--- 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 has_accepted_license: '1' intvolume: ' 3' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ 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 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_place: repository _id: '21427' abstract: - lang: eng text: While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo. acknowledgement: "European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360" article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Erik full_name: Sahai, Erik last_name: Sahai - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - 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: Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. doi:10.1101/2025.05.20.655037 apa: Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., & Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv. https://doi.org/10.1101/2025.05.20.655037 chicago: Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” bioRxiv, n.d. https://doi.org/10.1101/2025.05.20.655037. ieee: Z. Dunajova et al., “Substrate heterogeneity promotes cancer cell dissemination through interface roughening.” bioRxiv. ista: Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. 10.1101/2025.05.20.655037. mla: Dunajova, Zuzana, et al. Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening. bioRxiv, doi:10.1101/2025.05.20.655037. short: Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, (n.d.). corr_author: '1' date_created: 2026-03-11T08:40:06Z date_published: 2025-09-25T00:00:00Z date_updated: 2026-03-18T14:11:35Z day: '25' ddc: - '539' - '570' department: - _id: GradSch - _id: EdHa - _id: MiSi - _id: NanoFab - _id: AnSa doi: 10.1101/2025.05.20.655037 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.20.655037 month: '09' oa: 1 oa_version: Preprint project: - _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd grant_number: '101071793' name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces' - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication_status: draft publisher: bioRxiv related_material: record: - id: '21423' relation: dissertation_contains status: public - id: '21439' relation: research_data status: public status: public title: Substrate heterogeneity promotes cancer cell dissemination through interface roughening 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: '2025' ... --- OA_place: publisher _id: '20441' abstract: - lang: eng text: "Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium." acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences." alternative_title: - ISTA Thesis 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. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:10.15479/AT-ISTA-20441 apa: Naik, S. (2025). Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20441 chicago: Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20441. ieee: S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025. ista: Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria. mla: Naik, Suyash. Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20441. short: S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-10T14:58:30Z date_published: 2025-10-12T00:00:00Z date_updated: 2026-04-07T11:58:57Z day: '12' ddc: - '596' - '597' - '532' degree_awarded: PhD department: - _id: GradSch - _id: CaHe - _id: EdHa doi: 10.15479/AT-ISTA-20441 file: - access_level: open_access checksum: 2892f04d4a5c18677871c3e06ac1244a content_type: application/pdf creator: snaik date_created: 2025-10-28T13:10:08Z date_updated: 2025-10-28T13:10:08Z file_id: '20567' file_name: Thesis_PDFA_.pdf file_size: 6846189 relation: main_file success: 1 - access_level: open_access checksum: 15934d4465cd0e9b7c32678da9a33a2f content_type: application/zip creator: snaik date_created: 2025-10-28T13:10:26Z date_updated: 2025-10-28T13:10:26Z file_id: '20568' file_name: Thesis.zip file_size: 8839300 relation: source_file file_date_updated: 2025-10-28T13:10:26Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '10' oa: 1 oa_version: Published Version page: '105' project: - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 25AA5F24-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W 1250-B20 name: Nano-Analytics of Cellular Systems publication_identifier: isbn: - 978-3-99078-069-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20465' relation: part_of_dissertation status: public status: public supervisor: - 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 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Keratins act as global coordinators of tissue spreading through mechanosensitive feedback 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: repository _id: '20465' abstract: - lang: eng text: For tissues to spread, they must be deformable while maintaining their structural integrity. How these opposing requirements are balanced within spreading tissues is not yet well understood. Here, we show that keratin intermediate filaments function in epithelial spreading by adapting tissue mechanical resilience to the stresses arising in the tissue during the spreading process. By analysing the expansion of the enveloping cell layer (EVL) over the large yolk cell in early zebrafish embryos in vivo, we found 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, which is essential for preventing tissue rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the force-generating processes pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production in the yolk cell and the mechanical resilience of the EVL against stresses generated by these pulling forces, thereby ensuring uniform and robust tissue spreading. 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 - 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. bioRxiv. doi:10.1101/2025.02.14.638262 apa: Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., & Heisenberg, C.-P. J. (n.d.). Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.02.14.638262 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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2025.02.14.638262. 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,” bioRxiv. Cold Spring Harbor Laboratory. ista: 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. bioRxiv, 10.1101/2025.02.14.638262. mla: Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2025.02.14.638262. short: S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, BioRxiv (n.d.). corr_author: '1' date_created: 2025-10-14T07:25:27Z date_published: 2025-02-17T00:00:00Z date_updated: 2026-04-07T11:58:57Z day: '17' department: - _id: CaHe - _id: EdHa doi: 10.1101/2025.02.14.638262 language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.02.14.638262 month: '02' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: draft publisher: Cold Spring Harbor Laboratory related_material: record: - id: '20441' relation: dissertation_contains status: public status: public title: Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20393' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi orcid: 0000-0001-6060-4795 citation: ama: Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:10.15479/AT-ISTA-20393 apa: Kishi, K. (2025). Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20393 chicago: Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20393. ieee: K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025. ista: Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria. mla: Kishi, Kasumi. Regulation of Notochord and Floor Plate Size during Mouse Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20393. short: K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-25T10:08:10Z date_published: 2025-09-24T00:00:00Z date_updated: 2026-04-14T09:50:52Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi - _id: EdHa doi: 10.15479/AT-ISTA-20393 file: - access_level: closed checksum: 6bb5a7ce318dc3f7bd165f2523e77b89 content_type: application/x-zip-compressed creator: kkishi date_created: 2025-09-30T14:33:17Z date_updated: 2025-10-01T11:54:41Z file_id: '20413' file_name: 2025-Kishi-Kasumi-Thesis.zip file_size: 41847994 relation: source_file - access_level: closed checksum: 88349b9177e1dcbe1242cd3884b36fdb content_type: application/pdf creator: kkishi date_created: 2025-09-30T14:33:22Z date_updated: 2025-10-02T07:51:21Z embargo: 2026-09-30 embargo_to: open_access file_id: '20414' file_name: 2025-Kishi-Kasumi-Thesis.pdf file_size: 55747072 relation: main_file file_date_updated: 2025-10-02T07:51:21Z has_accepted_license: '1' language: - iso: eng month: '09' oa_version: Published Version page: '102' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18481' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Regulation of notochord and floor plate size during mouse development 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19670' abstract: - lang: eng text: “Pasta alla Cacio e pepe” is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. In this study, we systematically explore the phase behavior of Cacio e pepe sauce, focusing on its stability at increasing temperatures for various proportions of cheese, water, and starch. We identify starch concentration as the key factor influencing sauce stability, with direct implications for practical cooking. Specifically, we delineate a regime where starch concentrations below 1% (relative to cheese mass) lead to the formation of system-wide clumps, a condition determining what we term the “Mozzarella Phase” and corresponding to an unpleasant and separated sauce. Additionally, we examine the impact of cheese concentration relative to water at a fixed starch level, observing a lower critical solution temperature that we theoretically rationalized by means of a minimal effective free-energy model. We further analyze the effect of a less traditional stabilizer, trisodium citrate, and observe a sharp transition from the Mozzarella Phase to a completely smooth and stable sauce, in contrast to starch-stabilized mixtures, where the transition is more gradual. Finally, we present a scientifically optimized recipe based on our findings, enabling a consistently flawless execution of this classic dish. acknowledgement: he authors thank Frank Jülicher, for supporting the initiative and stimulating discussions. We thank Tetsuya Spippayashi for enlightening clarifications on the historical origins of Cacio e pepe and Giuseppe Ricchitelli for helping with the construction of the experimental apparatus. We further thank Martina Gaiba, Alessandro Gaiba, John D. Treado, Virginia Lepore, Eleonora Nanu, Julia Kirsch, Lara Koehler, Burak Budanur, Irina Pi-Jaumà, Elizabeth Brückner, M.J. Franco Oñate, Giorgio Nicoletti, and Marco Salvalaglio for their support and for eating up the sample leftovers. Finally, we thank Simone Frau for taking the photograph in Fig. 1(a). article_number: '044122' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: G. full_name: Bartolucci, G. last_name: Bartolucci - first_name: D. M. full_name: Busiello, D. M. last_name: Busiello - first_name: M. full_name: Ciarchi, M. last_name: Ciarchi - first_name: A. full_name: Corticelli, A. last_name: Corticelli - first_name: I. full_name: Di Terlizzi, I. last_name: Di Terlizzi - first_name: Fabrizio full_name: Olmeda, Fabrizio id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689 last_name: Olmeda - first_name: D. full_name: Revignas, D. last_name: Revignas - first_name: V. M. full_name: Schimmenti, V. M. last_name: Schimmenti citation: ama: Bartolucci G, Busiello DM, Ciarchi M, et al. Phase behavior of Cacio e Pepe sauce. Physics of Fluids. 2025;37(4). doi:10.1063/5.0255841 apa: Bartolucci, G., Busiello, D. M., Ciarchi, M., Corticelli, A., Di Terlizzi, I., Olmeda, F., … Schimmenti, V. M. (2025). Phase behavior of Cacio e Pepe sauce. Physics of Fluids. AIP Publishing. https://doi.org/10.1063/5.0255841 chicago: Bartolucci, G., D. M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, Fabrizio Olmeda, D. Revignas, and V. M. Schimmenti. “Phase Behavior of Cacio e Pepe Sauce.” Physics of Fluids. AIP Publishing, 2025. https://doi.org/10.1063/5.0255841. ieee: G. Bartolucci et al., “Phase behavior of Cacio e Pepe sauce,” Physics of Fluids, vol. 37, no. 4. AIP Publishing, 2025. ista: Bartolucci G, Busiello DM, Ciarchi M, Corticelli A, Di Terlizzi I, Olmeda F, Revignas D, Schimmenti VM. 2025. Phase behavior of Cacio e Pepe sauce. Physics of Fluids. 