-7114"],"issn":["0031-9007"]},"oa":1,"title":"Nonlocal decoding of positional and correlational information during development","doi":"10.1103/mbjk-v4ym","type":"journal_article","month":"07","department":[{"_id":"GaTk"},{"_id":"EdHa"},{"_id":"GradSch"}],"volume":137,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866"}],"quality_controlled":"1","date_created":"2026-07-14T05:38:28Z","supplementarymaterial":"no","article_processing_charge":"Yes (via OA deal)"},{"ddc":["570"],"date_published":"2026-01-01T00:00:00Z","OA_type":"hybrid","has_accepted_license":"1","PlanS_conform":"1","article_type":"original","fulldoi":"https://doi.org/10.1038/s41565-025-02052-6","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_place":"publisher","date_updated":"2026-07-27T08:24:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-07-27T08:22:57Z","abstract":[{"lang":"eng","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."}],"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.","external_id":{"isi":["001611698900001"],"pmid":["41219410"]},"file":[{"success":1,"file_id":"22412","file_size":10091503,"date_created":"2026-07-27T08:22:57Z","file_name":"2026_NatureNanotech_Mayer.pdf","access_level":"open_access","checksum":"ff9a5eafe60af1d97da545453bd53eca","relation":"main_file","creator":"dernst","date_updated":"2026-07-27T08:22:57Z","content_type":"application/pdf"}],"intvolume":"        21","_id":"20670","status":"public","researchdata_availability":"yes","oa_version":"Published Version","das_tickbox":"1","day":"01","isi":1,"year":"2026","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.","citation":{"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>","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>","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.","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.","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>."},"publisher":"Springer Nature","pmid":1,"publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"oa":1,"title":"Lumen charge governs gated ion transport in β-barrel nanopores","doi":"10.1038/s41565-025-02052-6","type":"journal_article","scopus_import":"1","publication":"Nature Nanotechnology","author":[{"first_name":"Simon","last_name":"Mayer","full_name":"Mayer, Simon"},{"full_name":"Mitsioni, Marianna Fanouria","last_name":"Mitsioni","first_name":"Marianna Fanouria"},{"full_name":"Robin, Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","last_name":"Robin","orcid":"0000-0002-5728-9189","first_name":"Paul"},{"first_name":"Lukas","full_name":"Van Den Heuvel, Lukas","last_name":"Van Den Heuvel"},{"first_name":"Nathan","full_name":"Ronceray, Nathan","last_name":"Ronceray"},{"first_name":"Maria Jose","full_name":"Marcaida, Maria Jose","last_name":"Marcaida"},{"last_name":"Abriata","full_name":"Abriata, Luciano A.","first_name":"Luciano A."},{"first_name":"Lucien F.","full_name":"Krapp, Lucien F.","last_name":"Krapp"},{"first_name":"Jana S.","last_name":"Anton","full_name":"Anton, Jana S."},{"first_name":"Sarah","full_name":"Soussou, Sarah","last_name":"Soussou"},{"last_name":"Jeanneret-Grosjean","full_name":"Jeanneret-Grosjean, Justin","first_name":"Justin"},{"full_name":"Fulciniti, Alessandro","last_name":"Fulciniti","first_name":"Alessandro"},{"last_name":"Möller","full_name":"Möller, Alexia","first_name":"Alexia"},{"first_name":"Sarah","full_name":"Vacle, Sarah","last_name":"Vacle"},{"last_name":"Feletti","full_name":"Feletti, Lely","first_name":"Lely"},{"first_name":"Henry","full_name":"Brinkerhoff, Henry","last_name":"Brinkerhoff"},{"first_name":"Andrew H.","full_name":"Laszlo, Andrew H.","last_name":"Laszlo"},{"first_name":"Jens H.","last_name":"Gundlach","full_name":"Gundlach, Jens H."},{"full_name":"Emmerich, Theo","last_name":"Emmerich","first_name":"Theo"},{"first_name":"Matteo","last_name":"Dal Peraro","full_name":"Dal Peraro, Matteo"},{"full_name":"Radenovic, Aleksandra","last_name":"Radenovic","first_name":"Aleksandra"}],"supplementarymaterial":"yes","date_created":"2025-11-23T23:01:40Z","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/lukasvandenheuvel/Biomemristors"}]},"page":"116-124","department":[{"_id":"EdHa"}],"volume":21,"language":[{"iso":"eng"}],"publication_status":"published","month":"01"},{"page":"931-940","volume":22,"department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","supplementarymaterial":"yes","date_created":"2026-05-10T22:02:16Z","article_processing_charge":"Yes (via OA deal)","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"quality_controlled":"1","scopus_import":"1","publication":"Nature Physics","author":[{"last_name":"Olmeda","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","full_name":"Olmeda, Fabrizio","first_name":"Fabrizio"},{"first_name":"Tim","full_name":"Lohoff, Tim","last_name":"Lohoff"},{"first_name":"Ioannis","full_name":"Kafetzopoulos, Ioannis","last_name":"Kafetzopoulos"},{"last_name":"Clark","full_name":"Clark, Stephen J.","first_name":"Stephen J."