[{"file_date_updated":"2026-03-02T09:34:18Z","file":[{"creator":"dernst","content_type":"application/pdf","checksum":"fa2b55b3a0d8978de7d2d061c7ad8779","file_id":"21377","file_name":"2026_NatureComm_Hu.pdf","file_size":4821073,"date_updated":"2026-03-02T09:34:18Z","date_created":"2026-03-02T09:34:18Z","relation":"main_file","access_level":"open_access","success":1}],"day":"20","OA_type":"gold","PlanS_conform":"1","article_type":"original","OA_place":"publisher","scopus_import":"1","oa":1,"fulldoi":"https://doi.org/10.1038/s41467-026-69377-1","citation":{"short":"J. Hu, T. Scheidt, D. Thacker, E. Axell, E. Stemme, U. Łapińska, S. Wennmalm, G. Meisl, S. Curk, M. Andreasen, M. Vendruscolo, P. Arosio, A. Šarić, J.D. Schmit, T.P.J. Knowles, E. Sparr, S. Linse, T.C.T. Michaels, A.J. Dear, Nature Communications 17 (2026).","chicago":"Hu, Jing, Tom Scheidt, Dev Thacker, Emil Axell, Elin Stemme, Urszula Łapińska, Stefan Wennmalm, et al. “Structural Defects in Amyloid-β Fibrils Drive Secondary Nucleation.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-69377-1\">https://doi.org/10.1038/s41467-026-69377-1</a>.","ista":"Hu J, Scheidt T, Thacker D, Axell E, Stemme E, Łapińska U, Wennmalm S, Meisl G, Curk S, Andreasen M, Vendruscolo M, Arosio P, Šarić A, Schmit JD, Knowles TPJ, Sparr E, Linse S, Michaels TCT, Dear AJ. 2026. Structural defects in amyloid-β fibrils drive secondary nucleation. Nature Communications. 17, 1933.","ieee":"J. Hu <i>et al.</i>, “Structural defects in amyloid-β fibrils drive secondary nucleation,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","apa":"Hu, J., Scheidt, T., Thacker, D., Axell, E., Stemme, E., Łapińska, U., … Dear, A. J. (2026). Structural defects in amyloid-β fibrils drive secondary nucleation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-69377-1\">https://doi.org/10.1038/s41467-026-69377-1</a>","mla":"Hu, Jing, et al. “Structural Defects in Amyloid-β Fibrils Drive Secondary Nucleation.” <i>Nature Communications</i>, vol. 17, 1933, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-69377-1\">10.1038/s41467-026-69377-1</a>.","ama":"Hu J, Scheidt T, Thacker D, et al. Structural defects in amyloid-β fibrils drive secondary nucleation. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-69377-1\">10.1038/s41467-026-69377-1</a>"},"publication_identifier":{"eissn":["2041-1723"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"DOAJ_listed":"1","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"pmid":1,"type":"journal_article","department":[{"_id":"AnSa"}],"ec_funded":1,"date_created":"2026-03-01T23:01:38Z","doi":"10.1038/s41467-026-69377-1","date_updated":"2026-03-02T09:36:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","ddc":["570"],"month":"02","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","status":"public","intvolume":"        17","acknowledgement":"This work was supported by the Swedish Research Council (2019-02397 to E.S., 2015-00143 to S.L., and 2022-06641 to S.L. and E.S.), and the GenerationNano project, the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 945378 (S.L. co-PI). We acknowledge support from the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the ERC PhysProt (agreement n 337969) (T.S., T.P.J.K., S.L.), ETC StG “NEPA” (A.Š. and S.C.), the Royal Society (S.C., A.S.), the ERASMUS Programme (T.S.), and The Danish Council for Independent Research ∣ Natural Sciences (FNU-11-113326) (M.A.). This work was also funded by the Novo Nordisk Foundation (#NNF19OC0054635 to S.L.), ETH Zürich (T.C.T.M.), and the Swiss National Science Foundation (grant no 219703 to A.J.D. and T.C.T.M.). We acknowledge the use of the nano-Characterisation and nano-Manufacturing Research Equipment (nCHREM) facility for access to microscopy instrumentation. We are grateful to the late Professor Sir Christopher Dobson for invaluable conversations regarding the microfluidic diffusional sizing experiments. We are also grateful to Quentin A. E. Peter and Thomas Müller for their guidance on microfluidic device design. The cuvette-filled icon in Fig. 3d is by Servier [https://smart.servier.com/]. It is licensed under CC-BY 3.0 Unported [https://creativecommons.org/licenses/by/3.0/]. The authors would like to acknowledge Umeå Centre for Electron Microscopy (UCEM) for technical assistance and access to electron microscopy. Support was provided by SciLifeLab national Cryo-EM Unit at Umeå University.","abstract":[{"lang":"eng","text":"Formation of new amyloid fibrils and oligomers from monomeric protein on the surfaces of existing fibrils is an important driver of many disorders such as Alzheimer’s and Parkinson’s diseases. The structural basis of this secondary nucleation process, however, is poorly understood. Here, we ask whether secondary nucleation sites are found predominantly at rare growth defects: irregularities in the fibril core structure incorporated during their original assembly. We first demonstrate using the specific inhibitor of secondary nucleation, Brichos, that secondary nucleation sites on Alzheimer’s disease-associated fibrils composed of Aβ40 and Aβ42 peptides are rare compared to the number of protein molecules they contain. We then grow Aβ40 fibrils under conditions designed to eliminate most growth defects while leaving the regular fibril morphology unchanged, and confirm the latter using cryo-electron microscopy. We measure both the ability of these annealed fibrils to promote secondary nucleation and the stoichiometry of their secondary nucleation sites, finding that both are greatly reduced as predicted. Re-analysis of published data for other proteins suggests that fibril growth defects may also drive secondary nucleation generally across most amyloids. These findings could unlock structure-based drug design of therapeutics that aim to halt amyloid disorders by inhibiting secondary nucleation sites."}],"publication":"Nature Communications","volume":17,"article_processing_charge":"Yes","publisher":"Springer Nature","_id":"21369","quality_controlled":"1","external_id":{"pmid":["41708600"]},"article_number":"1933","date_published":"2026-02-20T00:00:00Z","author":[{"last_name":"Hu","first_name":"Jing","full_name":"Hu, Jing"},{"first_name":"Tom","last_name":"Scheidt","full_name":"Scheidt, Tom"},{"full_name":"Thacker, Dev","first_name":"Dev","last_name":"Thacker"},{"first_name":"Emil","last_name":"Axell","full_name":"Axell, Emil"},{"first_name":"Elin","last_name":"Stemme","full_name":"Stemme, Elin"},{"last_name":"Łapińska","first_name":"Urszula","full_name":"Łapińska, Urszula"},{"full_name":"Wennmalm, Stefan","last_name":"Wennmalm","first_name":"Stefan"},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","full_name":"Curk, Samo","orcid":"0000-0001-6160-9766","first_name":"Samo","last_name":"Curk"},{"full_name":"Andreasen, Maria","last_name":"Andreasen","first_name":"Maria"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"full_name":"Arosio, Paolo","last_name":"Arosio","first_name":"Paolo"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Schmit","first_name":"Jeremy D.","full_name":"Schmit, Jeremy D."},{"full_name":"Knowles, Tuomas P.J.","first_name":"Tuomas P.J.","last_name":"Knowles"},{"full_name":"Sparr, Emma","last_name":"Sparr","first_name":"Emma"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"last_name":"Michaels","first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T."},{"last_name":"Dear","first_name":"Alexander J.","full_name":"Dear, Alexander J."}],"title":"Structural defects in amyloid-β fibrils drive secondary nucleation","year":"2026","has_accepted_license":"1","publication_status":"published"},{"article_processing_charge":"Yes (in subscription journal)","publisher":"AIP Publishing","_id":"21748","quality_controlled":"1","issue":"14","article_number":"144902","external_id":{"arxiv":["2603.15170"]},"abstract":[{"text":"Cells are defined by lipid membranes that differ in their structure across the tree of life. While the membranes of most bacteria and eukaryotes consist of single-headed bilayer lipids, the membranes of archaea are composed of mixtures of single-headed bilayer lipids and double-headed bolalipids. Archaeal bolalipids can adopt straight or u-shaped conformations, enabling them—together with bilayer lipids—to control whether membranes form bilayer or monolayer structures. Yet, the physical principles governing archaeal membranes remain largely unexplored, especially how membrane structure couples to externally imposed curvature during membrane remodeling. Here, we perform coarse-grained molecular dynamics simulations of toroidal vesicles to systematically probe the effects of all relevant combinations of mean and Gaussian curvatures on shape stability and lipid organization. We find that soft bilayer membranes can sustain all curvatures induced, whereas rigid bolalipid monolayer membranes either transition to different vesicle shapes or rupture. Bilayer-mimicking u-shaped bolalipids and bilayer lipids are spatially accumulated in regions of high mean membrane curvature independent of Gaussian curvature. Our work identifies curvature–composition coupling as a physical signature of archaeal membrane remodeling.","lang":"eng"}],"intvolume":"       164","status":"public","acknowledgement":"F.F. acknowledges the financial support from the NOMIS foundation. M.A. and A.Š. acknowledge the funding from the Volkswagen Foundation (Grant No. Az 96727). A.Š. acknowledges the funding from ERC Starting Grant “NEPA” (Grant No. 802960) and the Vallee Scholarship.","language":[{"iso":"eng"}],"volume":164,"publication":"Journal of Chemical Physics","has_accepted_license":"1","year":"2026","publication_status":"published","date_published":"2026-04-14T00:00:00Z","author":[{"last_name":"Frey","orcid":"0000-0001-8501-6017","first_name":"Felix F","full_name":"Frey, Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"last_name":"Santana de Freitas Amaral","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"title":"Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization","OA_place":"publisher","oa":1,"scopus_import":"1","publication_identifier":{"eissn":["1089-7690"],"issn":[" 0021-9606"]},"fulldoi":"https://doi.org/10.1063/5.0325170","citation":{"ista":"Frey FF, Santana de Freitas Amaral M, Šarić A. 2026. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. Journal of Chemical Physics. 164(14), 144902.","chicago":"Frey, Felix F, Miguel Santana de Freitas Amaral, and Anđela Šarić. “Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2026. <a href=\"https://doi.org/10.1063/5.0325170\">https://doi.org/10.1063/5.0325170</a>.","short":"F.F. Frey, M. Santana de Freitas Amaral, A. Šarić, Journal of Chemical Physics 164 (2026).","ama":"Frey FF, Santana de Freitas Amaral M, Šarić A. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. <i>Journal of Chemical Physics</i>. 2026;164(14). doi:<a href=\"https://doi.org/10.1063/5.0325170\">10.1063/5.0325170</a>","ieee":"F. F. Frey, M. Santana de Freitas Amaral, and A. Šarić, “Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization,” <i>Journal of Chemical Physics</i>, vol. 164, no. 14. AIP Publishing, 2026.","mla":"Frey, Felix F., et al. “Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization.” <i>Journal of Chemical Physics</i>, vol. 164, no. 14, 144902, AIP Publishing, 2026, doi:<a href=\"https://doi.org/10.1063/5.0325170\">10.1063/5.0325170</a>.","apa":"Frey, F. F., Santana de Freitas Amaral, M., &#38; Šarić, A. (2026). Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0325170\">https://doi.org/10.1063/5.0325170</a>"},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2026-05-05T12:35:24Z","file":[{"success":1,"access_level":"open_access","file_id":"21801","file_name":"2026_JourChemPhysics_Frey.pdf","file_size":8764791,"date_created":"2026-05-05T12:35:24Z","date_updated":"2026-05-05T12:35:24Z","relation":"main_file","creator":"dernst","content_type":"application/pdf","checksum":"2e10c4f4531676e0771ef3730e4b63a9"}],"day":"14","PlanS_conform":"1","article_type":"original","OA_type":"hybrid","date_updated":"2026-05-05T12:40:41Z","doi":"10.1063/5.0325170","date_created":"2026-04-19T22:07:45Z","oa_version":"Published Version","ddc":["540"],"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","month":"04","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"related_material":{"record":[{"id":"21800","relation":"research_data","status":"public"}]},"type":"journal_article","ec_funded":1,"department":[{"_id":"AnSa"}]},{"day":"13","article_type":"original","OA_type":"green","OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.1101/2025.02.15.637692","open_access":"1"}],"oa":1,"scopus_import":"1","publication_identifier":{"eissn":["1526-4602"]},"fulldoi":"https://doi.org/10.1021/acs.biomac.6c00345","citation":{"ama":"Cole CC, Kreutzberger MAB, Klein K, et al. Supramolecular assembly of collagen-mimetic eptide D-periodic fibrils and nanoassemblies. <i>Biomacromolecules</i>. 2026;27(4):2956-2965. doi:<a href=\"https://doi.org/10.1021/acs.biomac.6c00345\">10.1021/acs.biomac.6c00345</a>","mla":"Cole, Carson C., et al. “Supramolecular Assembly of Collagen-Mimetic Eptide D-Periodic Fibrils and Nanoassemblies.” <i>Biomacromolecules</i>, vol. 27, no. 4, American Chemical Society, 2026, pp. 2956–65, doi:<a href=\"https://doi.org/10.1021/acs.biomac.6c00345\">10.1021/acs.biomac.6c00345</a>.","ieee":"C. C. Cole <i>et al.</i>, “Supramolecular assembly of collagen-mimetic eptide D-periodic fibrils and nanoassemblies,” <i>Biomacromolecules</i>, vol. 27, no. 4. American Chemical Society, pp. 2956–2965, 2026.","apa":"Cole, C. C., Kreutzberger, M. A. B., Klein, K., Cahue, K. A., Pogostin, B. H., Farsheed, A. C., … Hartgerink, J. D. (2026). Supramolecular assembly of collagen-mimetic eptide D-periodic fibrils and nanoassemblies. <i>Biomacromolecules</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biomac.6c00345\">https://doi.org/10.1021/acs.biomac.6c00345</a>","short":"C.C. Cole, M.A.B. Kreutzberger, K. Klein, K.A. Cahue, B.H. Pogostin, A.C. Farsheed, J.W.R. Swain, T.H. Bui, A. Dey, J.T. Makhoul, M. Dubackic, A. Pal, U. Olsson, A. Šarić, E.H. Egelman, J.D. Hartgerink, Biomacromolecules 27 (2026) 2956–2965.","ista":"Cole CC, Kreutzberger MAB, Klein K, Cahue KA, Pogostin BH, Farsheed AC, Swain JWR, Bui TH, Dey A, Makhoul JT, Dubackic M, Pal A, Olsson U, Šarić A, Egelman EH, Hartgerink JD. 2026. Supramolecular assembly of collagen-mimetic eptide D-periodic fibrils and nanoassemblies. Biomacromolecules. 27(4), 2956–2965.","chicago":"Cole, Carson C., Mark A.B. Kreutzberger, Kevin Klein, Kiana A. Cahue, Brett H. Pogostin, Adam C. Farsheed, Joseph W.R. Swain, et al. “Supramolecular Assembly of Collagen-Mimetic Eptide D-Periodic Fibrils and Nanoassemblies.” <i>Biomacromolecules</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acs.biomac.6c00345\">https://doi.org/10.1021/acs.biomac.6c00345</a>."},"page":"2956-2965","type":"journal_article","department":[{"_id":"AnSa"}],"date_created":"2026-04-19T22:07:46Z","date_updated":"2026-05-06T05:43:44Z","doi":"10.1021/acs.biomac.6c00345","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","abstract":[{"text":"The collagen triple helix assembles hierarchically into bundled oligomers, solvated networks, and fibers. Synthetic peptide assemblies, driven by supramolecular interactions, can form single triple helices through intrahelical amino acid pairs; however, the principles guiding interhelical associations into higher-order structures remain unclear. Here, we incorporate cation−π and electrostatic charge pairs to probe interhelical interactions and elucidate the mechanisms driving triple helix assembly into fibrils, nanotubes, and nanosheets. Introducing cation−π pairs into a fibrillating collagen mimetic resulted in D-periodic fibrils with pH-sensitive gelation. By alternating the presentation of electrostatic and cation−π pairs, the assembly of another D-periodic fibril featuring inner and outer triple-helical layers was resolved by cryo electron microscopy to a resolution of 8 Å. At physiological pH, antiparallel association of these triple helices leads to the formation of nanotubes. The packing behavior of triple helices correlates with the interhelical interactions, where parallel associations favor fibril formation and antiparallel interactions drive nanotube and nanosheet assembly. These self-assembling triple-helical peptides demonstrate how packing of higher-order structures can be tailored with supramolecular interactions and establish the relationship of different hierarchical collagen-mimetic assemblies as pH-dependent.","lang":"eng"}],"intvolume":"        27","status":"public","acknowledgement":"The authors acknowledge Crispin Hetherington and L. Tracy Yu for their technical assistance and insights. This work was funded in part by the National Science Foundation (CHE 2203937), the National Science Foundation Graduate Research Fellowship (Grant No. 1842494), the Welch Foundation (C-2141), the Swedish Research Council (2020-04633), and the NIH (GM122510). This work benefited from using the SasView application, originally developed under NSF award DMR-0520547. SasView contains code developed with funding from the European Union’s Horizon 2020 research and innovation program under the SINE2020 project, Grant Agreement No. 654000. This work was partly done using the Shared Equipment Authority resources at Rice University.","language":[{"iso":"eng"}],"volume":27,"publication":"Biomacromolecules","article_processing_charge":"No","publisher":"American Chemical Society","_id":"21749","quality_controlled":"1","issue":"4","date_published":"2026-04-13T00:00:00Z","title":"Supramolecular assembly of collagen-mimetic eptide D-periodic fibrils and nanoassemblies","author":[{"last_name":"Cole","first_name":"Carson C.","full_name":"Cole, Carson C."},{"full_name":"Kreutzberger, Mark A.B.","last_name":"Kreutzberger","first_name":"Mark A.B."},{"last_name":"Klein","first_name":"Kevin","full_name":"Klein, Kevin","id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398"},{"first_name":"Kiana A.","last_name":"Cahue","full_name":"Cahue, Kiana A."},{"first_name":"Brett H.","last_name":"Pogostin","full_name":"Pogostin, Brett H."},{"full_name":"Farsheed, Adam C.","first_name":"Adam C.","last_name":"Farsheed"},{"full_name":"Swain, Joseph W.R.","last_name":"Swain","first_name":"Joseph W.R."},{"last_name":"Bui","first_name":"Thi H.","full_name":"Bui, Thi H."},{"full_name":"Dey, Arghadip","last_name":"Dey","first_name":"Arghadip"},{"full_name":"Makhoul, Jonathan T.","first_name":"Jonathan T.","last_name":"Makhoul"},{"full_name":"Dubackic, Marija","last_name":"Dubackic","first_name":"Marija"},{"last_name":"Pal","first_name":"Antara","full_name":"Pal, Antara"},{"full_name":"Olsson, Ulf","first_name":"Ulf","last_name":"Olsson"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Edward H.","last_name":"Egelman","full_name":"Egelman, Edward H."},{"last_name":"Hartgerink","first_name":"Jeffrey D.","full_name":"Hartgerink, Jeffrey D."}],"year":"2026","publication_status":"published"},{"date_published":"2026-04-20T00:00:00Z","author":[{"first_name":"Fernanda L","last_name":"Perez Verdugo","id":"4ecec223-9070-11ef-a0a9-bc76077bea8d","full_name":"Perez Verdugo, Fernanda L"},{"first_name":"Eirini","last_name":"Maniou","full_name":"Maniou, Eirini"},{"first_name":"Gabriel L.","last_name":"Galea","full_name":"Galea, Gabriel L."},{"full_name":"Banerjee, Shiladitya","last_name":"Banerjee","first_name":"Shiladitya"}],"title":"Mechanosensitive feedback organizes cell shape and motion during hindbrain neuropore morphogenesis","publication_status":"published","year":"2026","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"acknowledgement":"S.B. acknowledges support from the National Institutes of Health (NIH R35 GM143042) and the National Science Foundation (NSF MCB-2203601). G.L.G. acknowledges support from the Wellcome Trust (211112/Z/18/Z), the Royal Society (RG\\R2\\232082), and the Leverhulme Trust (RPG-2024-147). E.M. acknowledges support from European Union’s Horizon 2021 Marie Sklodowska-Curie grant agreement no. 101067028. F.P.-V. acknowledges support from the NOMIS foundation. The surface subtraction macro is courtesy of Dr. Dale Moulding and available on GitHub (https://github.com/DaleMoulding/Fiji-Macros).","intvolume":"        36","status":"public","abstract":[{"lang":"eng","text":"Neural tube closure is a critical morphogenetic process in vertebrate development, and failure to close cranial regions such as the hindbrain neuropore (HNP) leads to severe congenital malformations. While mechanical forces such as actomyosin purse-string contraction and directional cell crawling have been implicated in driving HNP closure, how these forces organize local cell shape and motion to produce large-scale tissue remodeling remains poorly understood. Using live and fixed imaging of mouse embryos combined with cell-based biophysical modeling, we show that these force-generating mechanisms are insufficient to explain the reproducible patterns of cell elongation and nematic alignment observed at the HNP border. Instead, we show that local anisotropic stress and cytoskeletal organization are required to generate these patterns and promote midline cell motion. Our model captures key features of cell shape dynamics and emergent nematic order, which we confirm experimentally, including the alignment of actin fibers with cell shape and enhanced midline cell speed. Comparative analysis with chick embryos, which lack supracellular purse strings, supports a conserved link between tension generation and cellular patterning. These findings establish a physical framework connecting force generation, cell shape anisotropy, and tissue morphodynamics during epithelial gap closure."}],"publication":"Current Biology","volume":36,"_id":"21761","article_processing_charge":"Yes (in subscription journal)","publisher":"Elsevier","external_id":{"pmid":["41881011"]},"issue":"8","quality_controlled":"1","pmid":1,"page":"1903-1917.e5","department":[{"_id":"AnSa"}],"type":"journal_article","date_created":"2026-04-26T22:01:46Z","doi":"10.1016/j.cub.2026.02.068","date_updated":"2026-04-28T13:15:42Z","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa_version":"Published Version","file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","creator":"dernst","checksum":"80ae45457b4682c50c84f54de15aa9a8","file_name":"2026_CurrentBiology_PerezVerdugo.pdf","file_size":13402043,"file_id":"21774","relation":"main_file","date_created":"2026-04-28T13:13:40Z","date_updated":"2026-04-28T13:13:40Z"}],"file_date_updated":"2026-04-28T13:13:40Z","article_type":"original","OA_type":"hybrid","day":"20","scopus_import":"1","oa":1,"OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"fulldoi":"https://doi.org/10.1016/j.cub.2026.02.068","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"citation":{"ama":"Perez Verdugo FL, Maniou E, Galea GL, Banerjee S. Mechanosensitive feedback organizes cell shape and motion during hindbrain neuropore morphogenesis. <i>Current Biology</i>. 2026;36(8):1903-1917.e5. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.02.068\">10.1016/j.cub.2026.02.068</a>","ieee":"F. L. Perez Verdugo, E. Maniou, G. L. Galea, and S. Banerjee, “Mechanosensitive feedback organizes cell shape and motion during hindbrain neuropore morphogenesis,” <i>Current Biology</i>, vol. 36, no. 8. Elsevier, p. 1903–1917.e5, 2026.","mla":"Perez Verdugo, Fernanda L., et al. “Mechanosensitive Feedback Organizes Cell Shape and Motion during Hindbrain Neuropore Morphogenesis.” <i>Current Biology</i>, vol. 36, no. 8, Elsevier, 2026, p. 1903–1917.e5, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.02.068\">10.1016/j.cub.2026.02.068</a>.","apa":"Perez Verdugo, F. L., Maniou, E., Galea, G. L., &#38; Banerjee, S. (2026). Mechanosensitive feedback organizes cell shape and motion during hindbrain neuropore morphogenesis. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2026.02.068\">https://doi.org/10.1016/j.cub.2026.02.068</a>","ista":"Perez Verdugo FL, Maniou E, Galea GL, Banerjee S. 2026. Mechanosensitive feedback organizes cell shape and motion during hindbrain neuropore morphogenesis. Current Biology. 