--- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21015' abstract: - lang: eng 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. acknowledged_ssus: - _id: PreCl - _id: Bio - _id: ScienComp - _id: LifeSc 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). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nikhil full_name: Mishra, Nikhil id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E last_name: Mishra orcid: 0000-0002-6425-5788 - first_name: Yuting I full_name: Li, Yuting I id: ee7a5ca8-8b71-11ed-b662-b3341c05b7eb last_name: Li - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: 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. Nature Physics. 2026;22:139-150. doi:10.1038/s41567-025-03122-1 apa: Mishra, N., Li, Y. I., Hannezo, E. B., & Heisenberg, C.-P. J. (2026). Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03122-1 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.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-025-03122-1. 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,” Nature Physics, vol. 22. Springer Nature, pp. 139–150, 2026. 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. mla: Mishra, Nikhil, et al. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” Nature Physics, vol. 22, Springer Nature, 2026, pp. 139–50, doi:10.1038/s41567-025-03122-1. short: N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026) 139–150. corr_author: '1' date_created: 2026-01-20T10:12:19Z date_published: 2026-01-05T00:00:00Z date_updated: 2026-04-28T12:55:30Z day: '05' ddc: - '570' department: - _id: EdHa - _id: CaHe doi: 10.1038/s41567-025-03122-1 ec_funded: 1 external_id: oaworkid: - W7118187193 file: - access_level: open_access checksum: 0ab7ac2fbcb61a364dba57152db64ed7 content_type: application/pdf creator: dernst date_created: 2026-01-21T08:21:11Z date_updated: 2026-01-21T08:21:11Z file_id: '21026' file_name: 2026_NaturePhysics_Mishra.pdf file_size: 7335694 relation: main_file success: 1 file_date_updated: 2026-01-21T08:21:11Z fulldoi: https://doi.org/10.1038/s41567-025-03122-1 has_accepted_license: '1' intvolume: ' 22' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version oaworkid: 1 page: 139-150 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 917c023a-16d5-11f0-9cad-eb5cafc52090 name: Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 issnl: - ' 1745-2473' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: research_data url: https://ista.ac.at/en/news/geometry-shapes-life/ scopus_import: '1' status: public title: Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 22 year: '2026' ... --- OA_place: repository _id: '21137' acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: ScienComp - _id: LifeSc 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. article_processing_charge: No author: - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 citation: ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137 apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137 chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137. ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026. ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137. mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137. short: S. Naik, (2026). contributor: - contributor_type: researcher first_name: Yann-Edwin last_name: Keta - contributor_type: supervisor first_name: 'Silke ' last_name: Henkes - contributor_type: supervisor first_name: Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - contributor_type: supervisor first_name: Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 corr_author: '1' date_created: 2026-02-04T16:38:02Z date_published: 2026-03-24T00:00:00Z date_updated: 2026-06-10T09:44:10Z day: '24' department: - _id: GradSch - _id: CaHe - _id: EdHa doi: 10.15479/AT-ISTA-21137 ec_funded: 1 file: - access_level: open_access checksum: 5d1fda7e410f24c311fcf6bcf725698f content_type: application/zip creator: snaik date_created: 2026-03-16T11:51:10Z date_updated: 2026-03-16T11:51:10Z 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. ' file_id: '21461' file_name: cells-main.zip file_size: 725916 relation: main_file title: Cell git repository - access_level: open_access checksum: ee350c8eaed99f3ca348c47c8b190d3c content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-18T14:52:02Z date_updated: 2026-03-18T14:52:02Z file_id: '21464' file_name: DevBranchDataRepo.zip file_size: 282168895 relation: main_file success: 1 - access_level: open_access checksum: 1ecaf2c1a2ce8ff9c75a128cc02d0b8f content_type: text/markdown creator: snaik date_created: 2026-03-18T15:01:32Z date_updated: 2026-03-18T15:01:32Z file_id: '21466' file_name: ReadMe.md file_size: 2231 relation: main_file success: 1 - access_level: open_access checksum: da9a4687e5144b61a64ca341f922046a content_type: image/svg+xml creator: snaik date_created: 2026-03-18T15:12:57Z date_updated: 2026-03-18T15:12:57Z file_id: '21467' file_name: PaperSchematics.svg file_size: 1951210 relation: main_file success: 1 - access_level: open_access checksum: 9ac1054b16c212c6f34d402dce2c80e0 content_type: application/octet-stream creator: snaik date_created: 2026-03-21T03:37:43Z date_updated: 2026-03-21T03:37:43Z file_id: '21468' file_name: maxwell_sketch.tex file_size: 1897 relation: main_file success: 1 - access_level: open_access checksum: 7c9ecf78e2593b3830d96fa94baa08df content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-24T07:21:43Z date_updated: 2026-03-24T07:21:43Z file_id: '21495' file_name: DataRepo.zip file_size: 749368723 relation: main_file success: 1 file_date_updated: 2026-03-24T07:21:43Z fulldoi: https://doi.org/10.15479/AT-ISTA-21137 has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '3' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 252C3B08-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1250-B20 name: Nano-Analytics of Cellular Systems publisher: Institute of Science and Technology Austria status: public title: 'Data associated with Keratins coordinate tissue spreading ' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21275' abstract: - lang: eng 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. 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. article_number: '013018' article_processing_charge: Yes article_type: original author: - first_name: Fabrizio full_name: Olmeda, Fabrizio id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689 last_name: Olmeda - first_name: Misha full_name: Gupta, Misha last_name: Gupta - first_name: Onurcan full_name: Bektas, Onurcan last_name: Bektas - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands citation: ama: Olmeda F, Gupta M, Bektas O, Rulands S. Spatiotemporal patterns of active epigenetic turnover. PRX Life. 2026;4. doi:10.1103/89bj-79g5 apa: Olmeda, F., Gupta, M., Bektas, O., & Rulands, S. (2026). Spatiotemporal patterns of active epigenetic turnover. PRX Life. American Physical Society. https://doi.org/10.1103/89bj-79g5 chicago: Olmeda, Fabrizio, Misha Gupta, Onurcan Bektas, and Steffen Rulands. “Spatiotemporal Patterns of Active Epigenetic Turnover.” PRX Life. American Physical Society, 2026. https://doi.org/10.1103/89bj-79g5. ieee: F. Olmeda, M. Gupta, O. Bektas, and S. Rulands, “Spatiotemporal patterns of active epigenetic turnover,” PRX Life, vol. 4. American Physical Society, 2026. ista: Olmeda F, Gupta M, Bektas O, Rulands S. 2026. Spatiotemporal patterns of active epigenetic turnover. PRX Life. 4, 013018. mla: Olmeda, Fabrizio, et al. “Spatiotemporal Patterns of Active Epigenetic Turnover.” PRX Life, vol. 4, 013018, American Physical Society, 2026, doi:10.1103/89bj-79g5. short: F. Olmeda, M. Gupta, O. Bektas, S. Rulands, PRX Life 4 (2026). corr_author: '1' date_created: 2026-02-17T08:17:53Z date_published: 2026-02-09T00:00:00Z date_updated: 2026-02-24T06:54:32Z day: '09' ddc: - '570' department: - _id: EdHa doi: 10.1103/89bj-79g5 ec_funded: 1 file: - access_level: open_access checksum: df9776422862d1d02c66d98e2d620849 content_type: application/pdf creator: dernst date_created: 2026-02-24T06:53:05Z date_updated: 2026-02-24T06:53:05Z file_id: '21351' file_name: 2026_PRXLife_Olmeda.pdf file_size: 5857833 relation: main_file success: 1 file_date_updated: 2026-02-24T06:53:05Z fulldoi: https://doi.org/10.1103/89bj-79g5 has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: PRX Life publication_identifier: eissn: - 2835-8279 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Spatiotemporal patterns of active epigenetic turnover tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21847' 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. 