},{"first_name":"Laura","last_name":"Benson","full_name":"Benson, Laura"},{"full_name":"Santos, Fatima","last_name":"Santos","first_name":"Fatima"},{"first_name":"Felix","full_name":"Krueger, Felix","last_name":"Krueger"},{"first_name":"Simon","full_name":"Walker, Simon","last_name":"Walker"},{"full_name":"Reik, Wolf","last_name":"Reik","first_name":"Wolf"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"}],"pmid":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"title":"Scaling and self-similarity in the formation of the embryonic epigenome","oa":1,"doi":"10.1038/s41567-026-03263-x","type":"journal_article","status":"public","_id":"21849","researchdata_availability":"yes","oa_version":"Published Version","day":"01","das_tickbox":"1","citation":{"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>","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>","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.","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>.","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>."},"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.","year":"2026","publisher":"Springer Nature","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.","external_id":{"pmid":["42318073"]},"file":[{"relation":"main_file","access_level":"open_access","checksum":"58e7734f1ebaf6def642140cb489f08f","creator":"dernst","content_type":"application/pdf","date_updated":"2026-07-27T13:54:58Z","file_id":"22591","success":1,"date_created":"2026-07-27T13:54:58Z","file_size":7932222,"file_name":"2026_NaturePhysics_Olmeda.pdf"}],"intvolume":"        22","date_updated":"2026-07-27T13:56:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-07-27T13:54:58Z","ec_funded":1,"abstract":[{"lang":"eng","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."}],"ddc":["570"],"OA_type":"hybrid","PlanS_conform":"1","date_published":"2026-06-01T00:00:00Z","has_accepted_license":"1","article_type":"original","fulldoi":"https://doi.org/10.1038/s41567-026-03263-x","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_place":"publisher"},{"external_id":{"pmid":["42143048"]},"file":[{"checksum":"f26d96e180c1d034d9c9c8f57c3c258b","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2026-07-29T10:27:25Z","content_type":"application/pdf","success":1,"file_id":"22609","date_created":"2026-07-29T10:27:25Z","file_size":15363936,"file_name":"2026_NatureComm_Naik.pdf"}],"intvolume":"        17","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"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.","day":"17","das_tickbox":"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.","citation":{"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>.","short":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, Nature Communications 17 (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>.","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>","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.","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."},"year":"2026","publisher":"Springer Nature","_id":"22608","researchdata_availability":"yes","status":"public","oa_version":"Published Version","OA_place":"publisher","ddc":["570"],"OA_type":"gold","date_published":"2026-07-17T00:00:00Z","PlanS_conform":"1","has_accepted_license":"1","article_type":"original","fulldoi":"https://doi.org/10.1038/s41467-026-72366-z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-07-29T10:27:25Z","abstract":[{"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.","lang":"eng"}],"date_updated":"2026-07-29T10:33:31Z","project":[{"name":"Keratins in epithelial tissue spreading","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","grant_number":"PAT 5044023"},{"name":"Nano-Analytics of Cellular Systems","_id":"252C3B08-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1250-B20"}],"related_material":{"record":[{"id":"20465","relation":"earlier_version","status":"public"}]},"quality_controlled":"1","supplementarymaterial":"yes","date_created":"2026-07-29T09:10:35Z","article_processing_charge":"Yes","month":"07","volume":17,"department":[{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EdHa"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"6499","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"title":"Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties","oa":1,"doi":"10.1038/s41467-026-72366-z","type":"journal_article","publication":"Nature Communications","author":[{"orcid":"0000-0001-8421-5508","first_name":"Suyash","full_name":"Naik, Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","last_name":"Naik"},{"full_name":"Keta, Yann-Edwin","last_name":"Keta","first_name":"Yann-Edwin"},{"first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"first_name":"Silke","full_name":"Henkes, Silke","last_name":"Henkes"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"corr_author":"1","scopus_import":"1"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"file_name":"Supplemental video 1.mp4","date_created":"2026-09-08T11:31:32Z","file_size":1513964,"success":1,"file_id":"22853","content_type":"video/mp4","date_updated":"2026-09-08T11:31:32Z","creator":"aehrmann","access_level":"open_access","checksum":"966417b3eab49523068bb0dfba4ecc07","relation":"main_file"},{"success":1,"file_id":"22854","date_created":"2026-09-08T11:31:37Z","file_size":2634179,"file_name":"Supplemental video 