36(8), 1903–1917.e5.","chicago":"Perez Verdugo, Fernanda L, Eirini Maniou, Gabriel L. Galea, and Shiladitya Banerjee. “Mechanosensitive Feedback Organizes Cell Shape and Motion during Hindbrain Neuropore Morphogenesis.” <i>Current Biology</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.02.068\">https://doi.org/10.1016/j.cub.2026.02.068</a>.","short":"F.L. Perez Verdugo, E. Maniou, G.L. Galea, S. Banerjee, Current Biology 36 (2026) 1903–1917.e5."}},{"status":"public","intvolume":"       136","acknowledgement":"The authors thank Ms. Katrin Muck for her guidance related to the use of HPC. The MC\r\ncomputer simulation results presented here were enabled via a generous share of CPU time, offered by the Vienna Scientific Cluster (VSC) under Project No. 71263. A. J. A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1. This research was funded in part by the Austrian Science Fund (FWF) [Grant DOI: 10.55776/PIN8759524], gratefully acknowledged by G. K .","language":[{"iso":"eng"}],"abstract":[{"text":"Colloidal fluids can exhibit complex phase behavior and determining phase diagrams via experiments or computer simulations can be laborious. We demonstrate that the dispersion relation ω(k), obtained from dynamical density functional theory for the uniform density system, is a highly versatile tool for predicting where in the phase diagram complex crystals form. The sign of ω(k) determines whether density modes with wave number k grow or decay over time. We demonstrate the predictive power by investigating the complex phase behavior of particles interacting via core-shoulder pair potentials. With complementary Monte Carlo simulations, we show that regions of the phase diagram where ωðkÞ has one or several unstable (growing) wave numbers are also where crystalline phases occur. Going further, by tuning these\r\nunstable wave numbers via the interaction-potential and state-point parameters, we design systems with quasicrystals in the phase diagram. We identify a system with a certain shoulder range exhibiting at least ten different phases. Our general approach accelerates considerably the mapping of complex phase diagrams, crucial for the design of new materials.","lang":"eng"}],"publication":"Physical Review Letters","volume":136,"_id":"21764","article_processing_charge":"Yes (in subscription journal)","publisher":"American Physical Society","external_id":{"arxiv":["2603.18918"]},"issue":"14","article_number":"148203","quality_controlled":"1","date_published":"2026-04-10T00:00:00Z","title":"Navigating complex phase diagrams in soft matter systems","author":[{"last_name":"Wassermair","orcid":"0009-0003-6339-4051","first_name":"Michael","id":"23d132c4-4e98-11ef-b275-9e8d4cd8c917","full_name":"Wassermair, Michael"},{"full_name":"Kahl, Gerhard","last_name":"Kahl","first_name":"Gerhard"},{"full_name":"Roth, Roland","first_name":"Roland","last_name":"Roth"},{"full_name":"Archer, Andrew J.","last_name":"Archer","first_name":"Andrew J."}],"publication_status":"published","year":"2026","has_accepted_license":"1","file":[{"creator":"dernst","content_type":"application/pdf","checksum":"8ffb139122a185fcddbe6a9c901a287c","file_id":"21769","file_name":"2026_PhysicalReviewLetters_Wassermair.pdf","file_size":4336488,"relation":"main_file","date_updated":"2026-04-28T06:58:40Z","date_created":"2026-04-28T06:58:40Z","access_level":"open_access","success":1}],"file_date_updated":"2026-04-28T06:58:40Z","OA_type":"hybrid","article_type":"original","PlanS_conform":"1","day":"10","oa":1,"scopus_import":"1","OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"fulldoi":"https://doi.org/10.1103/nbvt-fgjy","citation":{"ama":"Wassermair M, Kahl G, Roth R, Archer AJ. Navigating complex phase diagrams in soft matter systems. <i>Physical Review Letters</i>. 2026;136(14). doi:<a href=\"https://doi.org/10.1103/nbvt-fgjy\">10.1103/nbvt-fgjy</a>","ieee":"M. Wassermair, G. Kahl, R. Roth, and A. J. Archer, “Navigating complex phase diagrams in soft matter systems,” <i>Physical Review Letters</i>, vol. 136, no. 14. American Physical Society, 2026.","apa":"Wassermair, M., Kahl, G., Roth, R., &#38; Archer, A. J. (2026). Navigating complex phase diagrams in soft matter systems. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/nbvt-fgjy\">https://doi.org/10.1103/nbvt-fgjy</a>","mla":"Wassermair, Michael, et al. “Navigating Complex Phase Diagrams in Soft Matter Systems.” <i>Physical Review Letters</i>, vol. 136, no. 14, 148203, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/nbvt-fgjy\">10.1103/nbvt-fgjy</a>.","short":"M. Wassermair, G. Kahl, R. Roth, A.J. Archer, Physical Review Letters 136 (2026).","ista":"Wassermair M, Kahl G, Roth R, Archer AJ. 2026. Navigating complex phase diagrams in soft matter systems. Physical Review Letters. 136(14), 148203.","chicago":"Wassermair, Michael, Gerhard Kahl, Roland Roth, and Andrew J. Archer. “Navigating Complex Phase Diagrams in Soft Matter Systems.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/nbvt-fgjy\">https://doi.org/10.1103/nbvt-fgjy</a>."},"department":[{"_id":"AnSa"},{"_id":"GradSch"}],"type":"journal_article","doi":"10.1103/nbvt-fgjy","date_updated":"2026-04-28T07:03:48Z","date_created":"2026-04-26T22:01:47Z","month":"04","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","ddc":["530"]},{"status":"public","abstract":[{"lang":"eng","text":"LAMMPS input scripts to simulate toroidal vesicles composed of pure bolalipid membranes and archaeal mixture membranes for the following publication: \"Cracking donuts and sorting lipids: geometry controls archaeal membrane stability and lipid organization\" by Felix Frey, Miguel Amaral, and Andela Saric."}],"OA_type":"green","day":"25","oa":1,"_id":"21800","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.18772086","open_access":"1"}],"publisher":"Zenodo","OA_place":"repository","article_processing_charge":"No","fulldoi":"https://doi.org/10.5281/ZENODO.18772086","citation":{"short":"F.F. Frey, M. Santana de Freitas Amaral, A. Šarić, (2026).","ista":"Frey FF, Santana de Freitas Amaral M, Šarić A. 2026. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.18772086\">10.5281/ZENODO.18772086</a>.","chicago":"Frey, Felix F, Miguel Santana de Freitas Amaral, and Anđela Šarić. “Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization.” Zenodo, 2026. <a href=\"https://doi.org/10.5281/ZENODO.18772086\">https://doi.org/10.5281/ZENODO.18772086</a>.","ama":"Frey FF, Santana de Freitas Amaral M, Šarić A. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. 2026. doi:<a href=\"https://doi.org/10.5281/ZENODO.18772086\">10.5281/ZENODO.18772086</a>","mla":"Frey, Felix F., et al. <i>Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization</i>. Zenodo, 2026, doi:<a href=\"https://doi.org/10.5281/ZENODO.18772086\">10.5281/ZENODO.18772086</a>.","ieee":"F. F. Frey, M. Santana de Freitas Amaral, and A. Šarić, “Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization.” Zenodo, 2026.","apa":"Frey, F. F., Santana de Freitas Amaral, M., &#38; Šarić, A. (2026). Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.18772086\">https://doi.org/10.5281/ZENODO.18772086</a>"},"date_published":"2026-02-25T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"21748"}]},"author":[{"last_name":"Frey","orcid":"0000-0001-8501-6017","first_name":"Felix F","full_name":"Frey, Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"last_name":"Santana de Freitas Amaral","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"department":[{"_id":"AnSa"}],"title":"Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization","type":"research_data_reference","date_created":"2026-05-05T12:11:52Z","doi":"10.5281/ZENODO.18772086","date_updated":"2026-05-05T12:40:41Z","month":"02","year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","ddc":["540"],"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"An important quantity in liquid state theory is the radial distribution function g(r). It can be calculated within the framework of classical density functional theory in two very distinct ways. In the test-particle route, one fixes a single fluid particle, turning it into an external potential in which the inhomogeneous structure of the fluid is calculated by minimizing the functional. The second route to g(r) in density functional theory employs the Ornstein–Zernike equation and the pair direct correlation function, that can be obtained from the second functional derivatives of the excess (over the ideal gas) free energy functional. Since typically an approximate excess free energy functional is employed, the test-particle route, which requires only one functional derivative, is more accurate than the Ornstein–Zernike route. Here we study a two-dimensional core-shoulder particle system and find that in some circumstances the results from the Ornstein–Zernike route can be comparable in accuracy to the test-particle results for r > σ, the core diameter. We also examine in detail the asymptotic r → ∞ decay of g(r), finding a variety of possible decay wavelengths at different state points and state points where there is a crossover from one wavelength to a very different one. This behavior is a signature pointing to the rich phase behavior of the incipient solid phases."}],"language":[{"iso":"eng"}],"acknowledgement":"We are grateful to Florian Sanmüller and Matthias Schmidt for valuable comments on the manuscript and helpful discussions. The simulation results presented here were enabled via a generous allocation of CPU time by the Austrian Scientific Computing (ASC) under Project No. 71263. The authors thank Katrin Muck for her guidance related to the use of HPC. A.J.A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1. This research was funded in part by the Austrian Science Fund (FWF) under project no. PIN8759524 with Grant-DOI 10.55776/PIN8759524, gratefully acknowledged by GK.","intvolume":"       130","status":"public","volume":130,"publication":"Journal of Physical Chemistry B","_id":"22773","article_processing_charge":"Yes (in subscription journal)","publisher":"American Chemical Society","issue":"33","external_id":{"arxiv":["2603.24537"],"pmid":["42622279"]},"quality_controlled":"1","das_tickbox":"0","date_published":"2026-08-20T00:00:00Z","title":"Radial distribution function in a two-dimensional core-shoulder particle system","author":[{"full_name":"Wassermair, Michael","id":"23d132c4-4e98-11ef-b275-9e8d4cd8c917","last_name":"Wassermair","first_name":"Michael","orcid":"0009-0003-6339-4051"},{"full_name":"Kahl, Gerhard","last_name":"Kahl","first_name":"Gerhard"},{"full_name":"Archer, Andrew J.","last_name":"Archer","first_name":"Andrew J."},{"full_name":"Roth, Roland","last_name":"Roth","first_name":"Roland"}],"researchdata_availability":"no","publication_status":"published","has_accepted_license":"1","year":"2026","file":[{"checksum":"67313d68ab13b553a38e8b4bf99983d2","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_created":"2026-09-09T11:05:02Z","date_updated":"2026-09-09T11:05:02Z","file_id":"22871","file_size":7472078,"file_name":"2026_JourPhysicChemistryB_Wassermair.pdf","access_level":"open_access","success":1}],"file_date_updated":"2026-09-09T11:05:02Z","article_type":"original","OA_type":"hybrid","PlanS_conform":"1","day":"20","oa":1,"scopus_import":"1","OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Wassermair M, Kahl G, Archer AJ, Roth R. Radial distribution function in a two-dimensional core-shoulder particle system. <i>Journal of Physical Chemistry B</i>. 2026;130(33):8514-8526. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.6c00653\">10.1021/acs.jpcb.6c00653</a>","mla":"Wassermair, Michael, et al. “Radial Distribution Function in a Two-Dimensional Core-Shoulder Particle System.” <i>Journal of Physical Chemistry B</i>, vol. 130, no. 33, American Chemical Society, 2026, pp. 8514–26, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.6c00653\">10.1021/acs.jpcb.6c00653</a>.","ieee":"M. Wassermair, G. Kahl, A. J. Archer, and R. Roth, “Radial distribution function in a two-dimensional core-shoulder particle system,” <i>Journal of Physical Chemistry B</i>, vol. 130, no. 33. American Chemical Society, pp. 8514–8526, 2026.","apa":"Wassermair, M., Kahl, G., Archer, A. J., &#38; Roth, R. (2026). Radial distribution function in a two-dimensional core-shoulder particle system. <i>Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.6c00653\">https://doi.org/10.1021/acs.jpcb.6c00653</a>","ista":"Wassermair M, Kahl G, Archer AJ, Roth R. 2026. Radial distribution function in a two-dimensional core-shoulder particle system. Journal of Physical Chemistry B. 130(33), 8514–8526.","chicago":"Wassermair, Michael, Gerhard Kahl, Andrew J. Archer, and Roland Roth. “Radial Distribution Function in a Two-Dimensional Core-Shoulder Particle System.” <i>Journal of Physical Chemistry B</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acs.jpcb.6c00653\">https://doi.org/10.1021/acs.jpcb.6c00653</a>.","short":"M. Wassermair, G. Kahl, A.J. Archer, R. Roth, Journal of Physical Chemistry B 130 (2026) 8514–8526."},"fulldoi":"https://doi.org/10.1021/acs.jpcb.6c00653","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"pmid":1,"page":"8514-8526","department":[{"_id":"AnSa"}],"supplementarymaterial":"yes","type":"journal_article","date_updated":"2026-09-09T11:11:12Z","date_created":"2026-08-30T22:01:44Z","doi":"10.1021/acs.jpcb.6c00653","month":"08","oa_version":"Published Version","ddc":["530","540"],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1},{"publication":"arXiv","acknowledgement":"We thank Maitane Muñoz-Basagoiti for stimulating\r\ndiscussions. This research was funded in part by the\r\nAustrian Science Fund (FWF) [10.55776/PAT8537123].\r\n","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"Many biological machines function through controlled conformational transitions, yet designing synthetic nanostructures with prescribed dynamical behavior remains a major challenge. Here, we develop a modular inverse-design framework for bistable nanostructures whose function is controlled by an energy profile along a geometric reaction coordinate. Inspired by proteins with rigid domains connected by flexible hinges, we introduce a hinge-arm paradigm in which a small bistable hinge controls the energetics of a conformational transition, while rigid arms map this transition onto the separation between external binding sites. Specifically, we ask which features of a target energy profile can be programmed under different design constraints. We find that the energy barriers and the binding-site separations in the two metastable states can be readily designed, while controlling the location of the transition state or the full shape of the energy profile requires additional design freedom. Using a differentiable design framework, we find that some optimized solutions are numerically inexact but still display the functional behavior for which the target profile was selected, emphasizing the importance of function-based evaluation criteria. These results establish a practical hierarchy of designability for bistable nanostructures and provide a route toward synthetic nanomachines that couple conformational transitions to target behavior."}],"external_id":{"arxiv":["2606.31620"]},"_id":"22893","article_processing_charge":"No","title":"Designing bistable nanostructures for target behavior","author":[{"first_name":"Andreas","orcid":"0000-0002-0997-5678","last_name":"Ehrmann","full_name":"Ehrmann, Andreas","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2"},{"id":"a8f6d1c6-3200-11ee-973b-dab948eace26","full_name":"Krstić, Marija","first_name":"Marija","last_name":"Krstić"},{"id":"0099896b-5fb8-11ef-8420-b30b14627e93","full_name":"Samadzadeh, Sahar","first_name":"Sahar","last_name":"Samadzadeh"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","first_name":"Carl Peter"}],"date_published":"2026-06-30T00:00:00Z","publication_status":"draft","year":"2026","OA_type":"green","day":"30","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"fulldoi":"https://doi.org/10.48550/arXiv.2606.31620","citation":{"chicago":"Ehrmann, Andreas, Marija Krstić, Sahar Samadzadeh, and Carl Peter Goodrich. “Designing Bistable Nanostructures for Target Behavior.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2606.31620\">https://doi.org/10.48550/arXiv.2606.31620</a>.","ista":"Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2606.31620\">10.48550/arXiv.2606.31620</a>.","short":"A. Ehrmann, M. Krstić, S. Samadzadeh, C.P. Goodrich, ArXiv (n.d.).","ieee":"A. Ehrmann, M. Krstić, S. Samadzadeh, and C. P. Goodrich, “Designing bistable nanostructures for target behavior,” <i>arXiv</i>. .","mla":"Ehrmann, Andreas, et al. “Designing Bistable Nanostructures for Target Behavior.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2606.31620\">10.48550/arXiv.2606.31620</a>.","apa":"Ehrmann, A., Krstić, M., Samadzadeh, S., &#38; Goodrich, C. P. (n.d.). Designing bistable nanostructures for target behavior. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2606.31620\">https://doi.org/10.48550/arXiv.2606.31620</a>","ama":"Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2606.31620\">10.48550/arXiv.2606.31620</a>"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2606.31620","open_access":"1"}],"OA_place":"repository","department":[{"_id":"CaGo"},{"_id":"EdHa"},{"_id":"AnSa"}],"type":"preprint","related_material":{"record":[{"id":"22873","status":"for_moderation","relation":"dissertation_contains"}]},"project":[{"_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","grant_number":"PAT 8537123","name":"Functional bio-inspired nanomachines from sticky colloids"}],"month":"06","corr_author":"1","arxiv":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","date_updated":"2026-09-11T07:37:58Z","date_created":"2026-09-09T13:19:13Z","doi":"10.48550/arXiv.2606.31620"},{"title":"Charge distribution of the coating brush drives interchromosome attraction","author":[{"full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","first_name":"Valerio","last_name":"Sorichetti"},{"last_name":"Robin","orcid":"0000-0002-5728-9189","first_name":"Paul","full_name":"Robin, Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d"},{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","last_name":"Palaia"},{"first_name":"Alberto","last_name":"Hernandez-Armendariz","full_name":"Hernandez-Armendariz, Alberto"},{"full_name":"Cuylen-Haering, Sara","first_name":"Sara","last_name":"Cuylen-Haering"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"date_published":"2025-08-11T00:00:00Z","year":"2025","has_accepted_license":"1","publication_status":"published","publication":"PRX Life","volume":3,"intvolume":"         3","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.).","language":[{"iso":"eng"}],"status":"public","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."}],"quality_controlled":"1","issue":"3","article_number":"033010","publisher":"American Physical Society","article_processing_charge":"Yes","_id":"21235","type":"journal_article","department":[{"_id":"AnSa"},{"_id":"EdHa"}],"ec_funded":1,"project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"name":"EMBO Young Investigator Program - Andela Saric","_id":"349b6ff1-11ca-11ed-8bc3-f006047c2eeb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","oa_version":"Published Version","ddc":["570"],"month":"08","date_updated":"2026-02-17T11:16:26Z","date_created":"2026-02-16T14:50:32Z","doi":"10.1103/41fd-r847","day":"11","article_type":"original","OA_type":"gold","PlanS_conform":"1","file_date_updated":"2026-02-17T11:12:30Z","file":[{"success":1,"access_level":"open_access","file_id":"21287","file_name":"2025_PRXLife_Sorichetti.pdf","file_size":3732843,"relation":"main_file","date_created":"2026-02-17T11:12:30Z","date_updated":"2026-02-17T11:12:30Z","creator":"dernst","content_type":"application/pdf","checksum":"1702b9bdbfd902a7c08aa4f1479b390d"}],"citation":{"short":"V. Sorichetti, P. Robin, I. Palaia, A. Hernandez-Armendariz, S. Cuylen-Haering, A. Šarić, PRX Life 3 (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.","chicago":"Sorichetti, Valerio, Paul Robin, Ivan Palaia, Alberto Hernandez-Armendariz, Sara Cuylen-Haering, and Anđela Šarić. “Charge Distribution of the Coating Brush Drives Interchromosome Attraction.” <i>PRX Life</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/41fd-r847\">https://doi.org/10.1103/41fd-r847</a>.","ama":"Sorichetti V, Robin P, Palaia I, Hernandez-Armendariz A, Cuylen-Haering S, Šarić A. Charge distribution of the coating brush drives interchromosome attraction. <i>PRX Life</i>. 2025;3(3). doi:<a href=\"https://doi.org/10.1103/41fd-r847\">10.1103/41fd-r847</a>","ieee":"V. Sorichetti, P. Robin, I. Palaia, A. Hernandez-Armendariz, S. Cuylen-Haering, and A. Šarić, “Charge distribution of the coating brush drives interchromosome attraction,” <i>PRX Life</i>, vol. 3, no. 3. American Physical Society, 2025.","apa":"Sorichetti, V., Robin, P., Palaia, I., Hernandez-Armendariz, A., Cuylen-Haering, S., &#38; Šarić, A. (2025). Charge distribution of the coating brush drives interchromosome attraction. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/41fd-r847\">https://doi.org/10.1103/41fd-r847</a>","mla":"Sorichetti, Valerio, et al. “Charge Distribution of the Coating Brush Drives Interchromosome Attraction.” <i>PRX Life</i>, vol. 3, no. 3, 033010, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/41fd-r847\">10.1103/41fd-r847</a>."},"fulldoi":"https://doi.org/10.1103/41fd-r847","publication_identifier":{"eissn":["2835-8279"]},"DOAJ_listed":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","oa":1},{"OA_place":"publisher","oa":1,"fulldoi":"https://doi.org/10.7554/elife.105432","citation":{"short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, ELife 14 (2025).","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. 2025. Balancing stability and flexibility when reshaping archaeal membranes. eLife. 14, 105432.","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Balancing Stability and Flexibility When Reshaping Archaeal Membranes.” <i>ELife</i>. eLife Sciences Publications, 2025. <a href=\"https://doi.org/10.7554/elife.105432\">https://doi.org/10.7554/elife.105432</a>.","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Balancing stability and flexibility when reshaping archaeal membranes. <i>eLife</i>. 2025;14. doi:<a href=\"https://doi.org/10.7554/elife.105432\">10.7554/elife.105432</a>","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (2025). Balancing stability and flexibility when reshaping archaeal membranes. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.105432\">https://doi.org/10.7554/elife.105432</a>","mla":"Santana de Freitas Amaral, Miguel, et al. “Balancing Stability and Flexibility When Reshaping Archaeal Membranes.” <i>ELife</i>, vol. 14, 105432, eLife Sciences Publications, 2025, doi:<a href=\"https://doi.org/10.7554/elife.105432\">10.7554/elife.105432</a>.","ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Balancing stability and flexibility when reshaping archaeal membranes,” <i>eLife</i>, vol. 14. eLife Sciences Publications, 2025."