[{"publisher":"Proceedings of the National Academy of Sciences","intvolume":"       121","status":"public","department":[{"_id":"AnSa"}],"quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2024-02-18T23:01:00Z","month":"02","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","pmid":1,"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"related_material":{"record":[{"relation":"research_data","id":"15027","status":"public"}]},"ddc":["570"],"doi":"10.1073/pnas.2220075121","language":[{"iso":"eng"}],"title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","ec_funded":1,"citation":{"mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>.","ieee":"S. Curk <i>et al.</i>, “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>.","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(7). doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"type":"journal_article","author":[{"orcid":"0000-0001-6160-9766","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"last_name":"Meisl","full_name":"Meisl, Georg","first_name":"Georg"},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"},{"first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T.","last_name":"Michaels"},{"full_name":"Knowles, Tuomas P.J.","first_name":"Tuomas P.J.","last_name":"Knowles"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"}],"day":"13","oa":1,"publication_status":"published","volume":121,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2024-02-26T08:20:00Z","issue":"7","article_processing_charge":"Yes","_id":"15001","date_published":"2024-02-13T00:00:00Z","abstract":[{"lang":"eng","text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor."}],"file":[{"content_type":"application/pdf","file_id":"15026","relation":"main_file","success":1,"date_created":"2024-02-26T08:20:00Z","file_name":"2024_PNAS_Curk.pdf","file_size":7699487,"creator":"dernst","date_updated":"2024-02-26T08:20:00Z","access_level":"open_access","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b"}],"article_number":"e2220075121","publication_identifier":{"eissn":["1091-6490"]},"date_updated":"2024-02-26T08:45:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38335256"]},"scopus_import":"1","oa_version":"Published Version","year":"2024","has_accepted_license":"1","article_type":"original"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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","short":"CC BY-NC-ND (4.0)"},"publication_status":"inpress","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.bpj.2023.12.020","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"_id":"14844","date_published":"2023-12-29T00:00:00Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-23T09:26:35Z","scopus_import":"1","publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"article_type":"original","oa_version":"Published Version","year":"2023","quality_controlled":"1","department":[{"_id":"AnSa"}],"publication":"Biophysical Journal","status":"public","publisher":"Elsevier","month":"12","date_created":"2024-01-21T23:00:56Z","language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2023.12.020","ddc":["570"],"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).","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"day":"29","type":"journal_article","author":[{"first_name":"Ali","full_name":"Azadbakht, Ali","last_name":"Azadbakht"},{"orcid":"0000-0003-3441-1337","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","first_name":"Billie","full_name":"Meadowcroft, Billie","last_name":"Meadowcroft"},{"id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","first_name":"Juraj","full_name":"Majek, Juraj","last_name":"Majek"},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Daniela J.","full_name":"Kraft, Daniela J.","last_name":"Kraft"}],"ec_funded":1,"citation":{"mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>, Elsevier, 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>. Elsevier.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal.","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, n.d. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>.","apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., &#38; Kraft, D. J. (n.d.). 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>","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.)."},"title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres"},{"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T14:51:25Z","external_id":{"isi":["000985481400001"],"pmid":["37141427"]},"scopus_import":"1","oa_version":"Published Version","year":"2023","has_accepted_license":"1","article_type":"letter_note","oa":1,"publication_status":"published","volume":23,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-05-30T07:55:31Z","issue":"10","article_processing_charge":"No","_id":"13094","abstract":[{"lang":"eng","text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states."}],"date_published":"2023-05-04T00:00:00Z","file":[{"checksum":"9734d4c617bab3578ef62916b764547a","access_level":"open_access","date_updated":"2023-05-30T07:55:31Z","file_size":3654910,"creator":"dernst","file_name":"2023_NanoLetters_Azadbakht.pdf","date_created":"2023-05-30T07:55:31Z","success":1,"file_id":"13100","relation":"main_file","content_type":"application/pdf"}],"acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","pmid":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"}],"ddc":["540"],"doi":"10.1021/acs.nanolett.3c00375","language":[{"iso":"eng"}],"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","ec_funded":1,"citation":{"mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>.","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” <i>Nano Letters</i>, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>.","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., &#38; Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. 