2.mp4","access_level":"open_access","checksum":"deddcae30875bff8e59d5dc9ee3c196f","relation":"main_file","creator":"aehrmann","date_updated":"2026-09-08T11:31:37Z","content_type":"video/mp4"},{"relation":"main_file","access_level":"open_access","checksum":"721446b7595edc670d877185637cf15c","creator":"aehrmann","date_updated":"2026-09-08T11:31:42Z","content_type":"video/mp4","file_id":"22855","success":1,"date_created":"2026-09-08T11:31:42Z","file_size":2080684,"file_name":"Supplemental video 3.mp4"},{"file_size":4047831,"date_created":"2026-09-08T11:31:48Z","file_name":"Supplemental video 4.mp4","success":1,"file_id":"22856","creator":"aehrmann","content_type":"video/mp4","date_updated":"2026-09-08T11:31:48Z","checksum":"da44153821aa4f8f3cbc2860ef6d1bad","access_level":"open_access","relation":"main_file"},{"content_type":"text/plain","date_updated":"2026-09-08T18:36:14Z","creator":"aehrmann","access_level":"open_access","checksum":"1e94cd067809e1a93e21676181b4c102","relation":"main_file","file_name":"README.txt","file_size":1122,"date_created":"2026-09-08T18:36:14Z","success":1,"file_id":"22860"}],"status":"public","_id":"22852","oa_version":"None","day":"09","year":"2026","citation":{"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>","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>.","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>","ieee":"A. Ehrmann, “Supplemental videos for Designing bistable nanostructures for target behavior.” Institute of Science and Technology Austria, 2026.","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).","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>."},"publisher":"Institute of Science and Technology Austria","date_published":"2026-09-09T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT-ISTA-22852","keyword":["functional nanostructures","bistability","target behavior","transition pathway"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"OA_place":"repository","date_updated":"2026-09-09T07:24:10Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2026-09-08T18:36:14Z","date_created":"2026-09-08T11:32:53Z","article_processing_charge":"No","project":[{"_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","name":"Functional bio-inspired nanomachines from sticky colloids","grant_number":"PAT 8537123"}],"department":[{"_id":"GradSch"},{"_id":"CaGo"},{"_id":"EdHa"}],"month":"09","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa":1,"title":"Supplemental videos for Designing bistable nanostructures for target behavior","doi":"10.15479/AT-ISTA-22852","type":"research_data","doi_confirm":"1","contributor":[{"orcid":"0000-0002-0997-5678","contributor_type":"data_collector","first_name":"Andreas","last_name":"Ehrmann","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2"}],"corr_author":"1","author":[{"first_name":"Andreas","orcid":"0000-0002-0997-5678","full_name":"Ehrmann, Andreas","last_name":"Ehrmann","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2"}]},{"OA_place":"publisher","ddc":["530","600","621","004","005"],"has_accepted_license":"1","date_published":"2026-09-04T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-22873","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"keyword":["PhD Thesis","functional nanomachines","biological functionality","nanotechnology","energy delivery","target behavior","dynamics","design principles","optimization","differentiable statistical physics","machine learning"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2026-09-17T08:59:39Z","alternative_title":["ISTA Thesis"],"date_updated":"2026-09-18T11:28:29Z","file":[{"checksum":"a5e3d79e0e5f3f4fb3c414e48116dc9e","access_level":"closed","relation":"main_file","creator":"aehrmann","date_updated":"2026-09-17T08:59:39Z","content_type":"application/pdf","embargo_to":"open_access","file_id":"22901","embargo":"2027-01-15","file_size":14782662,"date_created":"2026-09-11T07:23:57Z","file_name":"2026_Ehrmann_Andreas_Thesis.pdf"},{"creator":"aehrmann","content_type":"application/zip","date_updated":"2026-09-11T07:24:14Z","access_level":"closed","checksum":"0235b9c52fee0c97f402f1c3d4efc1eb","description":"All LaTeX files to compile my PhD Thesis.","relation":"source_file","file_size":155228,"date_created":"2026-09-11T07:24:14Z","file_name":"thesis_latex_files.zip","file_id":"22902"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"day":"04","das_tickbox":"0","supervisor":[{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}],"citation":{"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>","ista":"Ehrmann A. 2026. Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria.","ieee":"A. Ehrmann, “Biological functionality without biochemistry: Designing nanomachines for target behavior,” Institute of Science and Technology Austria, 2026.","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>","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>.","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>.","short":"A. Ehrmann, Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior, Institute of Science and Technology Austria, 2026."