37(4), 044122. mla: Bartolucci, G., et al. “Phase Behavior of Cacio e Pepe Sauce.” Physics of Fluids, vol. 37, no. 4, 044122, AIP Publishing, 2025, doi:10.1063/5.0255841. short: G. Bartolucci, D.M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, F. Olmeda, D. Revignas, V.M. Schimmenti, Physics of Fluids 37 (2025). date_created: 2025-05-11T22:02:40Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-04-28T13:24:53Z day: '01' ddc: - '530' department: - _id: EdHa doi: 10.1063/5.0255841 external_id: arxiv: - '2501.00536' isi: - '001482986200001' file: - access_level: open_access checksum: 242d05898aa0a2348b9c108747adb5ce content_type: application/pdf creator: dernst date_created: 2025-05-12T09:31:22Z date_updated: 2025-05-12T09:31:22Z file_id: '19681' file_name: 2025_PhysicsFluids_Bartolucci.pdf file_size: 4926853 relation: main_file success: 1 file_date_updated: 2025-05-12T09:31:22Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Physics of Fluids publication_identifier: eissn: - 1089-7666 issn: - 1070-6631 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: link: - description: News on ISTA relation: press_release url: https://ista.ac.at/en/news/2025-ig-nobel-prize-for-perfect-pasta-sauce/ scopus_import: '1' status: public title: Phase behavior of Cacio e Pepe sauce 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: 37 year: '2025' ... --- APC_amount: 3642,79 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20080' abstract: - lang: eng text: "Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: E-Lib acknowledgement: "The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler for the efforts to establish immunodetection method." article_number: '1612366' article_processing_charge: Yes article_type: original author: - first_name: Marçal full_name: Gallemi, Marçal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi orcid: 0000-0003-4675-6893 - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Nikola full_name: Zarevski, Nikola id: 18e95355-e05a-11ea-a9c0-8fba1b89e83a last_name: Zarevski - first_name: Jan full_name: Pribyl, Jan last_name: Pribyl - first_name: Petr full_name: Skládal, Petr last_name: Skládal - 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: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 2025;16. doi:10.3389/fpls.2025.1612366 apa: Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P., Hannezo, E. B., & Benková, E. (2025). Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. Frontiers Media. https://doi.org/10.3389/fpls.2025.1612366 chicago: Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl, Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” Frontiers in Plant Science. Frontiers Media, 2025. https://doi.org/10.3389/fpls.2025.1612366. ieee: M. Gallemi et al., “Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties,” Frontiers in Plant Science, vol. 16. Frontiers Media, 2025. ista: Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB, Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366. mla: Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” Frontiers in Plant Science, vol. 16, 1612366, Frontiers Media, 2025, doi:10.3389/fpls.2025.1612366. short: M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025). corr_author: '1' date_created: 2025-07-27T22:01:26Z date_published: 2025-07-04T00:00:00Z date_updated: 2026-05-20T07:53:03Z day: '04' ddc: - '580' department: - _id: EdHa - _id: EvBe - _id: CaGu doi: 10.3389/fpls.2025.1612366 ec_funded: 1 external_id: isi: - '001530690900001' pmid: - '40688689' file: - access_level: open_access checksum: 9e6b8b53ba56d4a24a9bd91cf6d2dc58 content_type: application/pdf creator: dernst date_created: 2025-07-31T07:28:54Z date_updated: 2025-07-31T07:28:54Z file_id: '20093' file_name: 2025_FrontiersPlantSc_Gallemi.pdf file_size: 3665187 relation: main_file success: 1 file_date_updated: 2025-07-31T07:28:54Z has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Frontiers in Plant Science publication_identifier: eissn: - 1664-462X publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical 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: 16 year: '2025' ... --- APC_amount: 5766,07 EUR OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20289' abstract: - lang: eng text: Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally directed by self-generated signaling gradients rather than long-range, prepatterned cues. However, how heterogeneous mixtures of cells interact nonreciprocally and navigate through self-generated gradients remains largely unexplored. Here, we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that the relative chemotactic sensitivities of different cell populations control their long-time coupling and comigration dynamics, with boundary conditions such as external cell and attractant reservoirs substantially influencing the migration patterns. Our model predicts an optimal parameter regime that enables robust and colocalized migration. We test our theoretical predictions with in vitro experiments demonstrating the comigration of distinct immune cell populations, and quantitatively reproduce observed migration patterns under wild-type and perturbed conditions. Interestingly, immune cell comigration occurs close to the predicted optimal regime. Finally, we incorporate mechanical interactions into our framework, revealing a nontrivial interplay between chemotactic and mechanical nonreciprocity in driving collective migration. Together, our findings suggest that self-generated chemotaxis is a robust strategy for the navigation of mixed cell populations. acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc - _id: NanoFab acknowledgement: We thank all members of the M.S. and E.H. groups for stimulating discussions.We thank the Imaging and Optics facility, the Pre-clinical and Lab Support facility of the Institute of Science and Technology Austria for their excellent support and provided resources for the experimental research. In particular, we thank Jack Merrin from the Nanofabrication facility who generated the microfabricated channel used in this study. This work received funding fromt he European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 851288 to E.H.). M.C.U.is funded by a University of Sheffield Strategic Research Fellowship in the Physics of Life and Quantitative Biology. article_number: e2504064122 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Alsberga full_name: Zane, Alsberga id: 60f7509a-f652-11ea-9d86-b963d6490d7c last_name: Zane orcid: 0009-0003-0415-7603 - first_name: Jonna H full_name: Alanko, Jonna H id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87 last_name: Alanko orcid: 0000-0002-7698-3061 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - 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: Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. Self-generated chemotaxis of mixed cell populations. Proceedings of the National Academy of Sciences. 2025;122(34). doi:10.1073/pnas.2504064122 apa: Ucar, M. C., Zane, A., Alanko, J. H., Sixt, M. K., & Hannezo, E. B. (2025). Self-generated chemotaxis of mixed cell populations. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2504064122 chicago: Ucar, Mehmet C, Alsberga Zane, Jonna H Alanko, Michael K Sixt, and Edouard B Hannezo. “Self-Generated Chemotaxis of Mixed Cell Populations.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2504064122. ieee: M. C. Ucar, A. Zane, J. H. Alanko, M. K. Sixt, and E. B. Hannezo, “Self-generated chemotaxis of mixed cell populations,” Proceedings of the National Academy of Sciences, vol. 122, no. 34. National Academy of Sciences, 2025. ista: Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. 