2023;23(10):4267–4273. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273."},"type":"journal_article","author":[{"first_name":"Ali","full_name":"Azadbakht, Ali","last_name":"Azadbakht"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","full_name":"Meadowcroft, Billie","first_name":"Billie","last_name":"Meadowcroft"},{"last_name":"Varkevisser","first_name":"Thijs","full_name":"Varkevisser, Thijs"},{"full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Daniela J.","full_name":"Kraft, Daniela J.","last_name":"Kraft"}],"day":"04","isi":1,"publisher":"American Chemical Society","intvolume":"        23","status":"public","department":[{"_id":"AnSa"}],"quality_controlled":"1","publication":"Nano Letters","page":"4267–4273","date_created":"2023-05-28T22:01:03Z","month":"05"},{"title":"Unconventional colloidal aggregation in chiral bacterial baths","ec_funded":1,"citation":{"chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>.","ista":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.","ieee":"D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1680–1688, 2023.","mla":"Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>.","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688.","ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. 2023;19:1680-1688. doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., &#38; Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>"},"author":[{"id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","first_name":"Daniel","full_name":"Grober, Daniel","last_name":"Grober"},{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","full_name":"Palaia, Ivan","last_name":"Palaia"},{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","full_name":"Ucar, Mehmet C","first_name":"Mehmet C"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić"},{"last_name":"Palacci","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"}],"type":"journal_article","day":"01","acknowledgement":"D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa for providing the E. coli strains. This material is based upon work supported by the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411.","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41567-023-02136-x","ddc":["530"],"language":[{"iso":"eng"}],"page":"1680-1688","date_created":"2023-08-06T22:01:11Z","month":"11","isi":1,"publisher":"Springer Nature","intvolume":"        19","status":"public","quality_controlled":"1","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"publication":"Nature Physics","oa_version":"Published Version","year":"2023","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"date_updated":"2024-01-30T12:26:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001037346400005"]},"scopus_import":"1","article_processing_charge":"Yes","date_published":"2023-11-01T00:00:00Z","_id":"13971","abstract":[{"lang":"eng","text":"When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases."}],"file":[{"success":1,"date_created":"2024-01-30T12:26:08Z","content_type":"application/pdf","file_id":"14906","relation":"main_file","date_updated":"2024-01-30T12:26:08Z","access_level":"open_access","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","file_name":"2023_NaturePhysics_Grober.pdf","file_size":6365607,"creator":"dernst"}],"oa":1,"publication_status":"published","volume":19,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2024-01-30T12:26:08Z"},{"ec_funded":1,"citation":{"short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. <i>Soft Matter</i>. 2023;19:1695-1704. doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","ieee":"N. A. M. Araújo <i>et al.</i>, “Steering self-organisation through confinement,” <i>Soft Matter</i>, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>."},"title":"Steering self-organisation through confinement","day":"06","author":[{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"last_name":"Janssen","full_name":"Janssen, Liesbeth M.C.","first_name":"Liesbeth M.C."},{"last_name":"Barois","first_name":"Thomas","full_name":"Barois, Thomas"},{"first_name":"Guido","full_name":"Boffetta, Guido","last_name":"Boffetta"},{"last_name":"Cohen","full_name":"Cohen, Itai","first_name":"Itai"},{"full_name":"Corbetta, Alessandro","first_name":"Alessandro","last_name":"Corbetta"},{"last_name":"Dauchot","full_name":"Dauchot, Olivier","first_name":"Olivier"},{"first_name":"Marjolein","full_name":"Dijkstra, Marjolein","last_name":"Dijkstra"},{"last_name":"Durham","first_name":"William M.","full_name":"Durham, William M."