},"acknowledgement":"I acknowledge funding by the Austrian Science Fund (FWF) [10.55776/PAT8537123].","year":"2026","publisher":"Institute of Science and Technology Austria","status":"public","_id":"22873","researchdata_availability":"upon request","oa_version":"Published Version","doi_confirm":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-092-3"]},"title":"Biological functionality without biochemistry: Designing nanomachines for target behavior","doi":"10.15479/AT-ISTA-22873","type":"dissertation","author":[{"first_name":"Andreas","orcid":"0000-0002-0997-5678","last_name":"Ehrmann","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","full_name":"Ehrmann, Andreas"}],"corr_author":"1","project":[{"grant_number":"PAT 8537123","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","name":"Functional bio-inspired nanomachines from sticky colloids"}],"degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"22893","status":"public"},{"relation":"part_of_dissertation","id":"22892","status":"public"}]},"date_created":"2026-09-09T12:18:24Z","supplementarymaterial":"not applicable","article_processing_charge":"No","month":"09","page":"168","department":[{"_id":"GradSch"},{"_id":"CaGo"},{"_id":"EdHa"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"oa_version":"Preprint","_id":"22893","status":"public","year":"2026","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","citation":{"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>.","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>.","short":"A. Ehrmann, M. Krstić, S. Samadzadeh, C.P. Goodrich, ArXiv (n.d.).","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>","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>.","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>","ieee":"A. Ehrmann, M. Krstić, S. Samadzadeh, and C. P. Goodrich, “Designing bistable nanostructures for target behavior,” <i>arXiv</i>. ."},"arxiv":1,"day":"30","external_id":{"arxiv":["2606.31620"]},"date_updated":"2026-09-18T11:28:28Z","abstract":[{"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.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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)"},"fulldoi":"https://doi.org/10.48550/arXiv.2606.31620","date_published":"2026-06-30T00:00:00Z","OA_type":"green","OA_place":"repository","publication_status":"draft","language":[{"iso":"eng"}],"department":[{"_id":"CaGo"},{"_id":"EdHa"},{"_id":"AnSa"}],"month":"06","article_processing_charge":"No","date_created":"2026-09-09T13:19:13Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"22873"}]},"project":[{"grant_number":"PAT 8537123","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","name":"Functional bio-inspired nanomachines from sticky colloids"}],"corr_author":"1","author":[{"first_name":"Andreas","orcid":"0000-0002-0997-5678","last_name":"Ehrmann","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","full_name":"Ehrmann, Andreas"},{"full_name":"Krstić, Marija","last_name":"Krstić","id":"a8f6d1c6-3200-11ee-973b-dab948eace26","first_name":"Marija"},{"last_name":"Samadzadeh","id":"0099896b-5fb8-11ef-8420-b30b14627e93","full_name":"Samadzadeh, Sahar","first_name":"Sahar"},{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"publication":"arXiv","type":"preprint","doi":"10.48550/arXiv.2606.31620","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2606.31620"}],"oa":1,"title":"Designing bistable nanostructures for target behavior"},{"external_id":{"arxiv":["2506.14266"]},"citation":{"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>","ieee":"A. Ehrmann and C. P. Goodrich, “Controlling energy delivery with bistable nanostructures,” <i>arXiv</i>. .","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>","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>.","short":"A. Ehrmann, C.P. Goodrich, ArXiv (n.d.).","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>."},"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].","year":"2026","day":"07","arxiv":1,"oa_version":"Preprint","status":"public","_id":"22892","OA_place":"repository","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)"},"fulldoi":"https://doi.org/10.48550/arXiv.2506.14266","date_published":"2026-06-07T00:00:00Z","abstract":[{"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.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-09-18T11:28:29Z","related_material":{"record":[{"relation":"dissertation_contains","id":"22873","status":"public"}]},"project":[{"grant_number":"PAT 8537123","name":"Functional bio-inspired nanomachines from sticky colloids","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d"}],"article_processing_charge":"No","date_created":"2026-09-09T13:16:54Z","month":"06","publication_status":"draft","department":[{"_id":"CaGo"},{"_id":"EdHa"}],"language":[{"iso":"eng"}],"type":"preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2506.14266","open_access":"1"}],"doi":"10.48550/arXiv.2506.14266","title":"Controlling energy delivery with bistable nanostructures","oa":1,"author":[{"orcid":"0000-0002-0997-5678","first_name":"Andreas","last_name":"Ehrmann","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","full_name":"Ehrmann, Andreas"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter"}],"publication":"arXiv","corr_author":"1"},{"dataavailabilitystatement":" All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials and the associated data and code repositories. Source data underlying all figures and supplementary figures have been deposited in a Zenodo repository (DOi: 10.5281/zenodo.21718217) and will be made publicly available upon publication. custom