2025. Self-generated chemotaxis of mixed cell populations. Proceedings of the National Academy of Sciences. 122(34), e2504064122. mla: Ucar, Mehmet C., et al. “Self-Generated Chemotaxis of Mixed Cell Populations.” Proceedings of the National Academy of Sciences, vol. 122, no. 34, e2504064122, National Academy of Sciences, 2025, doi:10.1073/pnas.2504064122. short: M.C. Ucar, A. Zane, J.H. Alanko, M.K. Sixt, E.B. Hannezo, Proceedings of the National Academy of Sciences 122 (2025). corr_author: '1' date_created: 2025-09-07T22:01:32Z date_published: 2025-08-26T00:00:00Z date_updated: 2026-05-20T08:59:54Z day: '26' ddc: - '570' department: - _id: EdHa - _id: MiSi doi: 10.1073/pnas.2504064122 ec_funded: 1 external_id: isi: - '001562181600001' pmid: - '40838890' file: - access_level: open_access checksum: b36abd92673b6d76376fc9434bad52cc content_type: application/pdf creator: dernst date_created: 2025-09-08T07:23:29Z date_updated: 2025-09-08T07:23:29Z file_id: '20307' file_name: 2025_PNAS_Ucar.pdf file_size: 16069140 relation: main_file success: 1 file_date_updated: 2025-09-08T07:23:29Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '34' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/mehmetcanucar/Self-generated-chemotaxis scopus_import: '1' status: public title: Self-generated chemotaxis of mixed cell populations 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: 122 year: '2025' ... --- APC_amount: 7068 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '20424' abstract: - lang: eng text: Homeostasis relies on a precise balance of fate choices between renewal and differentiation. Although progress has been done to characterize the dynamics of single-cell fate choices, their underlying mechanistic basis often remains unclear. Concentrating on skin epidermis as a paradigm for multilayered tissues with complex fate choices, we develop a 3D vertex-based model with proliferation in the basal layer, showing that mechanical competition for space naturally gives rise to homeostasis and neutral drift dynamics that are seen experimentally. We then explore the effect of introducing mechanical heterogeneities between cellular subpopulations. We uncover that relatively small tension heterogeneities, reflected by distinct morphological changes in single-cell shapes, can be sufficient to heavily tilt cellular dynamics towards exponential growth. We thus derive a master relationship between cell shape and long-term clonal dynamics, which we validated during basal cell carcinoma initiation in mouse epidermis. Altogether, we propose a theoretical framework to link mechanical forces, quantitative cellular morphologies and cellular fate outcomes in complex tissues. acknowledged_ssus: - _id: Bio acknowledgement: We thank Alois Schlögl, Paula Sanematsu, Susana Moreno Flores, Bernat Corominas-Murtra, Stefania Tavano, Gayathri Singharaju, and Hannezo group members for helpful discussions, the Bioimaging facility at ISTA, as well as Matthias Merkel and Lisa Manning for sharing the 3D Voronoi code. We also thank the Champalimaud animal facility, Anna Pezzarossa and the Champalimaud ABBE platform for the help with microscopy and image processing. This work was supported by EMBO (ALTF 522-2021), a Fundação para a Ciência e Tecnologia grant to A.S.D. (PTDC/MED-ONC/5553/2020), as well as the European Research Council (grant 851288 to EH). A.S.D., S.C., and R.M.S. are supported by QuantOCancer Project Horizon European Union’s Horizon 2020 program (grant agreement No 810653). article_number: '8440' article_processing_charge: Yes article_type: original author: - first_name: Preeti full_name: Sahu, Preeti id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E last_name: Sahu - first_name: Sara full_name: Monteiro-Ferreira, Sara last_name: Monteiro-Ferreira - first_name: Sara full_name: Canato, Sara last_name: Canato - first_name: Raquel Maia full_name: Soares, Raquel Maia last_name: Soares - first_name: Adriana full_name: Sánchez-Danés, Adriana last_name: Sánchez-Danés - 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: Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo EB. Mechanical control of cell fate decisions in the skin epidermis. Nature Communications. 2025;16. doi:10.1038/s41467-025-62882-9 apa: Sahu, P., Monteiro-Ferreira, S., Canato, S., Soares, R. M., Sánchez-Danés, A., & Hannezo, E. B. (2025). Mechanical control of cell fate decisions in the skin epidermis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-62882-9 chicago: Sahu, Preeti, Sara Monteiro-Ferreira, Sara Canato, Raquel Maia Soares, Adriana Sánchez-Danés, and Edouard B Hannezo. “Mechanical Control of Cell Fate Decisions in the Skin Epidermis.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-62882-9. ieee: P. Sahu, S. Monteiro-Ferreira, S. Canato, R. M. Soares, A. Sánchez-Danés, and E. B. Hannezo, “Mechanical control of cell fate decisions in the skin epidermis,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo EB. 2025. Mechanical control of cell fate decisions in the skin epidermis. Nature Communications. 16, 8440. mla: Sahu, Preeti, et al. “Mechanical Control of Cell Fate Decisions in the Skin Epidermis.” Nature Communications, vol. 16, 8440, Springer Nature, 2025, doi:10.1038/s41467-025-62882-9. short: P. Sahu, S. Monteiro-Ferreira, S. Canato, R.M. Soares, A. Sánchez-Danés, E.B. Hannezo, Nature Communications 16 (2025). corr_author: '1' date_created: 2025-10-05T22:01:34Z date_published: 2025-09-26T00:00:00Z date_updated: 2026-05-20T08:52:01Z day: '26' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41467-025-62882-9 ec_funded: 1 external_id: isi: - '001582555200011' pmid: - '41006218' file: - access_level: open_access checksum: d1656576883b23902545328e2d640234 content_type: application/pdf creator: dernst date_created: 2025-10-13T12:37:04Z date_updated: 2025-10-13T12:37:04Z file_id: '20464' file_name: 2025_NatureComm_Sahu.pdf file_size: 2816813 relation: main_file success: 1 file_date_updated: 2025-10-13T12:37:04Z has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 628f3fb1-2b32-11ec-9570-83ce778803f7 grant_number: ALTF 522-2021 name: Biomechanics of stem cell fate determination - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mechanical control of cell fate decisions in the skin epidermis 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- APC_amount: 4695,11 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20708' abstract: - lang: eng text: In equilibrium, the physical properties of matter are set by the interactions between the constituents. In contrast, the energy input of the individual components controls the behavior of synthetic or