},"publication_identifier":{"eissn":["2050-084X"]},"DOAJ_listed":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2026-02-17T13:02:02Z","file":[{"success":1,"access_level":"open_access","relation":"main_file","date_created":"2026-02-17T13:02:02Z","date_updated":"2026-02-17T13:02:02Z","file_id":"21305","file_name":"2025_elife_Amaral.pdf","file_size":10668225,"checksum":"4116cd5143558ded995fb9ff5fcbc7e0","creator":"dernst","content_type":"application/pdf"}],"day":"07","PlanS_conform":"1","OA_type":"gold","article_type":"original","doi":"10.7554/elife.105432","date_updated":"2026-02-23T11:49:05Z","date_created":"2026-02-16T15:43:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","oa_version":"Published Version","ddc":["570"],"month":"10","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"pmid":1,"related_material":{"record":[{"id":"21304","status":"public","relation":"software"}]},"type":"journal_article","department":[{"_id":"AnSa"}],"ec_funded":1,"article_processing_charge":"Yes","publisher":"eLife Sciences Publications","_id":"21251","quality_controlled":"1","external_id":{"pmid":["41056191 "]},"article_number":"105432","status":"public","intvolume":"        14","language":[{"iso":"eng"}],"acknowledgement":"MA, BB, and AŠ acknowledge funding by the Volkswagen Foundation Grant Az 96727. FF acknowledges financial support by the NOMIS foundation. AŠ acknowledges funding by ERC Starting Grant 'NEPA' 802960. We thank Claudia Flandoli for her help with illustrations.","abstract":[{"text":"Cellular membranes differ across the tree of life. In most bacteria and eukaryotes, single-headed lipids self-assemble into flexible bilayer membranes. By contrast, thermophilic archaea tend to possess bilayer lipids together with double-headed, monolayer spanning bolalipids, which are thought to enable cells to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we explore the trade-offs at play when forming membranes. We find that flexible bolalipids form membranes that resemble bilayer membranes because they are able to assume a U-shaped conformation. Conversely, rigid bolalipids, which resemble the bolalipids with cyclic groups found in thermophilic archaea, take on a straight conformation and form membranes that are stiff and prone to pore formation when they undergo changes in shape. Strikingly, however, the inclusion of small amounts of bilayer lipids in a bolalipid membrane is enough to achieve fluid bolalipid membranes that are both stable and flexible, resolving this trade-off. Our study suggests a mechanism by which archaea can tune the material properties of their membranes as and when required to enable them to survive in harsh environments and to undergo essential membrane remodelling events like cell division.","lang":"eng"}],"publication":"eLife","volume":14,"year":"2025","has_accepted_license":"1","publication_status":"published","date_published":"2025-10-07T00:00:00Z","author":[{"full_name":"Santana de Freitas Amaral, Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","last_name":"Santana de Freitas Amaral"},{"last_name":"Frey","orcid":"0000-0001-8501-6017","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F"},{"last_name":"Jiang","first_name":"Xiuyun","full_name":"Jiang, Xiuyun"},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"title":"Balancing stability and flexibility when reshaping archaeal membranes"},{"publication_status":"published","year":"2025","has_accepted_license":"1","date_published":"2025-09-05T00:00:00Z","author":[{"last_name":"Meadowcroft","orcid":"0000-0003-3441-1337","first_name":"Billie","full_name":"Meadowcroft, Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"last_name":"Sorichetti","first_name":"Valerio","orcid":"0000-0002-9645-6576","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","full_name":"Sorichetti, Valerio"},{"full_name":"Ratajczyk, Eryk","first_name":"Eryk","last_name":"Ratajczyk"},{"id":"4ecec223-9070-11ef-a0a9-bc76077bea8d","full_name":"Perez Verdugo, Fernanda L","last_name":"Perez Verdugo","first_name":"Fernanda L"},{"full_name":"Khalilgharibi, Nargess","last_name":"Khalilgharibi","first_name":"Nargess"},{"last_name":"Mao","first_name":"Yanlan","full_name":"Mao, Yanlan"},{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","full_name":"Palaia, Ivan","last_name":"Palaia","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"title":"Nonequilibrium remodeling of collagen IV networks in Silico","_id":"21256","article_processing_charge":"Yes","publisher":"American Physical Society","article_number":"033019","quality_controlled":"1","acknowledgement":"This work received funding from the European Research Council under the European Union's Horizon 2020 research and innovation program through Grant Agreement No. 802960 (B.M., V.S., I.P., and A.Š.), the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413 (I.P.), the NOMIS Foundation (F.P.-V.), the National Centre for the Replacement, Refinement and Reduction of Animals in Research Grant No. NC/T002425/1 (N.K.), Leverhulme Trust project Grant No. RPG-2020-068 (N.K.), MRC Fellowship No. MR/W027437/1 (Y.M.), a Lister Institute Research Prize (Y.M.) and EMBO Young Investigator Programme (Y.M. and A.Š.).","intvolume":"         3","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"Collagen IV is one of the main components of the basement membrane, a layer of material that lines the majority of tissues in multicellular organisms. Collagen IV molecules assemble into networks, providing stiffness and elasticity to tissues and informing cell and organ shape, especially during development. In this work, we develop two coarse-grained models for collagen IV molecules that retain biochemical bond specificity and coarse grain at different length scales. Through molecular-dynamics simulations, we test the assembly and mechanics of the resulting networks and measure their response to strain in terms of stress, microscopic alignment, and bond dynamics. Within the basement membrane, collagen IV networks rearrange by molecule turnover, which affects tissue organization and can be linked with enzyme activity. Here we explore network rearrangements via bond remodeling, the process of breaking and remaking of bonds between network molecules. We then investigate the effects of active (enzymatic) bond remodeling. We find that this nonequilibrium remodeling allows a network to keep its integrity under strain, while relaxing fully over a variety of timescales, a dynamic response that is unavailable to networks undergoing equilibrium remodeling.","lang":"eng"}],"publication":"PRX Life","volume":3,"date_updated":"2026-02-17T13:37:38Z","date_created":"2026-02-16T15:55:03Z","doi":"10.1103/gdd5-rnh7","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","oa_version":"Published Version","ddc":["570"],"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"},{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"},{"name":"EMBO Young Investigator Program - Andela Saric","_id":"349b6ff1-11ca-11ed-8bc3-f006047c2eeb"}],"department":[{"_id":"AnSa"}],"ec_funded":1,"type":"journal_article","oa":1,"OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"DOAJ_listed":"1","fulldoi":"https://doi.org/10.1103/gdd5-rnh7","publication_identifier":{"eissn":["2835-8279"]},"citation":{"chicago":"Meadowcroft, Billie, Valerio Sorichetti, Eryk Ratajczyk, Fernanda L Perez Verdugo, Nargess Khalilgharibi, Yanlan Mao, Ivan Palaia, and Anđela Šarić. “Nonequilibrium Remodeling of Collagen IV Networks in Silico.” <i>PRX Life</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/gdd5-rnh7\">https://doi.org/10.1103/gdd5-rnh7</a>.","ista":"Meadowcroft B, Sorichetti V, Ratajczyk E, Perez Verdugo FL, Khalilgharibi N, Mao Y, Palaia I, Šarić A. 2025. Nonequilibrium remodeling of collagen IV networks in Silico. PRX Life. 3, 033019.","short":"B. Meadowcroft, V. Sorichetti, E. Ratajczyk, F.L. Perez Verdugo, N. Khalilgharibi, Y. Mao, I. Palaia, A. Šarić, PRX Life 3 (2025).","mla":"Meadowcroft, Billie, et al. “Nonequilibrium Remodeling of Collagen IV Networks in Silico.” <i>PRX Life</i>, vol. 3, 033019, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/gdd5-rnh7\">10.1103/gdd5-rnh7</a>.","ieee":"B. Meadowcroft <i>et al.</i>, “Nonequilibrium remodeling of collagen IV networks in Silico,” <i>PRX Life</i>, vol. 3. American Physical Society, 2025.","apa":"Meadowcroft, B., Sorichetti, V., Ratajczyk, E., Perez Verdugo, F. L., Khalilgharibi, N., Mao, Y., … Šarić, A. (2025). Nonequilibrium remodeling of collagen IV networks in Silico. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/gdd5-rnh7\">https://doi.org/10.1103/gdd5-rnh7</a>","ama":"Meadowcroft B, Sorichetti V, Ratajczyk E, et al. Nonequilibrium remodeling of collagen IV networks in Silico. <i>PRX Life</i>. 2025;3. doi:<a href=\"https://doi.org/10.1103/gdd5-rnh7\">10.1103/gdd5-rnh7</a>"},"file":[{"success":1,"access_level":"open_access","date_updated":"2026-02-17T13:36:01Z","date_created":"2026-02-17T13:36:01Z","relation":"main_file","file_id":"21308","file_size":2277704,"file_name":"2025_PRXLife_Meadowcroft.pdf","checksum":"04cae5231d97e533145c493880fadbd9","creator":"dernst","content_type":"application/pdf"}],"file_date_updated":"2026-02-17T13:36:01Z","PlanS_conform":"1","OA_type":"gold","article_type":"original","day":"05"},{"publisher":"Elsevier","article_processing_charge":"Yes","_id":"19846","quality_controlled":"1","article_number":"102623","issue":"6","external_id":{"isi":["001516570500009"]},"abstract":[{"text":"The Ca2+-release-activated Ca2+ (CRAC) channel Orai1 is activated by interaction with the Ca2+ sensor Stromal Interaction Molecule 1 (STIM1). Owing to the lack of structurally resolved Orai1/STIM1 complexes, the impact of their coupling on individual Orai1 transmembrane domain (TM) movements is unclear. This study investigates STIM1-independent and STIM1-dependent Orai1-TM dynamics using photocrosslinking unnatural amino acids (UAAs) at each individual TM position. We primarily identify CRAC-channel-like currents directly after UAA incorporation or additional UV-light irradiation at TM3 sites that interface with non-pore-lining TMs. Using UAAs combined with conventional site-directed mutagenesis and molecular dynamics simulations, we discover that pore opening involves a widening of interfaces formed by TM3 with non-pore-lining TMs. Orai1 mutants with a UAA in TM3 exhibit weaker STIM1-induced activation after UV exposure, possibly caused by a restricted widening of non-pore-lining TM interfaces. We demonstrate that photocrosslinking UAAs are excellent tools for improving our understanding of key determinants and ion channel dynamics modulating pore opening.","lang":"eng"}],"status":"public","intvolume":"         6","language":[{"iso":"eng"}],"acknowledgement":"We thank S. Buchegger for excellent technical assistance. This research was funded by the Austrian Science Fund (FWF) projects https://doi.org/10.55776/P32851, https://doi.org/10.55776/P35900, and https://doi.org/10.55776/P36202 to I.D. and https://doi.org/10.55776/PAT6871323 to A.T. N.M. is funded within the DOC program of the OeAW (Austrian Academy of Science). For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","volume":6,"publication":"Cell Reports Physical Science","isi":1,"has_accepted_license":"1","year":"2025","publication_status":"published","date_published":"2025-06-18T00:00:00Z","author":[{"full_name":"Najjar, Hadil","first_name":"Hadil","last_name":"Najjar"},{"full_name":"Weiß, Sarah","first_name":"Sarah","last_name":"Weiß"},{"first_name":"Ferdinand","last_name":"Horvath","full_name":"Horvath, Ferdinand","id":"b0dc7f61-21a3-11ef-a9b4-e6ab1aa6f21e"},{"last_name":"Hopl","first_name":"Valentina","full_name":"Hopl, Valentina"},{"last_name":"Tiffner","first_name":"Adéla","full_name":"Tiffner, Adéla"},{"full_name":"Höbarth, Lorenz","first_name":"Lorenz","last_name":"Höbarth"},{"last_name":"Söllner","first_name":"Julia","full_name":"Söllner, Julia"},{"full_name":"Fröhlich, Maximilian","first_name":"Maximilian","last_name":"Fröhlich"},{"full_name":"Prantl, Magdalena","first_name":"Magdalena","last_name":"Prantl"},{"full_name":"Müller, Nora","first_name":"Nora","last_name":"Müller"},{"first_name":"Yuliia","last_name":"Nazarenko","full_name":"Nazarenko, Yuliia"},{"full_name":"Harant, Selina","last_name":"Harant","first_name":"Selina"},{"full_name":"Weissenböck, Lukas","first_name":"Lukas","last_name":"Weissenböck"},{"full_name":"Grabmayr, Herwig","first_name":"Herwig","last_name":"Grabmayr"},{"last_name":"Sallinger","first_name":"Matthias","full_name":"Sallinger, Matthias"},{"last_name":"Maltan","first_name":"Lena","full_name":"Maltan, Lena"},{"first_name":"Linda V.","last_name":"Echefu","full_name":"Echefu, Linda V."},{"first_name":"Tamara","last_name":"Radiskovic","full_name":"Radiskovic, Tamara"},{"full_name":"Leopold, Melanie","last_name":"Leopold","first_name":"Melanie"},{"full_name":"Lindinger, Sonja","last_name":"Lindinger","first_name":"Sonja"},{"last_name":"Humer","first_name":"Christina","full_name":"Humer, Christina"},{"full_name":"Höglinger, Carmen","last_name":"Höglinger","first_name":"Carmen"},{"first_name":"Heinrich","last_name":"Krobath","full_name":"Krobath, Heinrich"},{"last_name":"Renger","first_name":"Thomas","full_name":"Renger, Thomas"},{"first_name":"Isabella","last_name":"Derler","full_name":"Derler, Isabella"}],"title":"STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening","OA_place":"publisher","scopus_import":"1","oa":1,"fulldoi":"https://doi.org/10.1016/j.xcrp.2025.102623","citation":{"mla":"Najjar, Hadil, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces Is Crucial for Orai1 Pore Opening.” <i>Cell Reports Physical Science</i>, vol. 6, no. 6, 102623, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">10.1016/j.xcrp.2025.102623</a>.","ieee":"H. Najjar <i>et al.