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." article_number: '023094' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Frederik Skovbo full_name: Moller, Frederik Skovbo id: 43cbcc83-0564-11f0-a935-e37325525859 last_name: Moller - 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 full_name: De Schoulepnikoff, Paulin last_name: De Schoulepnikoff - first_name: Jörg full_name: Schmiedmayer, Jörg last_name: Schmiedmayer - first_name: Gorka full_name: Muñoz-Gil, Gorka last_name: Muñoz-Gil citation: 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. Physical Review Research. 2026;8(2). doi:10.1103/r7pj-gl7r apa: Moller, F. S., 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. American Physical Society. https://doi.org/10.1103/r7pj-gl7r 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.” Physical Review Research. American Physical Society, 2026. https://doi.org/10.1103/r7pj-gl7r. 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,” Physical Review Research, 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. mla: Moller, Frederik Skovbo, et al. “Learning Minimal Representations of Many-Body Physics from Snapshots of a Quantum Simulator.” Physical Review Research, vol. 8, no. 2, 023094, American Physical Society, 2026, doi:10.1103/r7pj-gl7r. short: F.S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff, J. Schmiedmayer, G. Muñoz-Gil, Physical Review Research 8 (2026). date_created: 2026-05-10T22:02:15Z date_published: 2026-04-29T00:00:00Z date_updated: 2026-05-11T06:58:56Z day: '29' ddc: - '530' department: - _id: EdHa doi: 10.1103/r7pj-gl7r external_id: arxiv: - '2509.13821' file: - access_level: open_access checksum: dbfc58e1e176f7b63e0d274eb0d1bffa content_type: application/pdf creator: dernst date_created: 2026-05-11T06:56:58Z date_updated: 2026-05-11T06:56:58Z file_id: '21852' file_name: 2026_PhysicalReviewResearch_Moller.pdf file_size: 1829628 relation: main_file success: 1 file_date_updated: 2026-05-11T06:56:58Z fulldoi: https://doi.org/10.1103/r7pj-gl7r has_accepted_license: '1' intvolume: ' 8' issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Physical Review Research publication_identifier: eissn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Learning minimal representations of many-body physics from snapshots of a quantum simulator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21899' abstract: - lang: eng 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. 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. article_number: '021023' article_processing_charge: Yes article_type: original author: - first_name: Oliver M full_name: Drozdowski, Oliver M id: cd4ed792-b872-11ef-bb90-b7b3a3f62f75 last_name: Drozdowski - first_name: Büşra full_name: "Kocameşe-Tamgac\U0001D6A4, Büşra" last_name: "Kocameşe-Tamgac\U0001D6A4" - first_name: Kim E. full_name: Boonekamp, Kim E. last_name: Boonekamp - first_name: Michael full_name: Boutros, Michael last_name: Boutros - first_name: Ulrich S. full_name: Schwarz, Ulrich S. last_name: Schwarz citation: ama: "Drozdowski OM, Kocameşe-Tamgac\U0001D6A4 B, Boonekamp KE, Boutros M, Schwarz US. Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. Physical Review X. 2026;16(2). doi:10.1103/x82g-cq7n" apa: "Drozdowski, O. M., Kocameşe-Tamgac\U0001D6A4, B., Boonekamp, K. E., Boutros, M., & Schwarz, U. S. (2026). Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. Physical Review X. American Physical Society. https://doi.org/10.1103/x82g-cq7n" chicago: "Drozdowski, Oliver M, Büşra Kocameşe-Tamgac\U0001D6A4, Kim E. Boonekamp, Michael Boutros, and Ulrich S. Schwarz. “Cell Bulging and Extrusion in a Three-Dimensional Bubbly Vertex Model for Curved Epithelial Sheets.” Physical Review X. American Physical Society, 2026. https://doi.org/10.1103/x82g-cq7n." ieee: "O. M. Drozdowski, B. Kocameşe-Tamgac\U0001D6A4, K. E. Boonekamp, M. Boutros, and U. S. Schwarz, “Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets,” Physical Review X, vol. 16, no. 2. American Physical Society, 2026." ista: "Drozdowski OM, Kocameşe-Tamgac\U0001D6A4 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." mla: Drozdowski, Oliver M., et al. “Cell Bulging and Extrusion in a Three-Dimensional Bubbly Vertex Model for Curved Epithelial Sheets.” Physical Review X, vol. 16, no. 2, 021023, American Physical Society, 2026, doi:10.1103/x82g-cq7n. short: "O.M. Drozdowski, B. Kocameşe-Tamgac\U0001D6A4, K.E. Boonekamp, M. Boutros, U.S. Schwarz, Physical Review X 16 (2026)." date_created: 2026-05-20T14:35:57Z date_published: 2026-04-30T00:00:00Z date_updated: 2026-05-21T06:08:11Z day: '30' ddc: - '530' department: - _id: EdHa doi: 10.1103/x82g-cq7n file: - access_level: open_access checksum: a90e905968648ac4425c256de901e9c3 content_type: application/pdf creator: dernst date_created: 2026-05-21T06:05:49Z date_updated: 2026-05-21T06:05:49Z file_id: '21901' file_name: 2026_PhysicalReviewX_Drozdowski.pdf file_size: 5603164 relation: main_file success: 1 file_date_updated: 2026-05-21T06:05:49Z fulldoi: https://doi.org/10.1103/x82g-cq7n has_accepted_license: '1' intvolume: ' 16' issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Physical Review X publication_identifier: issn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2026' ... --- OA_place: publisher OA_type: green _id: '22276' 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. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: EM-Fac 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. article_processing_charge: No author: - first_name: Naoya full_name: Hino, Naoya id: 5299a9ce-7679-11eb-a7bc-d1e62b936307 last_name: Hino - first_name: Tushna full_name: Kapoor, Tushna id: e3b3eda7-fd4d-11eb-8fd8-c40af7a478b1 last_name: Kapoor - first_name: Uday R full_name: Gubbala, Uday R id: bb4a0dc4-32c9-11ee-b5ce-a97ceedd5924 last_name: Gubbala - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Hino N, Kapoor T, Gubbala UR, Hannezo EB, Heisenberg C-PJ. Apical domain mechanosensation regulates tissue tension homeostasis. apa: Hino, N., Kapoor, T., Gubbala, U. R., Hannezo, E. B., & Heisenberg, C.-P. J. (n.d.). Apical domain mechanosensation regulates tissue tension homeostasis. Institute of Science and Technology Austria. chicago: Hino, Naoya, Tushna Kapoor, Uday R Gubbala, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Apical Domain Mechanosensation Regulates Tissue Tension Homeostasis.” Institute of Science and Technology Austria, n.d. 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. mla: Hino, Naoya, et al. Apical Domain Mechanosensation Regulates Tissue Tension Homeostasis. Institute of Science and Technology Austria. short: N. Hino, T. Kapoor, U.R. Gubbala, E.B. Hannezo, C.