[{"publication":"Soft Matter","date_created":"2025-09-10T05:34:36Z","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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>","short":"M. Muñoz Basagoiti, F.F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral, A. Prada, A. Šarić, Soft Matter 21 (2025) 7736–7756.","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>.","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>"},"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"arxiv":1,"language":[{"iso":"eng"}],"scopus_import":"1","day":"28","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222"}],"publisher":"Royal Society of Chemistry","publication_status":"published","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"date_updated":"2025-12-30T10:16:52Z","date_published":"2025-07-28T00:00:00Z","external_id":{"isi":["001562846800001"],"arxiv":["2502.09798"]},"OA_place":"publisher","article_type":"original","doi":"10.1039/d5sm00148j","month":"07","corr_author":"1","oa":1,"ddc":["540"],"license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"orcid":"0000-0003-1483-1457","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","first_name":"Maitane","last_name":"Muñoz Basagoiti","full_name":"Muñoz Basagoiti, Maitane"},{"first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey","orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","orcid":"0000-0003-3441-1337","full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","first_name":"Billie"},{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral","first_name":"Miguel"},{"id":"a43ed60a-dd22-11ed-9bf7-b34133792ea9","full_name":"Prada, Adam","last_name":"Prada","first_name":"Adam"},{"first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"title":"A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations","isi":1,"department":[{"_id":"AnSa"}],"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","_id":"20318","quality_controlled":"1","page":"7736-7756","issue":"40","has_accepted_license":"1","volume":21,"file_date_updated":"2025-12-30T10:16:40Z","year":"2025","ec_funded":1,"status":"public","intvolume":"        21","file":[{"file_id":"20912","file_size":4841140,"success":1,"checksum":"590bedad19b6f6d40a7ee036a056a6d9","access_level":"open_access","date_created":"2025-12-30T10:16:40Z","date_updated":"2025-12-30T10:16:40Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2025_SoftMatter_MunozBasagoiti.pdf"}]},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.05.10.490642 "}],"month":"12","corr_author":"1","doi":"10.1103/PhysRevLett.129.268101","article_type":"original","author":[{"last_name":"Meadowcroft","full_name":"Meadowcroft, Billie","first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","orcid":"0000-0003-3441-1337"},{"full_name":"Palaia, Ivan","last_name":"Palaia","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 "},{"last_name":"Pfitzner","full_name":"Pfitzner, Anna Katharina","first_name":"Anna Katharina"},{"first_name":"Aurélien","last_name":"Roux","full_name":"Roux, Aurélien"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"}],"date_published":"2022-12-23T00:00:00Z","date_updated":"2025-04-14T07:54:53Z","oa_version":"Preprint","external_id":{"isi":["000906721500001"],"pmid":["36608212"]},"article_number":"268101","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"},{"name":"The evolution of trafficking: from archaea to eukaryotes","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","grant_number":"96752"}],"day":"23","language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publisher":"American Physical Society","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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). ","date_created":"2023-01-08T23:00:53Z","publication":"Physical Review Letters","citation":{"short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (2022).","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>.","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>","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.","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.","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>","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>."},"ec_funded":1,"year":"2022","status":"public","intvolume":"       129","volume":129,"issue":"26","pmid":1,"article_processing_charge":"No","quality_controlled":"1","_id":"12108","title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","abstract":[{"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.","lang":"eng"}],"type":"journal_article","department":[{"_id":"AnSa"}],"isi":1},{"volume":18,"has_accepted_license":"1","issue":"10","pmid":1,"file_date_updated":"2023-01-24T10:45:01Z","ec_funded":1,"year":"2022","file":[{"relation":"main_file","file_name":"2022_PLoSCompBio_Jiang.pdf","date_updated":"2023-01-24T10:45:01Z","creator":"dernst","date_created":"2023-01-24T10:45:01Z","content_type":"application/pdf","file_size":2641067,"file_id":"12359","access_level":"open_access","checksum":"bada6a7865e470cf42bbdfa67dd471d2","success":1}],"intvolume":"        18","status":"public","title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","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."}],"type":"journal_article","related_material":{"link":[{"url":"https://github.com/sharonJXY/3-filament-model","relation":"software"}]},"keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"department":[{"_id":"AnSa"}],"isi":1,"article_processing_charge":"No","quality_controlled":"1","_id":"12152","date_published":"2022-10-17T00:00:00Z","date_updated":"2025-06-12T06:19:28Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","external_id":{"isi":["000924885500005"],"pmid":["36251703"]},"article_number":"e1010586","oa":1,"ddc":["570"],"corr_author":"1","month":"10","doi":"10.1371/journal.pcbi.1010586","article_type":"original","author":[{"first_name":"Xiuyun","full_name":"Jiang, Xiuyun","last_name":"Jiang"},{"first_name":"Lena","full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck"},{"full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"first_name":"Anna-Katharina","last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina"},{"first_name":"Elene","last_name":"Lominadze","full_name":"Lominadze, Elene"},{"full_name":"Roux, Aurélien","last_name":"Roux","first_name":"Aurélien"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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_created":"2023-01-12T12:08:10Z","publication":"PLOS Computational Biology","citation":{"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>","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.","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>","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).","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.","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>."},"day":"17","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020"},{"grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"publisher":"Public Library of Science","publication_status":"published"}]