simulation and analysis codes used in this study are available at https://codeocean.com/capsule/1237446/tree. no unique biological materials were generated in this study. Microfluidic mask designs generated for this work are available from the corresponding authors upon reasonable request.","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":"        12","file":[{"access_level":"open_access","checksum":"79f419b659650a39b3dfa58c782690a8","relation":"main_file","creator":"dernst","date_updated":"2026-10-06T11:30:48Z","content_type":"application/pdf","success":1,"file_id":"23062","file_size":11691064,"date_created":"2026-10-06T11:30:48Z","file_name":"2026_ScienceAdv_Dunajova.pdf"}],"issue":"37","external_id":{"pmid":["42715298"]},"oa_version":"Published Version","_id":"22963","status":"public","researchdata_availability":"yes","publisher":"AAAS","year":"2026","citation":{"chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Robert P. Jenkins, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>Science Advances</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/sciadv.aed0587\">https://doi.org/10.1126/sciadv.aed0587</a>.","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, R.P. Jenkins, E. Sahai, M.K. Sixt, E.B. Hannezo, Science Advances 12 (2026).","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>Science Advances</i>, vol. 12, no. 37, eaed0587, AAAS, 2026, doi:<a href=\"https://doi.org/10.1126/sciadv.aed0587\">10.1126/sciadv.aed0587</a>.","ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>Science Advances</i>. 2026;12(37). doi:<a href=\"https://doi.org/10.1126/sciadv.aed0587\">10.1126/sciadv.aed0587</a>","ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Jenkins RP, Sahai E, Sixt MK, Hannezo EB. 2026. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. Science Advances. 12(37), eaed0587.","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Jenkins, R. P., Sahai, E., … Hannezo, E. B. (2026). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.aed0587\">https://doi.org/10.1126/sciadv.aed0587</a>","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>Science Advances</i>, vol. 12, no. 37. AAAS, 2026."},"acknowledgement":"We thank all the members of the Hannezo and Sixt groups for fruitful discussions and t. Kato for advice on the experimental setup. We are also thankful for support from the Scientific Service Units (SSU) of IST Austria through resources provided by the imaging and Optics Facility (iOF) and the Lab Support Facility (lSF). We used chatGPt (GPt- 5,OpenAi, 2025) to make minor grammatical and stylistic revisions to the original manuscript, which was written by us. We carefully reviewed and verified all changes and are solely responsible for all scientific content, data, interpretation, and conclusions. Funding: Z.D. has received funding from the Doctoral Programme of the Austrian Academy of Sciences (OeAW):grant agreement 26360. this work was supported by the European Research council (grant ERC- SyG 101071793 to M.S.). E.S. and R.P.J. are supported by the Francis Crick Institute, which receives its core funding from cancer Research UK (cc2040), the UK Medical Research council(cc2040), and the Wellcome trust (cc2040) and the European Research council (ERC Advanced Grant cAn_ORGAniSe, grant agreement number 101019366).","das_tickbox":"1","day":"09","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1126/sciadv.aed0587","article_type":"original","OA_type":"gold","PlanS_conform":"1","date_published":"2026-09-09T00:00:00Z","has_accepted_license":"1","ddc":["570"],"DOAJ_listed":"1","OA_place":"publisher","date_updated":"2026-10-06T11:36:34Z","abstract":[{"lang":"eng","text":"Although studies of tumor invasion have mainly emphasized the evolution of genetic and epigenetic heterogeneity, cellular behaviors also depend on the physical microenvironment. Yet, the tumor microenvironment is both complex and continuously remodeled, making it hard to rigorously test its causal influence on tumor dissemination. Here, we adopted a reductionist approach to studying tumor cell invasion in microengineered environments of tunable patterned geometries. We find that not only the presence of obstacles but more unexpectedly their spatial disorder causes a drastic shift from a collective to a single-cell mode of invasion—comparable in strength to loss of cell-cell adhesion. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell dissemination results both from local geometrical constraints and a global integration of spatial disorder over time. We identify generic universality classes of invasion dynamics dependent on environmental geometry, enabling us to identify quantitative physical principles for tumor dissemination."