-P.J. Heisenberg, (n.d.). corr_author: '1' das_tickbox: '1' 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." date_created: 2026-07-13T09:03:26Z date_published: 2026-07-14T00:00:00Z date_updated: 2026-07-14T07:07:41Z day: '14' ddc: - '570' department: - _id: CaHe - _id: EdHa - _id: GradSch file: - access_level: open_access checksum: 66444afd243dce7d383d52d44e8d34a4 content_type: application/pdf creator: nhino date_created: 2026-07-13T09:16:20Z date_updated: 2026-07-13T09:16:20Z file_id: '22283' file_name: Main_text_and_figures.pdf file_size: 12477675 relation: main_file success: 1 - access_level: open_access checksum: 90bceb34de64ec792c5de117f0890d05 content_type: application/pdf creator: nhino date_created: 2026-07-13T09:16:25Z date_updated: 2026-07-13T09:16:25Z file_id: '22284' file_name: Supplementary_figures.pdf file_size: 4545901 relation: main_file success: 1 - access_level: open_access checksum: 9d9ab89c372142f2ffb6c8c625334d7f content_type: video/mp4 creator: nhino date_created: 2026-07-13T09:16:28Z date_updated: 2026-07-13T09:16:28Z file_id: '22285' file_name: Supplementary_Video1.mp4 file_size: 10349451 relation: main_file success: 1 file_date_updated: 2026-07-13T09:16:28Z has_accepted_license: '1' keyword: - Epithelial spreading - tissue tension - mechanosensation - aPKC - Kibra - zebrafish language: - iso: eng month: '07' oa: 1 oa_version: Preprint project: - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 34dd7f3b-11ca-11ed-8bc3-856f2c87f5da grant_number: LTF 16-2022 name: Mechanosensitive signaling activation in the crosstalk between mechanical force and tissuefluidity publication_status: draft publisher: Institute of Science and Technology Austria related_material: record: - id: '21864' relation: earlier_version status: public researchdata_availability: yes status: public supplementarymaterial: yes title: Apical domain mechanosensation regulates tissue tension homeostasis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22326' abstract: - lang: eng 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. 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." article_number: '038401' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Chen Y full_name: Zhang, Chen Y id: 81b43fb8-c9d5-11ef-bf68-ade532a1f204 last_name: Zhang - first_name: Pablo full_name: Mateu Hoyos, Pablo id: 50b236c7-50c1-11ef-bb9a-a2375694f8b5 last_name: Mateu Hoyos - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Zhang CY, Mateu Hoyos P, Brückner D, Tkačik G. Nonlocal decoding of positional and correlational information during development. Physical Review Letters. 2026;137. doi:10.1103/mbjk-v4ym apa: Zhang, C. Y., Mateu Hoyos, P., Brückner, D., & Tkačik, G. (2026). Nonlocal decoding of positional and correlational information during development. Physical Review Letters. American Physical Society. https://doi.org/10.1103/mbjk-v4ym chicago: Zhang, Chen Y, Pablo Mateu Hoyos, David Brückner, and Gašper Tkačik. “Nonlocal Decoding of Positional and Correlational Information during Development.” Physical Review Letters. American Physical Society, 2026. https://doi.org/10.1103/mbjk-v4ym. ieee: C. Y. Zhang, P. Mateu Hoyos, D. Brückner, and G. Tkačik, “Nonlocal decoding of positional and correlational information during development,” Physical Review Letters, vol. 137. American Physical Society, 2026. 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. mla: Zhang, Chen Y., et al. “Nonlocal Decoding of Positional and Correlational Information during Development.” Physical Review Letters, vol. 137, 038401, American Physical Society, 2026, doi:10.1103/mbjk-v4ym. short: C.Y. Zhang, P. Mateu Hoyos, D. Brückner, G. Tkačik, Physical Review Letters 137 (2026). corr_author: '1' das_tickbox: '1' 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." date_created: 2026-07-14T05:38:28Z date_published: 2026-07-15T00:00:00Z date_updated: 2026-07-16T09:58:04Z day: '15' ddc: - '530' department: - _id: GaTk - _id: EdHa - _id: GradSch doi: 10.1103/mbjk-v4ym file: - access_level: open_access checksum: 28861d31d0f6cf541aaca04faaed1767 content_type: application/pdf creator: dernst date_created: 2026-07-16T09:54:55Z date_updated: 2026-07-16T09:54:55Z file_id: '22352' file_name: 2026_PhysicalReviewLetters_Zhang.pdf file_size: 2550345 relation: main_file success: 1 file_date_updated: 2026-07-16T09:54:55Z fulldoi: https://doi.org/10.1103/mbjk-v4ym has_accepted_license: '1' intvolume: ' 137' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9 grant_number: '101118866' name: 'Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos' publication: Physical Review Letters publication_identifier: eissn: - ' 1079-7114' issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Nonlocal decoding of positional and correlational information during development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 137 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20670' 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.' 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Simon full_name: Mayer, Simon last_name: Mayer - first_name: Marianna Fanouria full_name: Mitsioni, Marianna Fanouria last_name: Mitsioni - first_name: Paul full_name: Robin, Paul id: 48c58128-57b0-11ee-9095-dc28fd97fc1d last_name: Robin orcid: 0000-0002-5728-9189 - 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 - first_name: Luciano A. full_name: Abriata, Luciano A. last_name: Abriata - first_name: Lucien F. full_name: Krapp, Lucien F. last_name: Krapp - first_name: Jana S. full_name: Anton, Jana S. last_name: Anton - first_name: Sarah full_name: Soussou, Sarah last_name: Soussou - first_name: Justin full_name: Jeanneret-Grosjean, Justin last_name: Jeanneret-Grosjean - first_name: Alessandro full_name: Fulciniti, Alessandro last_name: Fulciniti - first_name: Alexia full_name: Möller, Alexia last_name: Möller - first_name: Sarah full_name: Vacle, Sarah last_name: Vacle - first_name: Lely full_name: Feletti, Lely last_name: Feletti - 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. full_name: Gundlach, Jens H. last_name: Gundlach - first_name: Theo full_name: Emmerich, Theo last_name: Emmerich - first_name: Matteo full_name: Dal Peraro, Matteo last_name: Dal Peraro - first_name: Aleksandra full_name: Radenovic, Aleksandra last_name: Radenovic citation: ama: Mayer S, Mitsioni MF, Robin P, et al. Lumen charge governs gated ion transport in β-barrel nanopores. Nature Nanotechnology. 2026;21:116-124. doi:10.1038/s41565-025-02052-6 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. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-025-02052-6 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.” Nature Nanotechnology. Springer Nature, 2026. https://doi.org/10.1038/s41565-025-02052-6. ieee: S. Mayer et al., “Lumen charge governs gated ion transport in β-barrel nanopores,” Nature Nanotechnology, vol. 21. Springer Nature, pp. 116–124, 2026. 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. mla: Mayer, Simon, et al. “Lumen Charge Governs Gated Ion Transport in β-Barrel Nanopores.” Nature Nanotechnology, vol. 21, Springer Nature, 2026, pp. 116–24, doi:10.1038/s41565-025-02052-6. 