</i>, “STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening,” <i>Cell Reports Physical Science</i>, vol. 6, no. 6. Elsevier, 2025.","apa":"Najjar, H., Weiß, S., Horvath, F., Hopl, V., Tiffner, A., Höbarth, L., … Derler, I. (2025). STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. <i>Cell Reports Physical Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">https://doi.org/10.1016/j.xcrp.2025.102623</a>","ama":"Najjar H, Weiß S, Horvath F, et al. STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. <i>Cell Reports Physical Science</i>. 2025;6(6). doi:<a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">10.1016/j.xcrp.2025.102623</a>","short":"H. Najjar, S. Weiß, F. Horvath, V. Hopl, A. Tiffner, L. Höbarth, J. Söllner, M. Fröhlich, M. Prantl, N. Müller, Y. Nazarenko, S. Harant, L. Weissenböck, H. Grabmayr, M. Sallinger, L. Maltan, L.V. Echefu, T. Radiskovic, M. Leopold, S. Lindinger, C. Humer, C. Höglinger, H. Krobath, T. Renger, I. Derler, Cell Reports Physical Science 6 (2025).","chicago":"Najjar, Hadil, Sarah Weiß, Ferdinand Horvath, Valentina Hopl, Adéla Tiffner, Lorenz Höbarth, Julia Söllner, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces Is Crucial for Orai1 Pore Opening.” <i>Cell Reports Physical Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">https://doi.org/10.1016/j.xcrp.2025.102623</a>.","ista":"Najjar H, Weiß S, Horvath F, Hopl V, Tiffner A, Höbarth L, Söllner J, Fröhlich M, Prantl M, Müller N, Nazarenko Y, Harant S, Weissenböck L, Grabmayr H, Sallinger M, Maltan L, Echefu LV, Radiskovic T, Leopold M, Lindinger S, Humer C, Höglinger C, Krobath H, Renger T, Derler I. 2025. STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. Cell Reports Physical Science. 6(6), 102623."},"publication_identifier":{"eissn":["2666-3864"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"DOAJ_listed":"1","file_date_updated":"2025-06-23T10:20:22Z","file":[{"checksum":"37ff7c396f966d0ec363e4691d63d402","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_created":"2025-06-23T10:20:22Z","date_updated":"2025-06-23T10:20:22Z","file_id":"19868","file_name":"2025_CellReportsPhysicalScience_Najjar.pdf","file_size":9771117,"access_level":"open_access","success":1}],"day":"18","article_type":"original","OA_type":"gold","date_created":"2025-06-15T22:01:31Z","date_updated":"2025-09-30T12:53:15Z","doi":"10.1016/j.xcrp.2025.102623","oa_version":"Published Version","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"06","type":"journal_article","department":[{"_id":"AnSa"}]},{"file_date_updated":"2025-12-30T10:16:40Z","file":[{"access_level":"open_access","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"590bedad19b6f6d40a7ee036a056a6d9","file_id":"20912","file_name":"2025_SoftMatter_MunozBasagoiti.pdf","file_size":4841140,"date_updated":"2025-12-30T10:16:40Z","date_created":"2025-12-30T10:16:40Z","relation":"main_file"}],"day":"28","OA_type":"hybrid","article_type":"original","OA_place":"publisher","scopus_import":"1","oa":1,"fulldoi":"https://doi.org/10.1039/d5sm00148j","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"ama":"Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada A, Šarić A. A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>. 2025;21(40):7736-7756. doi:<a href=\"https://doi.org/10.1039/d5sm00148j\">10.1039/d5sm00148j</a>","mla":"Muñoz Basagoiti, Maitane, et al. “A Tutorial for Mesoscale Computer Simulations of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.” <i>Soft Matter</i>, vol. 21, no. 40, Royal Society of Chemistry, 2025, pp. 7736–56, doi:<a href=\"https://doi.org/10.1039/d5sm00148j\">10.1039/d5sm00148j</a>.","ieee":"M. Muñoz Basagoiti, F. F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral, A. Prada, and A. Šarić, “A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations,” <i>Soft Matter</i>, vol. 21, no. 40. Royal Society of Chemistry, pp. 7736–7756, 2025.","apa":"Muñoz Basagoiti, M., Frey, F. F., Meadowcroft, B., Santana de Freitas Amaral, M., Prada, A., &#38; Šarić, A. (2025). A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d5sm00148j\">https://doi.org/10.1039/d5sm00148j</a>","ista":"Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada A, Šarić A. 2025. A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. Soft Matter. 21(40), 7736–7756.","chicago":"Muñoz Basagoiti, Maitane, Felix F Frey, Billie Meadowcroft, Miguel Santana de Freitas Amaral, Adam Prada, and Anđela Šarić. “A Tutorial for Mesoscale Computer Simulations of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.” <i>Soft Matter</i>. Royal Society of Chemistry, 2025. <a href=\"https://doi.org/10.1039/d5sm00148j\">https://doi.org/10.1039/d5sm00148j</a>.","short":"M. Muñoz Basagoiti, F.F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral, A. Prada, A. Šarić, Soft Matter 21 (2025) 7736–7756."},"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"page":"7736-7756","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes"}],"type":"journal_article","ec_funded":1,"department":[{"_id":"AnSa"}],"doi":"10.1039/d5sm00148j","date_created":"2025-09-10T05:34:36Z","date_updated":"2025-12-30T10:16:52Z","oa_version":"Published Version","ddc":["540"],"arxiv":1,"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","abstract":[{"lang":"eng","text":"Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting up and using membrane simulations can come with barriers due to the multidisciplinary effort involved and the vast choice of existing simulations models. In this review, we introduce the non-expert reader to coarse-grained membrane simulations at the mesoscale. Firstly, we give a concise overview of the modelling approaches to study fluid membranes, together with guidance to more specialized references. Secondly, we provide a conceptual guide on how to develop mesoscale membrane simulations. Lastly, we construct a hands-on tutorial on how to apply mesoscale membrane simulations, by providing a pedagogical examination of membrane tether pulling, shape and mechanics of membrane tubes, and membrane fluctuations with three different membrane models, and discussing them in terms of their scope and how resource-intensive they are. To ease the reader's venture into the field, we provide a repository with ready-to-run tutorials."}],"intvolume":"        21","license":"https://creativecommons.org/licenses/by-nc/4.0/","status":"public","language":[{"iso":"eng"}],"acknowledgement":"We thank Oded Farago, Angelo Cacciuto, Jeriann Beiter and Pietro Sillano for helpful discussions and a critical reading of the manuscript. MMB and AP acknowledge funding by the European Unions Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. FF acknowledges financial support by the NOMIS foundation. BM and AŠ acknowledge funding by ERC Starting Grant “NEPA” 802960. MA and AŠ acknowledge funding by the Volkswagen Foundation Grant Az 96727.","volume":21,"publication":"Soft Matter","publisher":"Royal Society of Chemistry","article_processing_charge":"Yes (via OA deal)","_id":"20318","quality_controlled":"1","issue":"40","external_id":{"isi":["001562846800001"],"arxiv":["2502.09798"]},"date_published":"2025-07-28T00:00:00Z","title":"A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations","author":[{"last_name":"Muñoz Basagoiti","orcid":"0000-0003-1483-1457","first_name":"Maitane","full_name":"Muñoz Basagoiti, Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607"},{"last_name":"Frey","orcid":"0000-0001-8501-6017","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F"},{"full_name":"Meadowcroft, Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","first_name":"Billie","orcid":"0000-0003-3441-1337","last_name":"Meadowcroft"},{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral","first_name":"Miguel"},{"full_name":"Prada, Adam","id":"a43ed60a-dd22-11ed-9bf7-b34133792ea9","last_name":"Prada","first_name":"Adam"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"}],"isi":1,"has_accepted_license":"1","year":"2025","publication_status":"published"},{"_id":"20477","publisher":"American Physical Society","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2301.00610"],"isi":["001587121300010"]},"article_number":"148002","issue":"14","quality_controlled":"1","language":[{"iso":"eng"}],"acknowledgement":"This work has received funding from the European Union’s Horizon 2020 and Horizon Europe research and innovation programs under the Marie Skłodowska-Curie Grants No. 674979-NANOTRANS (I. P., P. B. W., B. R., E. T.), No. 101034413 (I. P.), and No. 101119598-FLUXIONIC (M. D., B. R., E. T.), as well as from the European Research Council under Grant No. 863473 (B. R.). B. R. acknowledges financial support from the French Agence Nationale de la Recherche (ANR) under Grant No. ANR-21-CE29-0021-02 (DIADEM). I. P. thanks Anđela Šarić for further support at ISTA.","intvolume":"       135","status":"public","abstract":[{"text":"An electric double-layer capacitor (EDLC) stores energy by modulating the spatial distribution of ions in the electrolytic solution that it contains. We determine the mean-field timescales for planar EDLC relaxation to equilibrium after a potential difference is applied. We tackle first the fully symmetric case, where positive and negative ionic species have the same valence and diffusivity, and then the general, more complex, asymmetric case. Depending on the applied voltage and salt concentration, different regimes appear, revealing a remarkably rich phenomenology relevant for nanocapacitors.","lang":"eng"}],"publication":"Physical Review Letters","volume":135,"isi":1,"publication_status":"published","year":"2025","has_accepted_license":"1","date_published":"2025-09-29T00:00:00Z","author":[{"last_name":"Palaia","first_name":"Ivan","orcid":" 0000-0002-8843-9485 ","full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"full_name":"Asta, Adelchi J.","last_name":"Asta","first_name":"Adelchi J."},{"last_name":"Dutta","first_name":"Megh","full_name":"Dutta, Megh"},{"full_name":"Warren, Patrick B.","first_name":"Patrick B.","last_name":"Warren"},{"full_name":"Rotenberg, Benjamin","first_name":"Benjamin","last_name":"Rotenberg"},{"first_name":"Emmanuel","last_name":"Trizac","full_name":"Trizac, Emmanuel"}],"title":"Charging dynamics of electric double-layer nanocapacitors in mean field","oa":1,"scopus_import":"1","OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.1103/72b9-c8cq","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"citation":{"short":"I. Palaia, A.J. Asta, M. Dutta, P.B. Warren, B. Rotenberg, E. Trizac, Physical Review Letters 135 (2025).","chicago":"Palaia, Ivan, Adelchi J. Asta, Megh Dutta, Patrick B. Warren, Benjamin Rotenberg, and Emmanuel Trizac. “Charging Dynamics of Electric Double-Layer Nanocapacitors in Mean Field.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/72b9-c8cq\">https://doi.org/10.1103/72b9-c8cq</a>.","ista":"Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. 2025. Charging dynamics of electric double-layer nanocapacitors in mean field. Physical Review Letters. 135(14), 148002.","ieee":"I. Palaia, A. J. Asta, M. Dutta, P. B. Warren, B. Rotenberg, and E. Trizac, “Charging dynamics of electric double-layer nanocapacitors in mean field,” <i>Physical Review Letters</i>, vol. 135, no. 14. American Physical Society, 2025.","apa":"Palaia, I., Asta, A. J., Dutta, M., Warren, P. B., Rotenberg, B., &#38; Trizac, E. (2025). Charging dynamics of electric double-layer nanocapacitors in mean field. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/72b9-c8cq\">https://doi.org/10.1103/72b9-c8cq</a>","mla":"Palaia, Ivan, et al. “Charging Dynamics of Electric Double-Layer Nanocapacitors in Mean Field.” <i>Physical Review Letters</i>, vol. 135, no. 14, 148002, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/72b9-c8cq\">10.1103/72b9-c8cq</a>.","ama":"Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. Charging dynamics of electric double-layer nanocapacitors in mean field. <i>Physical Review Letters</i>. 