living active matter. Great progress has been made in understanding the emergent phenomena in active fluids, though their inability to resist shear forces hinders their practical use. This motivates the exploration of active solids as shape-shifting materials, yet, we lack controlled synthetic systems to devise active solids with unconventional properties. Here we build active elastic beams from dozens of active colloids and unveil complex emergent behaviors such as self-oscillations or persistent rotations. Developing tensile tests at the microscale, we show that the active beams are ultrasoft materials, with large (nonequilibrium) fluctuations. Combining experiments, theory, and stochastic inference, we show that the dynamics of the active beams can be mapped on different phase transitions which are tuned by boundary conditions. More quantitatively, we assess all relevant parameters by independent measurements or first-principles calculations, and find that our theoretical description agrees with the experimental observations. Our results demonstrate that the simple addition of activity to an elastic beam unveils novel physics and can inspire design strategies for active solids and functional microscopic machines. acknowledgement: The authors thank Andela Saric, Christoph Zechner, and Paul Robin for helpful discussions. J. P. acknowledges support by ERC grant (VULCAN, 101086998) and U.S. ARO under Award No. W911NF2310008. Y. I. L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. article_number: '041017' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Quentin full_name: Martinet, Quentin id: b37485a8-d343-11eb-a0e9-df8c484ef8ab last_name: Martinet orcid: 0000-0002-2916-6632 - first_name: Yuting I full_name: Li, Yuting I id: ee7a5ca8-8b71-11ed-b662-b3341c05b7eb last_name: Li - first_name: A. full_name: Aubret, A. last_name: Aubret - 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: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. Emergent dynamics of active elastic microbeams. Physical Review X. 2025;15(4). doi:10.1103/rjk2-q2wh apa: Martinet, Q., Li, Y. I., Aubret, A., Hannezo, E. B., & Palacci, J. A. (2025). Emergent dynamics of active elastic microbeams. Physical Review X. American Physical Society. https://doi.org/10.1103/rjk2-q2wh chicago: Martinet, Quentin, Yuting I Li, A. Aubret, Edouard B Hannezo, and Jérémie A Palacci. “Emergent Dynamics of Active Elastic Microbeams.” Physical Review X. American Physical Society, 2025. https://doi.org/10.1103/rjk2-q2wh. ieee: Q. Martinet, Y. I. Li, A. Aubret, E. B. Hannezo, and J. A. Palacci, “Emergent dynamics of active elastic microbeams,” Physical Review X, vol. 15, no. 4. American Physical Society, 2025. ista: Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. 2025. Emergent dynamics of active elastic microbeams. Physical Review X. 15(4), 041017. mla: Martinet, Quentin, et al. “Emergent Dynamics of Active Elastic Microbeams.” Physical Review X, vol. 15, no. 4, 041017, American Physical Society, 2025, doi:10.1103/rjk2-q2wh. short: Q. Martinet, Y.I. Li, A. Aubret, E.B. Hannezo, J.A. Palacci, Physical Review X 15 (2025). corr_author: '1' date_created: 2025-11-30T23:02:08Z date_published: 2025-10-31T00:00:00Z date_updated: 2026-05-20T08:58:06Z day: '31' ddc: - '530' department: - _id: EdHa - _id: JePa doi: 10.1103/rjk2-q2wh ec_funded: 1 external_id: arxiv: - '2508.20642' file: - access_level: open_access checksum: bb64ea9f2c400205fd89e9bdd15cc850 content_type: application/pdf creator: dernst date_created: 2025-12-01T07:30:00Z date_updated: 2025-12-01T07:30:00Z file_id: '20714' file_name: 2025_PhysicalReviewX_Martinet.pdf file_size: 5902259 relation: main_file success: 1 file_date_updated: 2025-12-01T07:30:00Z has_accepted_license: '1' intvolume: ' 15' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: bdac72da-d553-11ed-ba76-eae56e802b74 grant_number: '101086998' name: 'VULCAN: matter, powered from within' - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Physical Review X publication_identifier: eissn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Emergent dynamics of active elastic microbeams 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: 15 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18807' abstract: - lang: eng text: Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues. acknowledgement: We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Thomas full_name: Minchington, Thomas id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f last_name: Minchington - first_name: Martina full_name: Greunz, Martina id: 48A59534-F248-11E8-B48F-1D18A9856A87 last_name: Greunz - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - 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: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 2025;60(4):567-580. doi:10.1016/j.devcel.2024.10.024 apa: Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., & Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.10.024 chicago: Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell. Elsevier, 2025. https://doi.org/10.1016/j.devcel.2024.10.024. ieee: S. Rus et al., “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” Developmental Cell, vol. 60, no. 4. Elsevier, pp. 567–580, 2025. ista: Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580. mla: Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell, vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:10.1016/j.devcel.2024.10.024. short: S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580. corr_author: '1' date_created: 2025-01-09T11:25:47Z date_published: 2025-02-24T00:00:00Z date_updated: 2026-05-20T22:31:11Z day: '24' ddc: - '570' department: - _id: AnKi - _id: EdHa - _id: NanoFab doi: 10.1016/j.devcel.2024.10.024 external_id: isi: - '001434279000001' pmid: - '39603235' file: - access_level: open_access checksum: bb58db4a908a1f4aabe4004706154541 content_type: application/pdf creator: dernst date_created: 2025-04-16T10:54:07Z date_updated: 2025-04-16T10:54:07Z file_id: '19584' file_name: 2025_DevelopmentalCell_Lehr.pdf file_size: 6994499 relation: main_file success: 1 file_date_updated: 2025-04-16T10:54:07Z has_accepted_license: '1' intvolume: ' 60' isi: 1 issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 567-580 pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F7802 name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19763' relation: dissertation_contains status: public scopus_import: '1' status: public title: Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling 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: 60 year: '2025' ... --- _id: '17892' abstract: - lang: eng text: "Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −\U0001D6FE. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−\U0001D6FE) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −\U0001D6FE on short distances and −(2/3)⁢(2−\U0001D6FE) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate." acknowledgement: We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413. article_number: '024404' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Fabrizio full_name: Olmeda, Fabrizio id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689 last_name: Olmeda - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands citation: ama: Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404 apa: Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404 chicago: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404. ieee: F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024. ista: Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404. mla: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404. short: F. Olmeda, S. Rulands, Physical Review E 110 (2024). corr_author: '1' date_created: 2024-09-08T22:01:12Z date_published: 2024-08-01T00:00:00Z date_updated: 2025-09-08T09:17:18Z day: '01' ddc: - '530' department: - _id: EdHa doi: 10.1103/PhysRevE.110.024404 ec_funded: 1 external_id: isi: - '001299670100004' pmid: - '39294986' file: - access_level: open_access checksum: 67fc2cc8eee3155e5c3b7380307d8284 content_type: application/pdf creator: dernst date_created: 2024-09-11T05:59:36Z date_updated: 2024-09-11T05:59:36Z file_id: '18053' file_name: 2024_PhysReviewE_Olmeda.pdf file_size: 445696 relation: main_file success: 1 file_date_updated: 2024-09-11T05:59:36Z has_accepted_license: '1' intvolume: ' 110' isi: 1 issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Field theory of enzyme-substrate systems with restricted long-range interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 110 year: '2024' ... --- OA_place: repository OA_type: green _id: '18446' abstract: - lang: eng text: How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning. acknowledgement: "We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)" article_number: eadh1145 article_processing_charge: No article_type: original author: - first_name: Dimitri full_name: Fabrèges, Dimitri last_name: Fabrèges - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 - first_name: Prachiti full_name: Moghe, Prachiti last_name: Moghe - first_name: Alison full_name: Kickuth, Alison last_name: Kickuth - first_name: Takafumi full_name: Ichikawa, Takafumi last_name: Ichikawa - first_name: Chizuru full_name: Iwatani, Chizuru last_name: Iwatani - first_name: Tomoyuki full_name: Tsukiyama, Tomoyuki last_name: Tsukiyama - first_name: Nathalie full_name: Daniel, Nathalie last_name: Daniel - first_name: Julie full_name: Gering, Julie last_name: Gering - first_name: Anniek full_name: Stokkermans, Anniek last_name: Stokkermans - first_name: Adrian full_name: Wolny, Adrian last_name: Wolny - first_name: Anna full_name: Kreshuk, Anna last_name: Kreshuk - first_name: Véronique full_name: Duranthon, Véronique last_name: Duranthon - first_name: Virginie full_name: Uhlman, Virginie last_name: Uhlman - 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: Takashi full_name: Hiiragi, Takashi last_name: Hiiragi citation: ama: Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718). doi:10.1126/science.adh1145 apa: Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145 chicago: Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science. AAAS, 2024. https://doi.org/10.1126/science.adh1145. ieee: D. Fabrèges et al., “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS, 2024. ista: Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145. mla: Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:10.1126/science.adh1145. short: D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024). corr_author: '1' date_created: 2024-10-20T22:02:06Z date_published: 2024-10-11T00:00:00Z date_updated: 2025-09-08T14:22:13Z day: '11' department: - _id: EdHa doi: 10.1126/science.adh1145 external_id: isi: - '001422132300018' pmid: - '39388574' intvolume: ' 386' isi: 1 issue: '6718' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf month: '10' oa: 1 oa_version: Submitted Version pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: AAAS quality_controlled: '1' scopus_import: '1' status: public title: Temporal variability and cell mechanics control robustness in mammalian embryogenesis type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 386 year: '2024' ... --- _id: '20121' abstract: - lang: eng text: PyDaddy is an open source package which is a key contribution of the manuscript Nabeel et al, arXiv:2205.02645. The basic scientific premise for this package is to discover the nature of stochasticity in ecological time series datasets. It is well known that the stochasticity can affect the dynamics of ecological systems in counter-intuitive ways. Without understanding the equations (typically, in the form of stochastic differential equations or SDEs, in short) that govern the dynamics of populations or ecosystems, it's challenging to determine the impact of randomness on real datasets. In this manuscript and accompanying package, we introduce a methodology for discovering equations (SDEs) that transforms time series data of state variables into stochastic differential equations. This approach merges traditional stochastic calculus with modern equation-discovery techniques. We showcase the generality of our method through various applications and discuss its limitations and potential pitfalls, offering diagnostic measures to address these challenges. acknowledgement: This study was partially funded by Science and Engineering Research Board, Department of Science and Technology, Government of India to Vishwesha Guttal. article_processing_charge: No author: - first_name: Arshed full_name: Nabeel, Arshed last_name: Nabeel - first_name: Ashwin full_name: Karichannavar, Ashwin last_name: Karichannavar - first_name: Shuaib full_name: Palathingal, Shuaib last_name: Palathingal - first_name: Jitesh full_name: Jhawar, Jitesh last_name: Jhawar - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Masila full_name: Danny Raj, Masila last_name: Danny Raj - first_name: Vishwesha full_name: Guttal, Vishwesha last_name: Guttal citation: ama: 'Nabeel A, Karichannavar A, Palathingal S, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. 