}],"file_date_updated":"2026-10-06T11:30:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","supplementarymaterial":"no","date_created":"2026-09-20T22:01:48Z","related_material":{"record":[{"status":"public","id":"21427","relation":"earlier_version"}]},"quality_controlled":"1","project":[{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"},{"grant_number":"101071793","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"}],"publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"GradSch"},{"_id":"AnSa"},{"_id":"NanoFab"}],"volume":12,"month":"09","type":"journal_article","doi":"10.1126/sciadv.aed0587","title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","oa":1,"pmid":1,"publication_identifier":{"eissn":["2375-2548"]},"article_number":"eaed0587","scopus_import":"1","corr_author":"1","author":[{"last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","first_name":"Zuzana"},{"first_name":"Saren","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan"},{"first_name":"Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","last_name":"Majek","full_name":"Majek, Juraj"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert P.","full_name":"Jenkins, Robert P.","last_name":"Jenkins"},{"first_name":"Erik","full_name":"Sahai, Erik","last_name":"Sahai"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}],"publication":"Science Advances"},{"corr_author":"1","author":[{"first_name":"Zuzana","full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova"}],"publication_identifier":{"isbn":["978-3-99078-076-3"],"issn":["2663-337X"]},"title":"Geometry-driven self-organization of migrating cells and chiral filaments","oa":1,"doi":"10.15479/AT-ISTA-21423","type":"dissertation","doi_confirm":"1","page":"110","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"03","date_created":"2026-03-11T08:30:49Z","article_processing_charge":"No","degree_awarded":"PhD","project":[{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"related_material":{"record":[{"status":"public","id":"13314","relation":"part_of_dissertation"},{"status":"public","id":"13116","relation":"research_data"},{"relation":"research_data","id":"21439","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"21427"}]},"date_updated":"2026-10-16T08:12:11Z","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Biological systems, such as cytoskeletal filaments and multicellular collectives, exhibit rich \r\nself-organization driven by their intrinsic activity and physical constraints. Across scales, \r\ngeometry plays a central role: the shape of active units and the structure of their environment \r\nstrongly influence how order emerges in these far-from-equilibrium systems. In this thesis, \r\nwe combine minimal active-matter models with bottom-up in vitro experiments to identify \r\nthe principles by which geometry and activity shape collective behavior in biological matter. \r\nAt the subcellular scale, we investigate how the physical properties of chiral FtsZ filaments \r\ngovern their large-scale organization. Using a mesoscopic model validated by reconstituted \r\nfilament assays, we show that filament shape, intrinsic curvature, and flexibility, together with \r\nactivity-driven straightening, determine whether filaments form chiral rings, polar bands, or \r\nnematic-like states. Our model shows that small changes in filament mechanics produce large \r\nshifts in collective structures, revealing how the geometry of individual filaments amplifies \r\nthrough activity to control patterns relevant for bacterial cytokinesis. \r\nAt the cellular scale, we examine how geometry of the external environment influences \r\ncollective cancer cell migration. Experiments in controlled microfabricated obstacle \r\nenvironments demonstrate that geometric disorder alone can induce a transition from \r\ncollective to single-cell invasion. A minimal model of active particles in disordered geometries \r\nreproduces these effects, demonstrating that cell dissemination results both from local \r\ngeometrical constraints and a global integration of spatial disorder over time. Surprisingly, \r\nthis transition is accompanied by a change in the universality class of interface dynamics, \r\nrevealing that cell-environment interactions can shift the collective behavior of an invasive \r\nfront purely through mechanics.  \r\nIn the last system, we study how cell-intrinsic geometry and chirality affect collective motion \r\nin confined and unconfined settings. Using a minimal model inspired by in vitro experiments, \r\nwe analyze motile cells that exhibit persistent rotation due to intrinsic left-right asymmetry. \r\nIn circular confinement, this simplified chiral model reproduces several experimentally \r\nobserved features within specific parameter regimes. At high densities in unconfined \r\nenvironments, however, intrinsic chirality becomes masked even before the onset of the \r\njamming transition. These results show that single-cell geometric asymmetry does not \r\nnecessarily translate into large-scale chiral flows, offering new insight into how forces and \r\nsymmetries shape collective motion in dense cellular systems. \r\nOverall, this work uncovers how geometric constraints – embedded in the intrinsic \r\narchitecture of an active filament or encoded in the complexity of a microenvironment \r\ncouple to active forces to generate different classes of complex behaviors. ","lang":"eng"}],"file_date_updated":"2026-09-11T22:30:02Z","ddc":["539","570"],"date_published":"2026-03-11T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT-ISTA-21423","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"OA_place":"repository","_id":"21423","status":"public","oa_version":"Published