},{"full_name":"Dussutour, Audrey","first_name":"Audrey","last_name":"Dussutour"},{"last_name":"Garnier","full_name":"Garnier, Simon","first_name":"Simon"},{"last_name":"Gelderblom","first_name":"Hanneke","full_name":"Gelderblom, Hanneke"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"full_name":"Isa, Lucio","first_name":"Lucio","last_name":"Isa"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"last_name":"Löwen","first_name":"Hartmut","full_name":"Löwen, Hartmut"},{"full_name":"Metzler, Ralf","first_name":"Ralf","last_name":"Metzler"},{"first_name":"Marco","full_name":"Polin, Marco","last_name":"Polin"},{"last_name":"Royall","full_name":"Royall, C. Patrick","first_name":"C. Patrick"},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Sengupta","first_name":"Anupam","full_name":"Sengupta, Anupam"},{"last_name":"Sykes","first_name":"Cécile","full_name":"Sykes, Cécile"},{"full_name":"Trianni, Vito","first_name":"Vito","last_name":"Trianni"},{"last_name":"Tuval","full_name":"Tuval, Idan","first_name":"Idan"},{"full_name":"Vogel, Nicolas","first_name":"Nicolas","last_name":"Vogel"},{"full_name":"Yeomans, Julia M.","first_name":"Julia M.","last_name":"Yeomans"},{"first_name":"Iker","full_name":"Zuriguel, Iker","last_name":"Zuriguel"},{"last_name":"Marin","full_name":"Marin, Alvaro","first_name":"Alvaro"},{"first_name":"Giorgio","full_name":"Volpe, Giorgio","last_name":"Volpe"}],"type":"journal_article","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"language":[{"iso":"eng"}],"ddc":["540"],"doi":"10.1039/d2sm01562e","page":"1695-1704","month":"02","date_created":"2023-03-05T23:01:06Z","publisher":"Royal Society of Chemistry","isi":1,"department":[{"_id":"AnSa"}],"quality_controlled":"1","publication":"Soft Matter","intvolume":"        19","status":"public","article_type":"original","oa_version":"Published Version","has_accepted_license":"1","year":"2023","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:28:39Z","external_id":{"isi":["000940388100001"],"arxiv":["2204.10059"]},"scopus_import":"1","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"arxiv":1,"article_processing_charge":"No","file":[{"creator":"cchlebak","file_size":3581939,"file_name":"2023_SoftMatter_Araujo.pdf","access_level":"open_access","date_updated":"2023-03-07T09:19:41Z","checksum":"af95aa18b9b01e32fb8f13477c0e2687","relation":"main_file","file_id":"12711","content_type":"application/pdf","success":1,"date_created":"2023-03-07T09:19:41Z"}],"_id":"12708","date_published":"2023-02-06T00:00:00Z","abstract":[{"lang":"eng","text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter."}],"publication_status":"published","oa":1,"file_date_updated":"2023-03-07T09:19:41Z","volume":19,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"external_id":{"isi":["000968083500010"]},"scopus_import":"1","date_updated":"2023-08-01T13:45:54Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["2375-2548"]},"article_type":"original","has_accepted_license":"1","oa_version":"Published Version","year":"2023","publication_status":"published","oa":1,"file_date_updated":"2023-03-27T06:24:49Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":9,"article_processing_charge":"No","issue":"11","article_number":"eade5224","file":[{"access_level":"open_access","date_updated":"2023-03-27T06:24:49Z","checksum":"6d7dbe9ed86a116c8a002d62971202c5","file_size":1826471,"creator":"dernst","file_name":"2023_ScienceAdvances_Hurtig.pdf","success":1,"date_created":"2023-03-27T06:24:49Z","file_id":"12768","relation":"main_file","content_type":"application/pdf"}],"_id":"12756","date_published":"2023-03-17T00:00:00Z","abstract":[{"lang":"eng","text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling."}],"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1126/sciadv.ade5224","citation":{"ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. 2023;9(11). doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>.","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>.","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","ieee":"F. Hurtig <i>et al.</i>, “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” <i>Science Advances</i>, vol. 9, no. 11. American Association for the Advancement of Science, 2023."},"ec_funded":1,"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","day":"17","author":[{"last_name":"Hurtig","first_name":"Fredrik","full_name":"Hurtig, Fredrik"},{"last_name":"Burgers","full_name":"Burgers, Thomas C.Q.","first_name":"Thomas C.Q."},{"full_name":"Cezanne, Alice","first_name":"Alice","last_name":"Cezanne"},{"full_name":"Jiang, Xiuyun","first_name":"Xiuyun","last_name":"Jiang"},{"last_name":"Mol","first_name":"Frank N.","full_name":"Mol, Frank N."},{"last_name":"Traparić","first_name":"Jovan","full_name":"Traparić, Jovan"},{"last_name":"Pulschen","first_name":"Andre Arashiro","full_name":"Pulschen, Andre Arashiro"},{"full_name":"Nierhaus, Tim","first_name":"Tim","last_name":"Nierhaus"},{"first_name":"Gabriel","full_name":"Tarrason-Risa, Gabriel","last_name":"Tarrason-Risa"},{"full_name":"Harker-Kirschneck, Lena","first_name":"Lena","last_name":"Harker-Kirschneck"},{"last_name":"Löwe","full_name":"Löwe, Jan","first_name":"Jan"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Vlijm, Rifka","first_name":"Rifka","last_name":"Vlijm"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"}],"type":"journal_article","publisher":"American Association for the Advancement of Science","isi":1,"publication":"Science Advances","quality_controlled":"1","department":[{"_id":"AnSa"}],"status":"public","intvolume":"         9","month":"03","date_created":"2023-03-26T22:01:06Z"},{"date_created":"2022-05-22T17:04:48Z","month":"05","status":"public","intvolume":"       156","publication":"The Journal of Chemical Physics","department":[{"_id":"AnSa"}],"quality_controlled":"1","isi":1,"publisher":"AIP Publishing","author":[{"last_name":"Palaia","full_name":"Palaia, Ivan","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 "},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"}],"type":"journal_article","day":"16","title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","citation":{"ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. 