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. das_tickbox: '1' 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. date_created: 2025-11-23T23:01:40Z date_published: 2026-01-01T00:00:00Z date_updated: 2026-07-27T08:24:20Z day: '01' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41565-025-02052-6 external_id: isi: - '001611698900001' pmid: - '41219410' file: - access_level: open_access checksum: ff9a5eafe60af1d97da545453bd53eca content_type: application/pdf creator: dernst date_created: 2026-07-27T08:22:57Z date_updated: 2026-07-27T08:22:57Z file_id: '22412' file_name: 2026_NatureNanotech_Mayer.pdf file_size: 10091503 relation: main_file success: 1 file_date_updated: 2026-07-27T08:22:57Z fulldoi: https://doi.org/10.1038/s41565-025-02052-6 has_accepted_license: '1' intvolume: ' 21' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 116-124 pmid: 1 publication: Nature Nanotechnology publication_identifier: eissn: - 1748-3395 issn: - 1748-3387 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/lukasvandenheuvel/Biomemristors researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Lumen charge governs gated ion transport in β-barrel nanopores tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21849' 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. 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Fabrizio full_name: Olmeda, Fabrizio id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689 last_name: Olmeda - first_name: Tim full_name: Lohoff, Tim last_name: Lohoff - first_name: Ioannis full_name: Kafetzopoulos, Ioannis last_name: Kafetzopoulos - first_name: Stephen J. full_name: Clark, Stephen J. last_name: Clark - first_name: Laura full_name: Benson, Laura last_name: Benson - first_name: Fatima full_name: Santos, Fatima last_name: Santos - first_name: Felix full_name: Krueger, Felix last_name: Krueger - first_name: Simon full_name: Walker, Simon last_name: Walker - first_name: Wolf full_name: Reik, Wolf last_name: Reik - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands citation: ama: Olmeda F, Lohoff T, Kafetzopoulos I, et al. Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. 2026;22:931-940. doi:10.1038/s41567-026-03263-x 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. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-026-03263-x 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.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-026-03263-x. ieee: F. Olmeda et al., “Scaling and self-similarity in the formation of the embryonic epigenome,” Nature Physics, vol. 22. Springer Nature, pp. 931–940, 2026. 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. mla: Olmeda, Fabrizio, et al. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” Nature Physics, vol. 22, Springer Nature, 2026, pp. 931–40, doi:10.1038/s41567-026-03263-x. 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. das_tickbox: '1' 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. date_created: 2026-05-10T22:02:16Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-27T13:56:09Z day: '01' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41567-026-03263-x ec_funded: 1 external_id: pmid: - '42318073' file: - access_level: open_access checksum: 58e7734f1ebaf6def642140cb489f08f content_type: application/pdf creator: dernst date_created: 2026-07-27T13:54:58Z date_updated: 2026-07-27T13:54:58Z file_id: '22591' file_name: 2026_NaturePhysics_Olmeda.pdf file_size: 7932222 relation: main_file success: 1 file_date_updated: 2026-07-27T13:54:58Z fulldoi: https://doi.org/10.1038/s41567-026-03263-x has_accepted_license: '1' intvolume: ' 22' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 931-940 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Scaling and self-similarity in the formation of the embryonic epigenome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2026' ... --- OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '22608' abstract: - lang: eng text: For tissues to spread, they must deform while staying intact. How spreading tissues balance flexibility with integrity is not yet well understood. Here, we show that keratin intermediate filaments adapt tissue mechanical resilience to the stresses arising in epithelial tissues during spreading. By analyzing the expansion of the enveloping cell layer (EVL) over the yolk cell in zebrafish embryos in vivo, we find that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, to prevent tissue rupture. Further, keratins are required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the forces pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production and EVL mechanical resilience, ensuring uniform and robust tissue spreading. acknowledged_ssus: - _id: Bio - _id: ScienComp - _id: LifeSc - _id: EM-Fac 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. article_number: '6499' article_processing_charge: Yes article_type: original author: - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 - first_name: Yann-Edwin full_name: Keta, Yann-Edwin last_name: Keta - first_name: Kornelija full_name: Pranjic-Ferscha, Kornelija id: 4362B3C2-F248-11E8-B48F-1D18A9856A87 last_name: Pranjic-Ferscha - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Silke full_name: Henkes, Silke last_name: Henkes - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: 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. Nature Communications. 2026;17. doi:10.1038/s41467-026-72366-z apa: Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., & Heisenberg, C.-P. J. (2026). Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-026-72366-z 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.” Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-72366-z. 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,” Nature Communications, vol. 17. Springer Nature, 2026. 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. mla: Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” Nature Communications, vol. 17, 6499, Springer Nature, 2026, doi:10.1038/s41467-026-72366-z. short: S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, Nature Communications 17 (2026). corr_author: '1' das_tickbox: '1' 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." date_created: 2026-07-29T09:10:35Z date_published: 2026-07-17T00:00:00Z date_updated: 2026-07-29T10:33:31Z day: '17' ddc: - '570' department: - _id: Bio - _id: CaHe - _id: EdHa doi: 10.1038/s41467-026-72366-z external_id: pmid: - '42143048' file: - access_level: open_access checksum: f26d96e180c1d034d9c9c8f57c3c258b content_type: application/pdf creator: dernst date_created: 2026-07-29T10:27:25Z date_updated: 2026-07-29T10:27:25Z file_id: '22609' file_name: 2026_NatureComm_Naik.pdf file_size: 15363936 relation: main_file success: 1 file_date_updated: 2026-07-29T10:27:25Z fulldoi: https://doi.org/10.1038/s41467-026-72366-z has_accepted_license: '1' intvolume: ' 17' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 252C3B08-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1250-B20 name: Nano-Analytics of Cellular Systems publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20465' relation: earlier_version status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2026' ... --- OA_place: repository _id: '22852' abstract: - lang: eng text: "This Research Data contains supplemental videos for Chapter 4 \"Designing bistable nanostructures for target behavior\" of my PhD Thesis \"Biological functionality without biochemistry: designing nanomachines for target behavior\".\r\nSupplemental video 1: Video showing the transition pathway of a bistable nanostructure with sphere-based arms, corresponding to the Machine in Scenario 4.\r\nSupplemental video 2: Video showing the transition pathway of the Source in Scenario 1. The arm tips change sides during the transition, demonstrating that the arms pass through each other.\r\nSupplemental video 3: Video showing the transition pathway of a fully polyhedral hinge structure with unconstrained arms. Note that we only show the ends of the arms.