Version","day":"11","supervisor":[{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360.","year":"2026","citation":{"short":"Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026.","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>.","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>.","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>","ieee":"Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026.","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>","ista":"Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"file_id":"21446","file_name":"2026_Dunajova_Zuzana_Thesis_pdfA.pdf","embargo":"2026-09-11","file_size":14662770,"date_created":"2026-03-12T20:38:52Z","checksum":"47ce6a48a0c63f28eca6e64c9ffd2c84","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2026-09-11T22:30:02Z","creator":"zdunajov"},{"access_level":"closed","checksum":"5dec5afdffd47c2b0b162d0fe1bed925","relation":"source_file","date_updated":"2026-09-11T22:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"zdunajov","embargo_to":"open_access","file_id":"21447","file_name":"Thesis-Dunajova_source_file.docx","file_size":32961408,"date_created":"2026-03-12T20:40:18Z"}]},{"ddc":["570"],"has_accepted_license":"1","OA_type":"free access","date_published":"2026-03-12T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-21439","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"OA_place":"repository","date_updated":"2026-10-26T23:31:06Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","file_date_updated":"2026-03-11T20:52:39Z","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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"file":[{"file_size":154465214,"date_created":"2026-03-11T20:41:28Z","file_name":"Supplementary_movies_Thesis_Dunajova.zip","file_id":"21440","success":1,"creator":"zdunajov","content_type":"application/zip","date_updated":"2026-03-11T20:41:28Z","relation":"main_file","checksum":"47809a9a31b748b16e21e92d11ddc87f","access_level":"open_access"},{"file_size":2289,"date_created":"2026-03-11T20:52:39Z","file_name":"readme.txt","success":1,"file_id":"21441","creator":"zdunajov","content_type":"text/plain","date_updated":"2026-03-11T20:52:39Z","access_level":"open_access","checksum":"a64a174bc6abf0a5e77631e4fd121f1f","relation":"main_file"}],"status":"public","_id":"21439","oa_version":"Published Version","day":"12","year":"2026","citation":{"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>.","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>.","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.","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>","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>.","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>"},"publisher":"Institute of Science and Technology Austria","title":"Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”","oa":1,"doi":"10.15479/AT-ISTA-21439","type":"research_data","contributor":[{"last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","orcid":"0000-0003-1671-393X","first_name":"Saren"},{"first_name":"Philipp","contributor_type":"researcher","orcid":"0000-0001-9198-2182 ","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","author":[{"first_name":"Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana"}],"date_created":"2026-03-11T21:05:20Z","article_processing_charge":"No","project":[{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"related_material":{"record":[{"relation":"used_in_publication","id":"13314","status":"public"},{"id":"21427","relation":"used_in_publication","status":"public"},{"id":"21423","relation":"used_in_publication","status":"public"}]},"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"month":"03"},{"oa_version":"Published Version","_id":"21235","status":"public","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.).","year":"2025","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).","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>.","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.","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>"},"publisher":"American Physical Society","day":"11","file":[{"success":1,"file_id":"21287","file_size":3732843,"date_created":"2026-02-17T11:12:30Z","file_name":"2025_PRXLife_Sorichetti.pdf","checksum":"1702b9bdbfd902a7c08aa4f1479b390d","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2026-02-17T11:12:30Z","content_type":"application/pdf"}],"intvolume":"         3","issue":"3","date_updated":"2026-02-17T11:16:26Z","file_date_updated":"2026-02-17T11:12:30Z","ec_funded":1,"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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1103/41fd-r847","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"OA_type":"gold","PlanS_conform":"1","date_published":"2025-08-11T00:00:00Z","has_accepted_license":"1","OA_place":"publisher","DOAJ_listed":"1","volume":3,"department":[{"_id":"AnSa"},{"_id":"EdHa"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"08","date_created":"2026-02-16T14:50:32Z","article_processing_charge":"Yes","quality_controlled":"1","project":[{"call_identifier":"H2020","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"},{"name":"EMBO Young Investigator Program - Andela