2022;156(19). doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>","apa":"Palaia, I., &#38; Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>.","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>.","ista":"Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 156(19), 194902.","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19. AIP Publishing, 2022."},"ec_funded":1,"doi":"10.1063/5.0087769","ddc":["540"],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"language":[{"iso":"eng"}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"acknowledgement":"The authors thank Longhui Zeng and Xiaolei Su (Yale University) for bringing the topic to their attention and for useful comments. This work has received funding from the European Research Council under the European Union’s Horizon\r\n2020 research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie Grant No. 101034413). The authors are grateful to the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by EPSRC (Grant Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and from the Royal Society (Grant No. UF160266).","abstract":[{"lang":"eng","text":"By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes."}],"_id":"11400","date_published":"2022-05-16T00:00:00Z","article_number":"194902","file":[{"content_type":"application/pdf","file_id":"11405","relation":"main_file","success":1,"date_created":"2022-05-23T07:45:33Z","file_name":"2022_JourChemPhysics_Palaia.pdf","creator":"dernst","file_size":6387208,"date_updated":"2022-05-23T07:45:33Z","access_level":"open_access","checksum":"7fada58059676a4bb0944b82247af740"}],"article_processing_charge":"No","issue":"19","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":156,"file_date_updated":"2022-05-23T07:45:33Z","oa":1,"publication_status":"published","oa_version":"Published Version","has_accepted_license":"1","year":"2022","article_type":"original","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"external_id":{"isi":["000797236000004"]},"date_updated":"2023-09-05T11:59:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_type":"original","has_accepted_license":"1","oa_version":"Published Version","year":"2022","external_id":{"isi":["000903753500002"]},"scopus_import":"1","date_updated":"2023-10-04T09:06:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_number":"e2109718119","file":[{"file_id":"14386","relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2023-10-04T09:05:44Z","creator":"dernst","file_size":2476021,"file_name":"2022_PNAS_Toprakcioglu.pdf","access_level":"open_access","date_updated":"2023-10-04T09:05:44Z","checksum":"0fe3878896cbeb6c44e29222ec2f336a"}],"abstract":[{"lang":"eng","text":"Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process."}],"_id":"11841","date_published":"2022-07-28T00:00:00Z","article_processing_charge":"No","issue":"31","file_date_updated":"2023-10-04T09:05:44Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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","short":"CC BY-NC-ND (4.0)"},"volume":119,"publication_status":"published","oa":1,"day":"28","author":[{"last_name":"Toprakcioglu","first_name":"Zenon","full_name":"Toprakcioglu, Zenon"},{"last_name":"Kamada","full_name":"Kamada, Ayaka","first_name":"Ayaka"},{"last_name":"Michaels","full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T."},{"first_name":"Mengqi","full_name":"Xie, Mengqi","last_name":"Xie"},{"full_name":"Krausser, Johannes","first_name":"Johannes","last_name":"Krausser"},{"full_name":"Wei, Jiapeng","first_name":"Jiapeng","last_name":"Wei"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."}],"type":"journal_article","citation":{"mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2109718119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>.","ieee":"Z. Toprakcioglu <i>et al.</i>, “Adsorption free energy predicts amyloid protein nucleation rates,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","ista":"Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A, Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2109718119.","chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>.","apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"ec_funded":1,"title":"Adsorption free energy predicts amyloid protein nucleation rates","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1073/pnas.2109718119","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969). We are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.), the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for Misfolding Diseases (CMD).","month":"07","date_created":"2022-08-14T22:01:45Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","department":[{"_id":"AnSa"}],"quality_controlled":"1","status":"public","intvolume":"       119","publisher":"Proceedings of the National Academy of Sciences","isi":1},{"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/2022.05.10.490642 ","open_access":"1"}],"oa":1,"volume":129,"article_processing_charge":"No","issue":"26","article_number":"268101","abstract":[{"lang":"eng","text":"The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation."}],"_id":"12108","date_published":"2022-12-23T00:00:00Z","external_id":{"pmid":["36608212"],"isi":["000906721500001"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T14:10:59Z","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_type":"original","oa_version":"Preprint","year":"2022","publisher":"American Physical Society","isi":1,"publication":"Physical Review Letters","quality_controlled":"1","department":[{"_id":"AnSa"}],"status":"public","intvolume":"       129","month":"12","date_created":"2023-01-08T23:00:53Z","pmid":1,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752"}],"acknowledgement":"We thank T. C. T. Michaels and J. Palacci for useful discussions. We thank Claudia Flandoli for the illustrations in Fig. 1(b) and Fig. 2. We acknowledge funding by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant\r\nAgreement No. 101034413 (I. P.), the Royal Society Grant No. UF160266 (A. Š.), the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant No. 802960; B. M., I. P., and A. Š.), and the Volkswagen Foundation\r\nLife Grant (B. B. and A. Š). ","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.129.268101","citation":{"ieee":"B. Meadowcroft, I. Palaia, A. K. Pfitzner, A. Roux, B. Baum, and A. Šarić, “Mechanochemical rules for shape-shifting filaments that remodel membranes,” <i>Physical Review Letters</i>, vol. 129, no. 26. American Physical Society, 2022.","ista":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. 2022. Mechanochemical rules for shape-shifting filaments that remodel membranes. Physical Review Letters. 129(26), 268101.","chicago":"Meadowcroft, Billie, Ivan Palaia, Anna Katharina Pfitzner, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>.","mla":"Meadowcroft, Billie, et al. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>, vol. 129, no. 26, 268101, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>.","short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (2022).","apa":"Meadowcroft, B., Palaia, I., Pfitzner, A. K., Roux, A., Baum, B., &#38; Šarić, A. (2022). Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>","ama":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. 2022;129(26). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>"},"ec_funded":1,"title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","day":"23","type":"journal_article","author":[{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","first_name":"Billie","full_name":"Meadowcroft, Billie","last_name":"Meadowcroft"},{"last_name":"Palaia","full_name":"Palaia, Ivan","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 "},{"first_name":"Anna Katharina","full_name":"Pfitzner, Anna Katharina","last_name":"Pfitzner"},{"last_name":"Roux","full_name":"Roux, Aurélien","first_name":"Aurélien"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"}]},{"date_created":"2023-01-12T12:08:10Z","month":"10","status":"public","intvolume":"        18","publication":"PLOS Computational Biology","quality_controlled":"1","department":[{"_id":"AnSa"}],"isi":1,"publisher":"Public Library of Science","type":"journal_article","author":[{"last_name":"Jiang","full_name":"Jiang, Xiuyun","first_name":"Xiuyun"},{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"first_name":"Christian Eduardo","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina","first_name":"Anna-Katharina"},{"full_name":"Lominadze, Elene","first_name":"Elene","last_name":"Lominadze"},{"full_name":"Roux, Aurélien","first_name":"Aurélien","last_name":"Roux"},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"},{"full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"day":"17","title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","citation":{"mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>.","chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>.","ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.","ieee":"X. Jiang <i>et al.</i>, “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” <i>PLOS Computational Biology</i>, vol. 18, no. 10. Public Library of Science, 2022.","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. 2022;18(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022)."},"ec_funded":1,"ddc":["570"],"doi":"10.1371/journal.pcbi.1010586","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222"}],"related_material":{"link":[{"url":"https://github.com/sharonJXY/3-filament-model","relation":"software"}]},"acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","date_published":"2022-10-17T00:00:00Z","_id":"12152","abstract":[{"lang":"eng","text":"ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks."}],"article_number":"e1010586","file":[{"success":1,"date_created":"2023-01-24T10:45:01Z","file_id":"12359","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-24T10:45:01Z","checksum":"bada6a7865e470cf42bbdfa67dd471d2","file_size":2641067,"creator":"dernst","file_name":"2022_PLoSCompBio_Jiang.pdf"}],"article_processing_charge":"No","issue":"10","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":18,"file_date_updated":"2023-01-24T10:45:01Z","oa":1,"publication_status":"published","has_accepted_license":"1","oa_version":"Published Version","year":"2022","article_type":"original","publication_identifier":{"issn":["1553-7358"]},"scopus_import":"1","external_id":{"isi":["000924885500005"]},"date_updated":"2023-08-04T09:03:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"}]