2024. doi:10.5281/ZENODO.7137151' apa: 'Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., & Guttal, V. (2024). PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo. https://doi.org/10.5281/ZENODO.7137151' chicago: 'Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Masila Danny Raj, and Vishwesha Guttal. “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.7137151.' ieee: 'A. Nabeel et al., “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.' ista: 'Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Danny Raj M, Guttal V. 2024. PyDaddy: A Python Package for Discovering SDEs from Time Series Data, Zenodo, 10.5281/ZENODO.7137151.' mla: 'Nabeel, Arshed, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo, 2024, doi:10.5281/ZENODO.7137151.' short: A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024). date_created: 2025-08-05T06:49:59Z date_published: 2024-09-18T00:00:00Z date_updated: 2025-09-30T14:14:42Z day: '18' ddc: - '570' department: - _id: EdHa doi: 10.5281/ZENODO.7137151 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7137151 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '20056' relation: used_for_analysis_in status: public status: public title: 'PyDaddy: A Python Package for Discovering SDEs from Time Series Data' 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: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '14795' abstract: - lang: eng text: Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells. acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: "We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - 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: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - 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: Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 2024;34(1):171-182.e8. doi:10.1016/j.cub.2023.11.067 apa: Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., & Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2023.11.067 chicago: Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.067. ieee: F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” Current Biology, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024. ista: Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8. mla: Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:10.1016/j.cub.2023.11.067. short: F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8. corr_author: '1' date_created: 2024-01-14T23:00:56Z date_published: 2024-01-08T00:00:00Z date_updated: 2025-09-04T11:39:10Z day: '08' ddc: - '570' department: - _id: CaHe - _id: EdHa - _id: MaLo - _id: NanoFab doi: 10.1016/j.cub.2023.11.067 ec_funded: 1 external_id: isi: - '001154500400001' pmid: - '38134934' file: - access_level: open_access checksum: 51220b76d72a614208f84bdbfbaf9b72 content_type: application/pdf creator: dernst date_created: 2024-01-16T10:53:31Z date_updated: 2024-01-16T10:53:31Z file_id: '14813' file_name: 2024_CurrentBiology_Arslan.pdf file_size: 5183861 relation: main_file success: 1 file_date_updated: 2024-01-16T10:53:31Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 171-182.e8 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 34 year: '2024' ... --- _id: '15024' abstract: - lang: eng text: Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions. acknowledgement: The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413. article_number: '064503' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Paul full_name: Robin, Paul id: 48c58128-57b0-11ee-9095-dc28fd97fc1d last_name: Robin orcid: 0000-0002-5728-9189 citation: ama: Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215 apa: Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215 chicago: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215. ieee: P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024. ista: Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503. mla: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215. short: P. Robin, Journal of Chemical Physics 160 (2024). corr_author: '1' date_created: 2024-02-25T23:00:55Z date_published: 2024-02-14T00:00:00Z date_updated: 2025-09-04T12:07:33Z day: '14' ddc: - '540' department: - _id: EdHa doi: 10.1063/5.0188215 ec_funded: 1 external_id: arxiv: - '2311.11784' isi: - '001161104900003' pmid: - '38349632' file: - access_level: open_access checksum: 0a5e0ae70849bce674466fc054390ec0 content_type: application/pdf creator: dernst date_created: 2024-02-27T08:12:52Z date_updated: 2024-02-27T08:12:52Z file_id: '15034' file_name: 2024_JourChemicalPhysics_Robin.pdf file_size: 5452738 relation: main_file success: 1 file_date_updated: 2024-02-27T08:12:52Z has_accepted_license: '1' intvolume: ' 160' 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: Correlation-induced viscous dissipation in concentrated electrolytes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 160 year: '2024' ... --- _id: '15315' abstract: - lang: eng text: Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description. acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (German Research Foundation)—Project-ID 201269156—SFB 1032 (Project B12). D B B was supported by an NOMIS Fellowship and an EMBO Fellowship (ALTF 343-2022). We thank Joachim Rädler, Alexandra Fink, Erwin Frey, Pierre Ronceray, Ricard Alert, Edouard Hannezo, Henrik Flyvbjerg, Ulrich Schwarz, Joshua Shaevitz, Greg Stephens, Andrea Cavagna, Grzegorz Gradziuk, Fridtjof Brauns, Nikolas Claussen, Tom Brandstätter, Johannes Flommersfeld, Christoph Schreiber, Nicolas Arlt, Matthew Schmitt, Joris Messelink, Federico Gnesotto, Federica Mura, Bram Hoogland, Manon Wigbers, Isabella Graf, Jessica Lober, and many others for inspiring discussions. We also thank Claudia Flandoli for the artwork in figures 1, 5, 8 and 9. article_number: '056601' article_processing_charge: Yes (in subscription journal) article_type: review arxiv: 1 author: - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Chase P. full_name: Broedersz, Chase P. last_name: Broedersz citation: ama: 'Brückner D, Broedersz CP. Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. 2024;87(5). doi:10.1088/1361-6633/ad36d2' apa: 'Brückner, D., & Broedersz, C. P. (2024). Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. IOP Publishing. https://doi.org/10.1088/1361-6633/ad36d2' chicago: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” Reports on Progress in Physics. IOP Publishing, 2024. https://doi.org/10.1088/1361-6633/ad36d2.' ieee: 'D. Brückner and C. P. Broedersz, “Learning dynamical models of single and collective cell migration: a review,” Reports on Progress in Physics, vol. 87, no. 5. IOP Publishing, 2024.' ista: 'Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. 