Saric","_id":"349b6ff1-11ca-11ed-8bc3-f006047c2eeb"}],"corr_author":"1","author":[{"full_name":"Sorichetti, Valerio","last_name":"Sorichetti","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","first_name":"Valerio"},{"first_name":"Paul","orcid":"0000-0002-5728-9189","full_name":"Robin, Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","last_name":"Robin"},{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan"},{"last_name":"Hernandez-Armendariz","full_name":"Hernandez-Armendariz, Alberto","first_name":"Alberto"},{"full_name":"Cuylen-Haering, Sara","last_name":"Cuylen-Haering","first_name":"Sara"},{"full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"}],"publication":"PRX Life","doi":"10.1103/41fd-r847","type":"journal_article","publication_identifier":{"eissn":["2835-8279"]},"oa":1,"title":"Charge distribution of the coating brush drives interchromosome attraction","article_number":"033010"},{"article_number":"033015","oa":1,"title":"Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells","publication_identifier":{"eissn":["2835-8279"]},"type":"journal_article","doi":"10.1103/3hhj-rt1n","publication":"PRX Life","author":[{"last_name":"Brandstätter","full_name":"Brandstätter, Tom","first_name":"Tom"},{"first_name":"Emily","full_name":"Brieger, Emily","last_name":"Brieger"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David"},{"first_name":"Georg","full_name":"Ladurner, Georg","last_name":"Ladurner"},{"first_name":"Joachim O.","last_name":"Rädler","full_name":"Rädler, Joachim O."},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."}],"quality_controlled":"1","article_processing_charge":"Yes","date_created":"2026-02-16T14:52:02Z","month":"08","publication_status":"published","department":[{"_id":"EdHa"}],"volume":3,"language":[{"iso":"eng"}],"DOAJ_listed":"1","OA_place":"publisher","has_accepted_license":"1","PlanS_conform":"1","date_published":"2025-08-26T00:00:00Z","OA_type":"gold","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1103/3hhj-rt1n","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2026-02-17T11:18:18Z","date_updated":"2026-02-17T11:20:20Z","issue":"3","external_id":{"arxiv":["2407.17268"]},"intvolume":"         3","file":[{"file_name":"2025_PRXLife_Brandstaetter.pdf","date_created":"2026-02-17T11:18:18Z","file_size":9366716,"file_id":"21288","success":1,"date_updated":"2026-02-17T11:18:18Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","checksum":"70c067ceef3a8262d9c430e85e3ba9ec","access_level":"open_access"}],"arxiv":1,"day":"26","publisher":"American Physical Society","citation":{"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.","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>","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>","short":"T. Brandstätter, E. Brieger, D. Brückner, G. Ladurner, J.O. Rädler, C.P. Broedersz, PRX Life 3 (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>.","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>."},"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).","year":"2025","status":"public","_id":"21236","oa_version":"Published Version"},{"_id":"19279","status":"public","oa_version":"Published Version","isi":1,"day":"14","arxiv":1,"publisher":"AIP Publishing","citation":{"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).","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>.","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.","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.","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>"},"year":"2025","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.","issue":"6","external_id":{"pmid":["39932241"],"arxiv":["2410.03316"],"isi":["001421300300001"]},"intvolume":"       162","file":[{"relation":"main_file","access_level":"open_access","checksum":"c9008c2c50c917673aa588f75acbcb40","creator":"dernst","content_type":"application/pdf","date_updated":"2025-03-04T10:29:36Z","file_id":"19290","success":1,"date_created":"2025-03-04T10:29:36Z","file_size":5807062,"file_name":"2025_JourChemicalPhysics_Toquer.pdf"}],"date_updated":"2025-09-30T10:44:48Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"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."}],"file_date_updated":"2025-03-04T10:29:36Z","OA_type":"hybrid","date_published":"2025-02-14T00:00:00Z","has_accepted_license":"1","ddc":["540"],"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)"},"article_type":"original","fulldoi":"https://doi.org/10.1063/5.0241949","OA_place":"publisher","publication_status":"published","department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"volume":162,"month":"02","article_processing_charge":"Yes (in subscription journal)","date_created":"2025-03-02T23:01:52Z","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"quality_controlled":"1","corr_author":"1","scopus_import":"1","publication":"Journal of Chemical Physics","author":[{"first_name":"Damien","full_name":"Toquer, Damien","last_name":"Toquer"},{"first_name":"Lydéric","last_name":"Bocquet","full_name":"Bocquet, Lydéric"},{"id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","last_name":"Robin","full_name":"Robin, Paul","first_name":"Paul","orcid":"0000-0002-5728-9189"}],"oa":1,"title":"Ionic association and Wien effect in 2D confined electrolytes","pmid":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"type":"journal_article","doi":"10.1063/5.0241949","article_number":"064703"}]