2025;135(14). doi:<a href=\"https://doi.org/10.1103/72b9-c8cq\">10.1103/72b9-c8cq</a>"},"file":[{"creator":"dernst","content_type":"application/pdf","checksum":"e29809fea48b18217d1779980f7117c4","file_id":"20526","file_name":"2025_PhysReviewLetters_Palaia.pdf","file_size":480414,"date_created":"2025-10-23T11:57:20Z","date_updated":"2025-10-23T11:57:20Z","relation":"main_file","access_level":"open_access","success":1}],"file_date_updated":"2025-10-23T11:57:20Z","PlanS_conform":"1","article_type":"original","OA_type":"hybrid","day":"29","date_created":"2025-10-16T13:09:30Z","doi":"10.1103/72b9-c8cq","date_updated":"2025-12-01T15:02:16Z","month":"09","corr_author":"1","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","ddc":["530"],"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"department":[{"_id":"AnSa"}],"ec_funded":1,"type":"journal_article"},{"abstract":[{"lang":"eng","text":"A parallel plate capacitor containing an electrolytic solution is the simplest model of a supercapacitor or electric double-layer capacitor. Using both analytical and numerical techniques, we solve the Poisson-Nernst-Planck equations for such a system, describing the mean-field charging dynamics of the capacitor, when a constant potential difference is abruptly applied to its plates. Working at constant total number of ions, we focus on the physical processes involved in the relaxation and, whenever possible, give its functional shape and exact time constants. We first review and study the case of a symmetric binary electrolyte, where we assume the two ionic species to have the same charges and diffusivities. We then relax these assumptions and present results for a generic strong (i.e fully dissociated) binary electrolyte. At low electrolyte concentration, the relaxation is simple to understand, as the dynamics of positive and negative ions appear decoupled. At higher electrolyte concentration, we distinguish several regimes. In the linear regime (low voltages), relaxation is multiexponential, it starts by the buildup of the equilibrium charge profile and continues with neutral mass diffusion, and the relevant timescales feature both the average and the Nernst-Hartley diffusion coefficients. In the purely nonlinear regime (intermediate voltages), the initial relaxation is slowed down exponentially due to increased capacitance, while bulk effects become more and more evident. In the fully nonlinear regime (high voltages), the dynamics of charge and mass are completely entangled and, asymptotically, the relaxation is linear in time. We finally discuss nonideal behavior in real capacitors and provide conditions for which mean-field is expected to hold."}],"intvolume":"       112","status":"public","acknowledgement":"This work has received funding from the European Union's Horizon 2020 and Horizon Europe research and innovation programs under the Marie Skłodowska-Curie Grants No. 674979-NANOTRANS (I.P., P.B.W., B.R., and E.T.), No. 101034413 (I.P.), and No. 101119598-FLUXIONIC (M.D., B.R., and E.T.), as well as from the European Research Council under Grant No. 863473 (B.R.). B.R. acknowledges financial support from the French Agence Nationale de la Recherche (ANR) under Grant No. ANR-21-CE29-0021-02 (DIADEM). I.P. thanks Anđela Šarić for further support at ISTA.","language":[{"iso":"eng"}],"volume":112,"publication":"Physical Review E","_id":"20483","article_processing_charge":"Yes (via OA deal)","publisher":"American Physical Society","article_number":"035417","issue":"3","external_id":{"arxiv":["2303.07859"],"isi":["001586173200001"]},"quality_controlled":"1","date_published":"2025-09-29T00:00:00Z","title":"Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes","author":[{"full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","last_name":"Palaia"},{"full_name":"Asta, Adelchi J.","first_name":"Adelchi J.","last_name":"Asta"},{"full_name":"Dutta, Megh","last_name":"Dutta","first_name":"Megh"},{"first_name":"Patrick B.","last_name":"Warren","full_name":"Warren, Patrick B."},{"full_name":"Rotenberg, Benjamin","last_name":"Rotenberg","first_name":"Benjamin"},{"full_name":"Trizac, Emmanuel","last_name":"Trizac","first_name":"Emmanuel"}],"isi":1,"publication_status":"published","has_accepted_license":"1","year":"2025","file":[{"success":1,"access_level":"open_access","relation":"main_file","date_updated":"2025-10-23T09:15:56Z","date_created":"2025-10-23T09:15:56Z","file_id":"20521","file_size":1211712,"file_name":"2025_PhysReviewE_Palaia.pdf","checksum":"658a9b1ce6b2edcf138b54c55a566f0e","creator":"dernst","content_type":"application/pdf"}],"file_date_updated":"2025-10-23T09:15:56Z","OA_type":"hybrid","PlanS_conform":"1","article_type":"original","day":"29","scopus_import":"1","oa":1,"OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.1103/p4dg-snqf","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"citation":{"short":"I. Palaia, A.J. Asta, M. Dutta, P.B. Warren, B. Rotenberg, E. Trizac, Physical Review E 112 (2025).","ista":"Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. 2025. Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes. Physical Review E. 112(3), 035417.","chicago":"Palaia, Ivan, Adelchi J. Asta, Megh Dutta, Patrick B. Warren, Benjamin Rotenberg, and Emmanuel Trizac. “Poisson-Nernst-Planck Charging Dynamics of an Electric Double-Layer Capacitor: Symmetric and Asymmetric Binary Electrolytes.” <i>Physical Review E</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/p4dg-snqf\">https://doi.org/10.1103/p4dg-snqf</a>.","ama":"Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes. <i>Physical Review E</i>. 2025;112(3). doi:<a href=\"https://doi.org/10.1103/p4dg-snqf\">10.1103/p4dg-snqf</a>","ieee":"I. Palaia, A. J. Asta, M. Dutta, P. B. Warren, B. Rotenberg, and E. Trizac, “Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes,” <i>Physical Review E</i>, vol. 112, no. 3. American Physical Society, 2025.","mla":"Palaia, Ivan, et al. “Poisson-Nernst-Planck Charging Dynamics of an Electric Double-Layer Capacitor: Symmetric and Asymmetric Binary Electrolytes.” <i>Physical Review E</i>, vol. 112, no. 3, 035417, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/p4dg-snqf\">10.1103/p4dg-snqf</a>.","apa":"Palaia, I., Asta, A. J., Dutta, M., Warren, P. B., Rotenberg, B., &#38; Trizac, E. (2025). Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/p4dg-snqf\">https://doi.org/10.1103/p4dg-snqf</a>"},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"ec_funded":1,"department":[{"_id":"AnSa"}],"type":"journal_article","doi":"10.1103/p4dg-snqf","date_created":"2025-10-16T13:15:16Z","date_updated":"2025-12-01T13:06:51Z","month":"09","ddc":["530"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"corr_author":"1"},{"isi":1,"year":"2025","has_accepted_license":"1","publication_status":"published","date_published":"2025-10-21T00:00:00Z","title":"Temporal and spatial coordination of DNA segregation and cell division in an archaeon","author":[{"full_name":"Parham, Joe","last_name":"Parham","first_name":"Joe"},{"full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","last_name":"Sorichetti","first_name":"Valerio","orcid":"0000-0002-9645-6576"},{"first_name":"Alice","last_name":"Cezanne","full_name":"Cezanne, Alice"},{"first_name":"Sherman","last_name":"Foo","full_name":"Foo, Sherman"},{"first_name":"Yin Wei","last_name":"Kuo","full_name":"Kuo, Yin Wei"},{"first_name":"Baukje","last_name":"Hoogenberg","full_name":"Hoogenberg, Baukje"},{"full_name":"Radoux-Mergault, Arthur","last_name":"Radoux-Mergault","first_name":"Arthur"},{"last_name":"Mawdesley","first_name":"Eloise","full_name":"Mawdesley, Eloise"},{"first_name":"Lydia Daniels","last_name":"Gatward","full_name":"Gatward, Lydia Daniels"},{"full_name":"Boulanger, Jerome","last_name":"Boulanger","first_name":"Jerome"},{"last_name":"Schulze","first_name":"Ulrike","full_name":"Schulze, Ulrike"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"}],"publisher":"National Academy of Sciences","article_processing_charge":"Yes (in subscription journal)","_id":"20530","quality_controlled":"1","external_id":{"pmid":["41091768"],"isi":["001620648600001"]},"issue":"42","language":[{"iso":"eng"}],"acknowledgement":"We thank Matthew Kenneth for his assistance with live cell imaging. We thank Arthur Charles-Orszag and Dyche Mullins for generously gifting the SegA and SegB antibodies, and Sonja-Verena Albers for gifting the CdvA-HA overexpression plasmid. We thank the Light Microscopy and Flow Cytometry facilities at the MRC-LMB, and all the core staff at the MRC-LMB for their support. We thank all members of the Baum lab for helpful discussions. We would like to thank Magdalena Lechowska, Gautam Dey, Laura Downie, and Iva Tolic for critical reading of the manuscript. J.P. was supported by the Medical Research Council—Laboratory of Molecular Biology (MC_UP_1201/27). A.C. was funded by an EMBO Postdoctoral fellowship (ALTF_1041-2021), a Marie Sklodowska-Curie Individual Fellowship (101068523) provided by UKRI and by the Wellcome Trust (222460/Z/21/Z). B.H. was supported by Wellcome Trust (203276/A/16/Z). Y.-W.K. was supported by an EMBO postdoctoral fellowship (ALTF 903-2021) and by the Medical Research Council—Laboratory of Molecular Biology (MC_UP_1201/27); S.F. was supported by the Wellcome Trust (222460/Z/21/Z); B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z) and (222460/Z/21/Z), the VW Foundation (94933), and from the Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). V.S. and A.Š. acknowledge funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant no.802960 to A.Š.), the Vallee Scholarship, and the EMBO Young Investigator Programme (A.Š.). The collaborative work of A.Š.’s and B.B. teams was also supported by a Moore–Simons Project on the Origin of the Eukaryotic Cell, Simons Foundation 735929LPI.","status":"public","intvolume":"       122","abstract":[{"text":"Cells must coordinate DNA segregation with cytokinesis to ensure that each daughter cell inherits a complete genome. Here, we explore how DNA segregation and division are mechanistically coupled in archaeal relatives of eukaryotes, which lack Cyclin-dependent kinase (CDK)/Cyclins. Using live cell imaging, we first describe the series of sequential changes in DNA organization that accompany cell division in Sulfolobus, which computational modeling shows likely aid genome segregation. Through a perturbation analysis we identify a regulatory checkpoint which ensures that the compaction of the genome into two spatially segregated nucleoids only occurs once cells have assembled a division ring—which also defines the axis of DNA segregation. Finally, we show that DNA compaction and segregation depend, in part, on a ParA homologue, SegA, and its partner SegB, whose absence leads to bridging DNA. Taken together, these data show how regulatory checkpoints like those operating in eukaryotes aid high-fidelity division in an archaeon.","lang":"eng"}],"publication":"Proceedings of the National Academy of Sciences","volume":122,"date_updated":"2026-02-16T12:32:31Z","date_created":"2025-10-26T23:01:33Z","doi":"10.1073/pnas.2513939122","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","ddc":["570"],"month":"10","page":"e2513939122","project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"_id":"349b6ff1-11ca-11ed-8bc3-f006047c2eeb","name":"EMBO Young Investigator Program - Andela Saric"}],"pmid":1,"type":"journal_article","department":[{"_id":"AnSa"}],"ec_funded":1,"OA_place":"publisher","oa":1,"scopus_import":"1","citation":{"ama":"Parham J, Sorichetti V, Cezanne A, et al. Temporal and spatial coordination of DNA segregation and cell division in an archaeon. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(42):e2513939122. doi:<a href=\"https://doi.org/10.1073/pnas.2513939122\">10.1073/pnas.2513939122</a>","mla":"Parham, Joe, et al. “Temporal and Spatial Coordination of DNA Segregation and Cell Division in an Archaeon.