87(5), 056601.' mla: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” Reports on Progress in Physics, vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:10.1088/1361-6633/ad36d2.' short: D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024). corr_author: '1' date_created: 2024-04-14T22:01:01Z date_published: 2024-04-04T00:00:00Z date_updated: 2025-09-04T13:39:07Z day: '04' ddc: - '530' department: - _id: EdHa doi: 10.1088/1361-6633/ad36d2 external_id: arxiv: - '2309.00545' isi: - '001196692400001' pmid: - '38518358' file: - access_level: open_access checksum: c5910078230ade20f4dd83592e862a72 content_type: application/pdf creator: dernst date_created: 2024-08-20T11:00:03Z date_updated: 2024-08-20T11:00:03Z file_id: '17451' file_name: 2024_ReportPhysics_Brueckner.pdf file_size: 4376898 relation: main_file success: 1 file_date_updated: 2024-08-20T11:00:03Z has_accepted_license: '1' intvolume: ' 87' isi: 1 issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '04' oa: 1 oa_version: Published Version 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 publication: Reports on Progress in Physics publication_identifier: eissn: - 1361-6633 issn: - 0034-4885 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Learning dynamical models of single and collective cell migration: a review' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 87 year: '2024' ... --- _id: '17104' abstract: - lang: eng text: 'The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth, the regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue steady-state are still poorly understood. Here, we develop a computational model that incorporates basic assumptions of stem cell renewal into distinct populations and mechanical interactions between cells. We find that the model generates unexpected dynamic features: stem cells repel each other in the bulk tissue and are thus found rather isolated, as in a number of in vivo contexts. By mapping the system onto a gas of passive Brownian particles with effective repulsive interactions, that arise from the generated flows of differentiated cells, we show that we can quantitatively describe such stem cell distribution in tissues. The interaction potential between a pair of stem cells decays exponentially with a characteristic length that spans several cell sizes, corresponding to the volume of cells generated per stem cell division. Our findings may help understanding the dynamics of normal and cancerous epithelial tissues.' acknowledgement: JE and JK gratefully acknowledge financial support from the Initiative and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed with computing resources granted by RWTH Aachen University under project ‘rwth0475’. article_number: '097' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Johannes C. full_name: Krämer, Johannes C. last_name: Krämer - 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: Gerhard full_name: Gompper, Gerhard last_name: Gompper - first_name: Jens full_name: Elgeti, Jens last_name: Elgeti citation: ama: Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 2024;16(4). doi:10.21468/scipostphys.16.4.097 apa: Krämer, J. C., Hannezo, E. B., Gompper, G., & Elgeti, J. (2024). Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.16.4.097 chicago: Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” SciPost Physics. SciPost Foundation, 2024. https://doi.org/10.21468/scipostphys.16.4.097. ieee: J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells,” SciPost Physics, vol. 16, no. 4. SciPost Foundation, 2024. ista: Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 16(4), 097. mla: Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” SciPost Physics, vol. 16, no. 4, 097, SciPost Foundation, 2024, doi:10.21468/scipostphys.16.4.097. short: J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024). date_created: 2024-06-03T08:58:44Z date_published: 2024-04-08T00:00:00Z date_updated: 2025-09-08T07:45:40Z day: '08' ddc: - '530' department: - _id: EdHa doi: 10.21468/scipostphys.16.4.097 external_id: arxiv: - '2310.04272' isi: - '001202370200001' file: - access_level: open_access checksum: 6fdeecd21c166db8dedb927ecc2e6025 content_type: application/pdf creator: dernst date_created: 2024-06-03T11:18:51Z date_updated: 2024-06-03T11:18:51Z file_id: '17109' file_name: 2024_SciPostPhys_Kraemer.pdf file_size: 4973291 relation: main_file success: 1 file_date_updated: 2024-06-03T11:18:51Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: SciPost Physics publication_identifier: issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' scopus_import: '1' status: public title: Mechanically-driven stem cell separation in tissues caused by proliferating daughter 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 16 year: '2024' ... --- APC_amount: 2570,79 EUR OA_place: publisher OA_type: hybrid _id: '17123' abstract: - lang: eng text: A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes. acknowledgement: We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02. article_number: e2322326121 article_processing_charge: Yes (in subscription journal) 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: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(23). doi:10.1073/pnas.2322326121 apa: Brückner, D., & Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2322326121 chicago: Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2322326121. ieee: D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23. National Academy of Sciences, 2024. ista: Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121. mla: Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:10.1073/pnas.2322326121. short: D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). corr_author: '1' date_created: 2024-06-09T22:01:02Z date_published: 2024-06-04T00:00:00Z date_updated: 2025-09-08T07:51:01Z day: '04' ddc: - '570' department: - _id: EdHa - _id: GaTk doi: 10.1073/pnas.2322326121 external_id: isi: - '001244835000006' pmid: - '38819997' file: - access_level: open_access checksum: 59797a75db7beb3721ed7a4d14c241f9 content_type: application/pdf creator: dernst date_created: 2024-06-10T10:27:37Z date_updated: 2024-06-10T10:27:37Z file_id: '17130' file_name: 2024_PNAS_Brueckner.pdf file_size: 12329234 relation: main_file success: 1 file_date_updated: 2024-06-10T10:27:37Z has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '23' language: - iso: eng month: '06' oa: 1 oa_version: Published Version 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 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/dbrueckner/SelforgInformation - description: News on the ISTA website relation: press_release url: https://ista.ac.at/en/news/the-embryo-assembles-itself/ scopus_import: '1' status: public title: Information content and optimization of self-organized developmental systems 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: 121 year: '2024' ...