\r\nSupplemental video 4: Video showing the transition pathway of the coupled energy-delivery reaction of a Machine (gray) and a Source (blue) nanostructure for the optimized parameters in Scenario 3. Note that we only show the ends of the arms." acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Andreas full_name: Ehrmann, Andreas id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2 last_name: Ehrmann orcid: 0000-0002-0997-5678 citation: ama: Ehrmann A. Supplemental videos for Designing bistable nanostructures for target behavior. 2026. doi:10.15479/AT-ISTA-22852 apa: Ehrmann, A. (2026). Supplemental videos for Designing bistable nanostructures for target behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22852 chicago: Ehrmann, Andreas. “Supplemental Videos for Designing Bistable Nanostructures for Target Behavior.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22852. ieee: A. Ehrmann, “Supplemental videos for Designing bistable nanostructures for target behavior.” Institute of Science and Technology Austria, 2026. ista: Ehrmann A. 2026. Supplemental videos for Designing bistable nanostructures for target behavior, Institute of Science and Technology Austria, 10.15479/AT-ISTA-22852. mla: Ehrmann, Andreas. Supplemental Videos for Designing Bistable Nanostructures for Target Behavior. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22852. short: A. Ehrmann, (2026). contributor: - contributor_type: data_collector first_name: Andreas id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2 last_name: Ehrmann orcid: 0000-0002-0997-5678 corr_author: '1' date_created: 2026-09-08T11:32:53Z date_published: 2026-09-09T00:00:00Z date_updated: 2026-09-09T07:24:10Z day: '09' department: - _id: GradSch - _id: CaGo - _id: EdHa doi: 10.15479/AT-ISTA-22852 doi_confirm: '1' file: - access_level: open_access checksum: 966417b3eab49523068bb0dfba4ecc07 content_type: video/mp4 creator: aehrmann date_created: 2026-09-08T11:31:32Z date_updated: 2026-09-08T11:31:32Z file_id: '22853' file_name: Supplemental video 1.mp4 file_size: 1513964 relation: main_file success: 1 - access_level: open_access checksum: deddcae30875bff8e59d5dc9ee3c196f content_type: video/mp4 creator: aehrmann date_created: 2026-09-08T11:31:37Z date_updated: 2026-09-08T11:31:37Z file_id: '22854' file_name: Supplemental video 2.mp4 file_size: 2634179 relation: main_file success: 1 - access_level: open_access checksum: 721446b7595edc670d877185637cf15c content_type: video/mp4 creator: aehrmann date_created: 2026-09-08T11:31:42Z date_updated: 2026-09-08T11:31:42Z file_id: '22855' file_name: Supplemental video 3.mp4 file_size: 2080684 relation: main_file success: 1 - access_level: open_access checksum: da44153821aa4f8f3cbc2860ef6d1bad content_type: video/mp4 creator: aehrmann date_created: 2026-09-08T11:31:48Z date_updated: 2026-09-08T11:31:48Z file_id: '22856' file_name: Supplemental video 4.mp4 file_size: 4047831 relation: main_file success: 1 - access_level: open_access checksum: 1e94cd067809e1a93e21676181b4c102 content_type: text/plain creator: aehrmann date_created: 2026-09-08T18:36:14Z date_updated: 2026-09-08T18:36:14Z file_id: '22860' file_name: README.txt file_size: 1122 relation: main_file success: 1 file_date_updated: 2026-09-08T18:36:14Z fulldoi: https://doi.org/10.15479/AT-ISTA-22852 has_accepted_license: '1' keyword: - functional nanostructures - bistability - target behavior - transition pathway license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '09' oa: 1 oa_version: None project: - _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d grant_number: PAT 8537123 name: Functional bio-inspired nanomachines from sticky colloids publisher: Institute of Science and Technology Austria status: public title: Supplemental videos for Designing bistable nanostructures for target behavior tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher _id: '22873' acknowledged_ssus: - _id: ScienComp - _id: CampIT acknowledgement: I acknowledge funding by the Austrian Science Fund (FWF) [10.55776/PAT8537123]. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andreas full_name: Ehrmann, Andreas id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2 last_name: Ehrmann orcid: 0000-0002-0997-5678 citation: ama: 'Ehrmann A. Biological functionality without biochemistry: Designing nanomachines for target behavior. 2026. doi:10.15479/AT-ISTA-22873' apa: 'Ehrmann, A. (2026). Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22873' chicago: 'Ehrmann, Andreas. “Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22873.' ieee: 'A. Ehrmann, “Biological functionality without biochemistry: Designing nanomachines for target behavior,” Institute of Science and Technology Austria, 2026.' ista: 'Ehrmann A. 2026. Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria.' mla: 'Ehrmann, Andreas. Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22873.' short: 'A. Ehrmann, Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior, Institute of Science and Technology Austria, 2026.' corr_author: '1' das_tickbox: '0' date_created: 2026-09-09T12:18:24Z date_published: 2026-09-04T00:00:00Z date_updated: 2026-09-18T11:28:29Z day: '04' ddc: - '530' - '600' - '621' - '004' - '005' degree_awarded: PhD department: - _id: GradSch - _id: CaGo - _id: EdHa doi: 10.15479/AT-ISTA-22873 doi_confirm: '1' file: - access_level: closed checksum: a5e3d79e0e5f3f4fb3c414e48116dc9e content_type: application/pdf creator: aehrmann date_created: 2026-09-11T07:23:57Z date_updated: 2026-09-17T08:59:39Z embargo: 2027-01-15 embargo_to: open_access file_id: '22901' file_name: 2026_Ehrmann_Andreas_Thesis.pdf file_size: 14782662 relation: main_file - access_level: closed checksum: 0235b9c52fee0c97f402f1c3d4efc1eb content_type: application/zip creator: aehrmann date_created: 2026-09-11T07:24:14Z date_updated: 2026-09-11T07:24:14Z description: All LaTeX files to compile my PhD Thesis. file_id: '22902' file_name: thesis_latex_files.zip file_size: 155228 relation: source_file file_date_updated: 2026-09-17T08:59:39Z fulldoi: https://doi.org/10.15479/AT-ISTA-22873 has_accepted_license: '1' keyword: - PhD Thesis - functional nanomachines - biological functionality - nanotechnology - energy delivery - target behavior - dynamics - design principles - optimization - differentiable statistical physics - machine learning language: - iso: eng month: '09' oa_version: Published Version page: '168' project: - _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d grant_number: PAT 8537123 name: Functional bio-inspired nanomachines from sticky colloids publication_identifier: isbn: - 978-3-99078-092-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '22893' relation: part_of_dissertation status: public - id: '22892' relation: part_of_dissertation status: public researchdata_availability: upon request status: public supervisor: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 supplementarymaterial: not applicable title: 'Biological functionality without biochemistry: Designing nanomachines for target behavior' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: green _id: '22893' abstract: - lang: eng text: Many biological machines function through controlled conformational transitions, yet designing synthetic nanostructures with prescribed dynamical behavior remains a major challenge. Here, we develop a modular inverse-design framework for bistable nanostructures whose function is controlled by an energy profile along a geometric reaction coordinate. Inspired by proteins with rigid domains connected by flexible hinges, we introduce a hinge-arm paradigm in which a small bistable hinge controls the energetics of a conformational transition, while rigid arms map this transition onto the separation between external binding sites. Specifically, we ask which features of a target energy profile can be programmed under different design constraints. We find that the energy barriers and the binding-site separations in the two metastable states can be readily designed, while controlling the location of the transition state or the full shape of the energy profile requires additional design freedom. Using a differentiable design framework, we find that some optimized solutions are numerically inexact but still display the functional behavior for which the target profile was selected, emphasizing the importance of function-based evaluation criteria. These results establish a practical hierarchy of designability for bistable nanostructures and provide a route toward synthetic nanomachines that couple conformational transitions to target behavior. 