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 42, National Academy of Sciences, 2025, p. e2513939122, doi:<a href=\"https://doi.org/10.1073/pnas.2513939122\">10.1073/pnas.2513939122</a>.","ieee":"J. Parham <i>et al.</i>, “Temporal and spatial coordination of DNA segregation and cell division in an archaeon,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 42. National Academy of Sciences, p. e2513939122, 2025.","apa":"Parham, J., Sorichetti, V., Cezanne, A., Foo, S., Kuo, Y. W., Hoogenberg, B., … Baum, B. (2025). Temporal and spatial coordination of DNA segregation and cell division in an archaeon. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2513939122\">https://doi.org/10.1073/pnas.2513939122</a>","short":"J. Parham, V. Sorichetti, A. Cezanne, S. Foo, Y.W. Kuo, B. Hoogenberg, A. Radoux-Mergault, E. Mawdesley, L.D. Gatward, J. Boulanger, U. Schulze, A. Šarić, B. Baum, Proceedings of the National Academy of Sciences 122 (2025) e2513939122.","ista":"Parham J, Sorichetti V, Cezanne A, Foo S, Kuo YW, Hoogenberg B, Radoux-Mergault A, Mawdesley E, Gatward LD, Boulanger J, Schulze U, Šarić A, Baum B. 2025. Temporal and spatial coordination of DNA segregation and cell division in an archaeon. Proceedings of the National Academy of Sciences. 122(42), e2513939122.","chicago":"Parham, Joe, Valerio Sorichetti, Alice Cezanne, Sherman Foo, Yin Wei Kuo, Baukje Hoogenberg, Arthur Radoux-Mergault, et al. “Temporal and Spatial Coordination of DNA Segregation and Cell Division in an Archaeon.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2513939122\">https://doi.org/10.1073/pnas.2513939122</a>."},"fulldoi":"https://doi.org/10.1073/pnas.2513939122","publication_identifier":{"eissn":["1091-6490"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2025-10-27T08:12:59Z","file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","creator":"dernst","checksum":"3555d51f438d2e356039a9b697eac3ee","file_size":2649194,"file_name":"2025_PNAS_Parham.pdf","file_id":"20543","date_created":"2025-10-27T08:12:59Z","date_updated":"2025-10-27T08:12:59Z","relation":"main_file"}],"day":"21","PlanS_conform":"1","OA_type":"hybrid","article_type":"original"},{"date_created":"2025-01-12T23:04:00Z","date_updated":"2026-08-07T09:43:12Z","doi":"10.1038/s41467-024-55449-7","oa_version":"Published Version","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"01","pmid":1,"supplementarymaterial":"no","type":"journal_article","department":[{"_id":"AnSa"},{"_id":"BiCh"}],"OA_place":"publisher","scopus_import":"1","oa":1,"fulldoi":"https://doi.org/10.1038/s41467-024-55449-7","publication_identifier":{"eissn":["2041-1723"]},"citation":{"mla":"Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>, vol. 16, 270, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>.","ieee":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","apa":"Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., &#38; Laio, A. (2025). Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>","ama":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>","short":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications 16 (2025).","chicago":"Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>.","ista":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 16, 270."},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"DOAJ_listed":"1","file_date_updated":"2025-01-14T06:59:25Z","file":[{"success":1,"access_level":"open_access","file_id":"18846","file_size":1216738,"file_name":"2025_NatureComm_Wild.pdf","date_created":"2025-01-14T06:59:25Z","relation":"main_file","date_updated":"2025-01-14T06:59:25Z","creator":"dernst","content_type":"application/pdf","checksum":"b3d0f3568d9a87c494cf231a5324029a"}],"day":"02","article_type":"original","OA_type":"gold","isi":1,"has_accepted_license":"1","year":"2025","publication_status":"published","date_published":"2025-01-02T00:00:00Z","researchdata_availability":"yes","title":"Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance","author":[{"full_name":"Wild, Romina","last_name":"Wild","first_name":"Romina"},{"first_name":"Felix","orcid":"0009-0000-1457-795X","last_name":"Wodaczek","full_name":"Wodaczek, Felix","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e"},{"first_name":"Vittorio","last_name":"Del Tatto","full_name":"Del Tatto, Vittorio"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng"},{"first_name":"Alessandro","last_name":"Laio","full_name":"Laio, Alessandro"}],"dataavailabilitystatement":"The data generated by feature selection in this study have been deposited on OSF at the following URL: https://osf.io/swtg5. The processed molecular dynamics and H2O structure data are also available at OSF. The data files necessary for carrying out all analyses and source data are available at the same OSF URL. Source data are provided with this paper.","publisher":"Springer Nature","article_processing_charge":"Yes","_id":"18820","das_tickbox":"1","quality_controlled":"1","article_number":"270","external_id":{"pmid":["39747013"],"isi":["001389959100009"]},"abstract":[{"lang":"eng","text":"Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy."}],"status":"public","intvolume":"        16","language":[{"iso":"eng"}],"acknowledgement":"The authors thank Dr. Matteo Carli for providing the CLN025 replica exchange MD trajectory and Matteo Allione for the fruitful discussions connected with the idea of the linear scaling estimator. This work was partially funded by NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial support by the region Friuli Venezia Giulia (project F53C22001770002 received by A.L.).","volume":16,"publication":"Nature Communications"},{"article_processing_charge":"No","_id":"21427","das_tickbox":"1","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","language":[{"iso":"eng"}],"status":"public","publication":"bioRxiv","has_accepted_license":"1","year":"2025","publication_status":"draft","date_published":"2025-09-25T00:00:00Z","title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","author":[{"last_name":"Dunajova","first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana"},{"first_name":"Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Majek, Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","last_name":"Majek","first_name":"Juraj"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Sahai, Erik","first_name":"Erik","last_name":"Sahai"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B"}],"OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.20.655037"}],"oa":1,"fulldoi":"https://doi.org/10.1101/2025.05.20.655037","citation":{"ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. .","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.).","ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","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.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>."},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"day":"25","doi":"10.1101/2025.05.20.655037","date_updated":"2026-09-12T22:30:04Z","date_created":"2026-03-11T08:40:06Z","ddc":["539","570"],"oa_version":"Preprint","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","project":[{"name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd","grant_number":"101071793"},{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"21439"},{"status":"public","relation":"dissertation_contains","id":"21423"}]},"type":"preprint","department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}]},{"oa":1,"_id":"21304","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.13934991"}],"article_processing_charge":"No","publisher":"Zenodo","OA_place":"repository","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Santana de Freitas Amaral, M. (2024). archaeal_membranes : code and examples. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>","ieee":"M. Santana de Freitas Amaral, “archaeal_membranes : code and examples.” Zenodo, 2024.","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal_membranes : Code and Examples</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>.","ama":"Santana de Freitas Amaral M. archaeal_membranes : code and examples. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>","short":"M. Santana de Freitas Amaral, (2024).","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal_membranes : Code and Examples.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>.","ista":"Santana de Freitas Amaral M. 2024. archaeal_membranes : code and examples, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>."},"fulldoi":"https://doi.org/10.5281/ZENODO.13934991","status":"public","abstract":[{"lang":"eng","text":"No description provided."}],"OA_type":"green","day":"15","date_created":"2026-02-17T12:52:26Z","doi":"10.5281/ZENODO.13934991","date_updated":"2026-02-23T11:49:05Z","month":"10","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","oa_version":"Published Version","has_accepted_license":"1","date_published":"2024-10-15T00:00:00Z","related_material":{"record":[{"relation":"used_for_analysis_in","status":"public","id":"21251"}]},"title":"archaeal_membranes : code and examples","department":[{"_id":"AnSa"}],"author":[{"first_name":"Miguel","last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel"}],"type":"research_data_reference"},{"doi":"10.1016/j.bpj.2023.12.020","date_created":"2024-01-21T23:00:56Z","date_updated":"2025-09-04T11:46:15Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"oa_version":"Published Version","month":"02","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"page":"307-316","pmid":1,"type":"journal_article","department":[{"_id":"AnSa"}],"ec_funded":1,"scopus_import":"1","oa":1,"fulldoi":"https://doi.org/10.1016/j.bpj.2023.12.020","publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"citation":{"chicago":"Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. 2024. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. 123(3), 307–316.","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal 123 (2024) 307–316.","apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., &#38; Kraft, D. J. (2024). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>","mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>, vol. 123, no. 3, Elsevier, 2024, pp. 307–16, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>.","ieee":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” <i>Biophysical Journal</i>, vol. 123, no. 3. Elsevier, pp. 307–316, 2024.","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. 2024;123(3):307-316. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>"},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file_date_updated":"2024-07-16T12:09:55Z","file":[{"success":1,"access_level":"open_access","date_created":"2024-07-16T12:09:55Z","date_updated":"2024-07-16T12:09:55Z","relation":"main_file","file_name":"2024_BiophysicalJournal_Azadbakht.pdf","file_size":3189926,"file_id":"17266","checksum":"1c8fe1cf950394875b65b90da86428ff","content_type":"application/pdf","creator":"dernst"}],"day":"06","article_type":"original","isi":1,"year":"2024","has_accepted_license":"1","publication_status":"published","date_published":"2024-02-06T00:00:00Z","title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","author":[{"first_name":"Ali","last_name":"Azadbakht","full_name":"Azadbakht, Ali"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337","first_name":"Billie","last_name":"Meadowcroft"},{"first_name":"Juraj","last_name":"Majek","full_name":"Majek, Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Daniela J.","last_name":"Kraft","full_name":"Kraft, Daniela J."}],"article_processing_charge":"Yes (in subscription journal)","publisher":"Elsevier","_id":"14844","quality_controlled":"1","external_id":{"isi":["001185235900001"],"pmid":["38158654"]},"issue":"3","intvolume":"       123","status":"public","acknowledgement":"We gratefully acknowledge useful discussions with Casper van der Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon Idema and George Dadunashvili for initial attempts to simulate the experimental system. D.J.K. would like to thank the physics department at Leiden University for funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules."}],"publication":"Biophysical Journal","volume":123}]