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" article_processing_charge: No arxiv: 1 author: - first_name: Andreas full_name: Ehrmann, Andreas id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2 last_name: Ehrmann orcid: 0000-0002-0997-5678 - first_name: Marija full_name: Krstić, Marija id: a8f6d1c6-3200-11ee-973b-dab948eace26 last_name: Krstić - first_name: Sahar full_name: Samadzadeh, Sahar id: 0099896b-5fb8-11ef-8420-b30b14627e93 last_name: Samadzadeh - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 citation: ama: Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. arXiv. doi:10.48550/arXiv.2606.31620 apa: Ehrmann, A., Krstić, M., Samadzadeh, S., & Goodrich, C. P. (n.d.). Designing bistable nanostructures for target behavior. arXiv. https://doi.org/10.48550/arXiv.2606.31620 chicago: Ehrmann, Andreas, Marija Krstić, Sahar Samadzadeh, and Carl Peter Goodrich. “Designing Bistable Nanostructures for Target Behavior.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2606.31620. ieee: A. Ehrmann, M. Krstić, S. Samadzadeh, and C. P. Goodrich, “Designing bistable nanostructures for target behavior,” arXiv. . ista: Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. arXiv, 10.48550/arXiv.2606.31620. mla: Ehrmann, Andreas, et al. “Designing Bistable Nanostructures for Target Behavior.” ArXiv, doi:10.48550/arXiv.2606.31620. short: A. Ehrmann, M. Krstić, S. Samadzadeh, C.P. Goodrich, ArXiv (n.d.). corr_author: '1' date_created: 2026-09-09T13:19:13Z date_published: 2026-06-30T00:00:00Z date_updated: 2026-09-18T11:28:28Z day: '30' department: - _id: CaGo - _id: EdHa - _id: AnSa doi: 10.48550/arXiv.2606.31620 external_id: arxiv: - '2606.31620' fulldoi: https://doi.org/10.48550/arXiv.2606.31620 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2606.31620 month: '06' oa: 1 oa_version: Preprint project: - _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d grant_number: PAT 8537123 name: Functional bio-inspired nanomachines from sticky colloids publication: arXiv publication_status: draft related_material: record: - id: '22873' relation: dissertation_contains status: public status: public title: Designing bistable nanostructures for target behavior tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository _id: '22892' abstract: - lang: eng text: 'Countless biological processes are fueled by energy-rich molecules like ATP and GTP that supply energy with extreme efficiency. However, designing similar energy-delivery schemes from the bottom up, essential for the development of powered nanostructures and other \emph{de novo} machinery, presents a significant challenge: how can an energy-rich structure be stable in solution yet still deliver this energy at precisely the right time? In this paper, we present a purely physical mechanism that solves this challenge, facilitating energy transfer akin to ATP hydrolysis, yet occurring between synthetic nanostructures without any biochemical interactions. This targeted energy delivery is achieved by exploiting a differentiable state-based model to balance the energy profiles that govern the structural transitions in the two nanostructures, creating a coupled relaxation pathway with minimal barriers that facilitates energy delivery. We verify the effectiveness and robustness of this mechanism through Langevin Dynamics simulations, demonstrating that a bath of the high-energy structures can systematically and repeatedly drive the target structure out of equilibrium, enabling it to perform tasks. As the mechanism operates only through explicit physical forces without any biochemistry or internal state variables, our results present generic and far-reaching design principles, setting the stage for the next generation of synthetic nanomachines.' 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]." article_processing_charge: No arxiv: 1 author: - first_name: Andreas full_name: Ehrmann, Andreas id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2 last_name: Ehrmann orcid: 0000-0002-0997-5678 - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 citation: ama: Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures. arXiv. doi:10.48550/arXiv.2506.14266 apa: Ehrmann, A., & Goodrich, C. P. (n.d.). Controlling energy delivery with bistable nanostructures. arXiv. https://doi.org/10.48550/arXiv.2506.14266 chicago: Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery with Bistable Nanostructures.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2506.14266. ieee: A. Ehrmann and C. P. Goodrich, “Controlling energy delivery with bistable nanostructures,” arXiv. . ista: Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures. arXiv, 10.48550/arXiv.2506.14266. mla: Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery with Bistable Nanostructures.” ArXiv, doi:10.48550/arXiv.2506.14266. short: A. Ehrmann, C.P. Goodrich, ArXiv (n.d.). corr_author: '1' date_created: 2026-09-09T13:16:54Z date_published: 2026-06-07T00:00:00Z date_updated: 2026-09-18T11:28:29Z day: '07' department: - _id: CaGo - _id: EdHa doi: 10.48550/arXiv.2506.14266 external_id: arxiv: - '2506.14266' fulldoi: https://doi.org/10.48550/arXiv.2506.14266 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2506.14266 month: '06' oa: 1 oa_version: Preprint project: - _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d grant_number: PAT 8537123 name: Functional bio-inspired nanomachines from sticky colloids publication: arXiv publication_status: draft related_material: record: - id: '22873' relation: dissertation_contains status: public status: public title: Controlling energy delivery with bistable nanostructures tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository _id: '21423' acknowledged_ssus: - _id: ScienComp acknowledgement: "Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova citation: ama: Dunajova Z. Geometry-driven self-organization of migrating cells and chiral filaments. 2026. doi:10.15479/AT-ISTA-21423 apa: Dunajova, Z. (2026). Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21423 chicago: Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423. ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026. ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria. mla: Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423. short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-03-11T08:30:49Z date_published: 2026-03-11T00:00:00Z date_updated: 2026-09-11T22:30:04Z day: '11' ddc: - '539' - '570' degree_awarded: PhD department: - _id: GradSch - _id: EdHa doi: 10.15479/AT-ISTA-21423 file: - access_level: open_access checksum: 47ce6a48a0c63f28eca6e64c9ffd2c84 content_type: application/pdf creator: zdunajov date_created: 2026-03-12T20:38:52Z date_updated: 2026-09-11T22:30:02Z embargo: 2026-09-11 file_id: '21446' file_name: 2026_Dunajova_Zuzana_Thesis_pdfA.pdf file_size: 14662770 relation: main_file - access_level: closed checksum: 5dec5afdffd47c2b0b162d0fe1bed925 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: zdunajov date_created: 2026-03-12T20:40:18Z date_updated: 2026-09-11T22:30:02Z embargo_to: open_access file_id: '21447' file_name: Thesis-Dunajova_source_file.docx file_size: 32961408 relation: source_file file_date_updated: 2026-09-11T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-21423 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '110' project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication_identifier: isbn: - 978-3-99078-076-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: part_of_dissertation status: public - id: '13116' relation: research_data status: public - id: '21439' relation: research_data status: public - id: '21427' relation: part_of_dissertation status: public status: public supervisor: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Geometry-driven self-organization of migrating cells and chiral filaments tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: free access _id: '21439' abstract: - lang: eng 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. acknowledged_ssus: - _id: Bio - _id: ScienComp article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova citation: ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:10.15479/AT-ISTA-21439 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. https://doi.org/10.15479/AT-ISTA-21439 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. https://doi.org/10.15479/AT-ISTA-21439. 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. 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, 10.15479/AT-ISTA-21439. mla: Dunajova, Zuzana. Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21439. short: Z. Dunajova, (2026). contributor: - contributor_type: researcher first_name: Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - contributor_type: researcher first_name: Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' corr_author: '1' date_created: 2026-03-11T21:05:20Z date_published: 2026-03-12T00:00:00Z date_updated: 2026-09-19T22:30:08Z day: '12' ddc: - '570' department: - _id: GradSch - _id: EdHa doi: 10.15479/AT-ISTA-21439 file: - access_level: open_access checksum: 47809a9a31b748b16e21e92d11ddc87f content_type: application/zip creator: zdunajov date_created: 2026-03-11T20:41:28Z date_updated: 2026-03-11T20:41:28Z file_id: '21440' file_name: Supplementary_movies_Thesis_Dunajova.zip file_size: 154465214 relation: main_file success: 1 - access_level: open_access checksum: a64a174bc6abf0a5e77631e4fd121f1f content_type: text/plain creator: zdunajov date_created: 2026-03-11T20:52:39Z date_updated: 2026-03-11T20:52:39Z file_id: '21441' file_name: readme.txt file_size: 2289 relation: main_file success: 1 file_date_updated: 2026-03-11T20:52:39Z fulldoi: https://doi.org/10.15479/AT-ISTA-21439 has_accepted_license: '1' month: '03' oa: 1 oa_version: Published Version project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: used_in_publication status: public - id: '21427' relation: used_in_publication status: public - id: '21423' relation: used_in_publication status: public status: public title: Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21235' 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. 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.)." article_number: '033010' article_processing_charge: Yes article_type: original author: - first_name: Valerio full_name: Sorichetti, Valerio id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b last_name: Sorichetti orcid: 0000-0002-9645-6576 - first_name: Paul full_name: Robin, Paul id: 48c58128-57b0-11ee-9095-dc28fd97fc1d last_name: Robin orcid: 0000-0002-5728-9189 - first_name: Ivan full_name: Palaia, Ivan id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa last_name: Palaia orcid: ' 0000-0002-8843-9485 ' - first_name: Alberto full_name: Hernandez-Armendariz, Alberto last_name: Hernandez-Armendariz - first_name: Sara full_name: Cuylen-Haering, Sara last_name: Cuylen-Haering - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Sorichetti V, Robin P, Palaia I, Hernandez-Armendariz A, Cuylen-Haering S, Šarić A. Charge distribution of the coating brush drives interchromosome attraction. PRX Life. 2025;3(3). doi:10.1103/41fd-r847 apa: 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. American Physical Society. https://doi.org/10.1103/41fd-r847 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.” PRX Life. American Physical Society, 2025. https://doi.org/10.1103/41fd-r847. 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,” PRX Life, vol. 3, no. 3. American Physical Society, 2025. 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. mla: Sorichetti, Valerio, et al. “Charge Distribution of the Coating Brush Drives Interchromosome Attraction.” PRX Life, vol. 3, no. 3, 033010, American Physical Society, 2025, doi:10.1103/41fd-r847. short: V. Sorichetti, P. Robin, I. Palaia, A. Hernandez-Armendariz, S. Cuylen-Haering, A. Šarić, PRX Life 3 (2025). corr_author: '1' date_created: 2026-02-16T14:50:32Z date_published: 2025-08-11T00:00:00Z date_updated: 2026-02-17T11:16:26Z day: '11' ddc: - '570' department: - _id: AnSa - _id: EdHa doi: 10.1103/41fd-r847 ec_funded: 1 file: - access_level: open_access checksum: 1702b9bdbfd902a7c08aa4f1479b390d content_type: application/pdf creator: dernst date_created: 2026-02-17T11:12:30Z date_updated: 2026-02-17T11:12:30Z file_id: '21287' file_name: 2025_PRXLife_Sorichetti.pdf file_size: 3732843 relation: main_file success: 1 file_date_updated: 2026-02-17T11:12:30Z fulldoi: https://doi.org/10.1103/41fd-r847 has_accepted_license: '1' intvolume: ' 3' issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 349b6ff1-11ca-11ed-8bc3-f006047c2eeb name: EMBO Young Investigator Program - Andela Saric publication: PRX Life publication_identifier: eissn: - 2835-8279 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Charge distribution of the coating brush drives interchromosome attraction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21236' abstract: - lang: eng text: 'The migration behavior of colliding cells is critically determined by transient contact interactions. During these interactions, the motility machinery, including the front-rear polarization of the cell, dynamically responds to surface protein-mediated transmission of forces and biochemical signals between cells. While biomolecular details of such contact interactions are increasingly well understood, it remains unclear what biophysical interaction mechanisms govern the cell-level dynamics of colliding cells and how these mechanisms vary across cell types. Here we develop a phenomenological theory based on 14 candidate contact-interaction mechanisms coupling cell position, protrusion, and polarity. Using high-throughput micropattern experiments, we detect which of these phenomenological contact interactions captures the interaction behaviors of cells. We find that various cell types—ranging from mesenchymal to epithelial cells—are accurately captured by a single model with only two interaction mechanisms: polarity-protrusion coupling and polarity-polarity coupling. Remarkably, the qualitatively different interaction behaviors of distinct cells, as well as cells subject to molecular perturbations of surface protein-mediated signaling, can all be quantitatively captured by varying the strength and sign of the polarity-polarity coupling mechanism. Altogether, our data-driven phenomenological theory of cell-cell interactions reveals polarity-polarity coupling as a versatile and general contact-interaction mechanism, which may underlie diverse collective migration behaviors of motile cells.' 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). article_number: '033015' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Tom full_name: Brandstätter, Tom last_name: Brandstätter - first_name: Emily full_name: Brieger, Emily last_name: Brieger - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Georg full_name: Ladurner, Georg last_name: Ladurner - first_name: Joachim O. full_name: Rädler, Joachim O. last_name: Rädler - first_name: Chase P. full_name: Broedersz, Chase P. last_name: Broedersz citation: 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. PRX Life. 2025;3(3). doi:10.1103/3hhj-rt1n apa: Brandstätter, T., Brieger, E., Brückner, D., Ladurner, G., Rädler, J. O., & Broedersz, C. P. (2025). Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. PRX Life. American Physical Society. https://doi.org/10.1103/3hhj-rt1n 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.” PRX Life. American Physical Society, 2025. https://doi.org/10.1103/3hhj-rt1n. 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,” PRX Life, vol. 3, no. 3. American Physical Society, 2025. ista: Brandstätter T, Brieger E, Brückner D, Ladurner G, Rädler JO, Broedersz CP. 2025. Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. PRX Life. 3(3), 033015. mla: Brandstätter, Tom, et al. “Data-Driven Theory Reveals Protrusion and Polarity Interactions Governing Collision Behavior of Distinct Motile Cells.” PRX Life, vol. 3, no. 3, 033015, American Physical Society, 2025, doi:10.1103/3hhj-rt1n. short: T. Brandstätter, E. Brieger, D. Brückner, G. Ladurner, J.O. Rädler, C.P. Broedersz, PRX Life 3 (2025). date_created: 2026-02-16T14:52:02Z date_published: 2025-08-26T00:00:00Z date_updated: 2026-02-17T11:20:20Z day: '26' ddc: - '570' department: - _id: EdHa doi: 10.1103/3hhj-rt1n external_id: arxiv: - '2407.17268' file: - access_level: open_access checksum: 70c067ceef3a8262d9c430e85e3ba9ec content_type: application/pdf creator: dernst date_created: 2026-02-17T11:18:18Z date_updated: 2026-02-17T11:18:18Z file_id: '21288' file_name: 2025_PRXLife_Brandstaetter.pdf file_size: 9366716 relation: main_file success: 1 file_date_updated: 2026-02-17T11:18:18Z fulldoi: https://doi.org/10.1103/3hhj-rt1n has_accepted_license: '1' intvolume: ' 3' issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: PRX Life publication_identifier: eissn: - 2835-8279 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2025' ... --- OA_type: closed access _id: '18960' abstract: - lang: eng text: The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter. acknowledgement: We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg for a critical reading of the manuscript and Claudia Flandoli for the artwork in the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from the European Research Council (ERC) under the European Union\u2019s Horizon 2020 Research and Innovation Programme Grant Agreement no. 851288. article_number: a041653 article_processing_charge: No article_type: original author: - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: 'Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 2025;17(4). doi:10.1101/cshperspect.a041653' apa: 'Brückner, D., & Hannezo, E. B. (2025). Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a041653' chicago: 'Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press, 2025. https://doi.org/10.1101/cshperspect.a041653.' ieee: 'D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics and signaling into dynamical models,” Cold Spring Harbor Perspectives in Biology, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.' ista: 'Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 17(4), a041653.' mla: 'Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives in Biology, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press, 2025, doi:10.1101/cshperspect.a041653.' short: D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17 (2025). corr_author: '1' date_created: 2025-01-29T13:33:47Z date_published: 2025-04-01T00:00:00Z date_updated: 2025-12-30T07:08:34Z day: '01' department: - _id: EdHa doi: 10.1101/cshperspect.a041653 ec_funded: 1 external_id: isi: - '001456660400001' pmid: - '38951023' fulldoi: https://doi.org/10.1101/cshperspect.a041653 intvolume: ' 17' isi: 1 issue: '4' language: - iso: eng month: '04' oa_version: None pmid: 1 project: - _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b grant_number: ALTF 343-2022 name: A mechano-chemical theory for stem cell fate decisions in organoid development - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Cold Spring Harbor Perspectives in Biology publication_identifier: issn: - 1943-0264 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: 'Tissue active matter: Integrating mechanics and signaling into dynamical models' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19279' 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. 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. article_number: '064703' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Damien full_name: Toquer, Damien last_name: Toquer - first_name: Lydéric full_name: Bocquet, Lydéric last_name: Bocquet - first_name: Paul full_name: Robin, Paul id: 48c58128-57b0-11ee-9095-dc28fd97fc1d last_name: Robin orcid: 0000-0002-5728-9189 citation: ama: Toquer D, Bocquet L, Robin P. Ionic association and Wien effect in 2D confined electrolytes. Journal of Chemical Physics. 2025;162(6). doi:10.1063/5.0241949 apa: Toquer, D., Bocquet, L., & Robin, P. (2025). Ionic association and Wien effect in 2D confined electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0241949 chicago: Toquer, Damien, Lydéric Bocquet, and Paul Robin. “Ionic Association and Wien Effect in 2D Confined Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2025. https://doi.org/10.1063/5.0241949. ieee: D. Toquer, L. Bocquet, and P. Robin, “Ionic association and Wien effect in 2D confined electrolytes,” Journal of Chemical Physics, vol. 162, no. 6. AIP Publishing, 2025. ista: Toquer D, Bocquet L, Robin P. 2025. Ionic association and Wien effect in 2D confined electrolytes. Journal of Chemical Physics. 162(6), 064703. mla: Toquer, Damien, et al. “Ionic Association and Wien Effect in 2D Confined Electrolytes.” Journal of Chemical Physics, vol. 162, no. 6, 064703, AIP Publishing, 2025, doi:10.1063/5.0241949. short: D. Toquer, L. Bocquet, P. Robin, Journal of Chemical Physics 162 (2025). corr_author: '1' date_created: 2025-03-02T23:01:52Z date_published: 2025-02-14T00:00:00Z date_updated: 2025-09-30T10:44:48Z day: '14' ddc: - '540' department: - _id: EdHa doi: 10.1063/5.0241949 ec_funded: 1 external_id: arxiv: - '2410.03316' isi: - '001421300300001' pmid: - '39932241' file: - access_level: open_access checksum: c9008c2c50c917673aa588f75acbcb40 content_type: application/pdf creator: dernst date_created: 2025-03-04T10:29:36Z date_updated: 2025-03-04T10:29:36Z file_id: '19290' file_name: 2025_JourChemicalPhysics_Toquer.pdf file_size: 5807062 relation: main_file success: 1 file_date_updated: 2025-03-04T10:29:36Z fulldoi: https://doi.org/10.1063/5.0241949 has_accepted_license: '1' intvolume: ' 162' isi: 1 issue: '6' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Ionic association and Wien effect in 2D confined electrolytes tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 162 year: '2025' ...