[{"article_processing_charge":"Yes (via OA deal)","publisher":"Royal Society of Chemistry","doi":"10.1039/d5sm00148j","corr_author":"1","ddc":["540"],"oa_version":"Published Version","file":[{"date_created":"2025-12-30T10:16:40Z","file_name":"2025_SoftMatter_MunozBasagoiti.pdf","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"590bedad19b6f6d40a7ee036a056a6d9","file_id":"20912","creator":"dernst","date_updated":"2025-12-30T10:16:40Z","file_size":4841140}],"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"}],"date_published":"2025-07-28T00:00:00Z","year":"2025","OA_type":"hybrid","intvolume":"        21","citation":{"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>","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>.","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>","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.","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."},"author":[{"full_name":"Muñoz Basagoiti, Maitane","last_name":"Muñoz Basagoiti","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","orcid":"0000-0003-1483-1457","first_name":"Maitane"},{"first_name":"Felix F","orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","last_name":"Frey"},{"full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","orcid":"0000-0003-3441-1337","first_name":"Billie"},{"first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"},{"id":"a43ed60a-dd22-11ed-9bf7-b34133792ea9","last_name":"Prada","full_name":"Prada, Adam","first_name":"Adam"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"ec_funded":1,"_id":"20318","publication":"Soft Matter","title":"A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations","file_date_updated":"2025-12-30T10:16:40Z","month":"07","scopus_import":"1","quality_controlled":"1","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.","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"external_id":{"isi":["001562846800001"],"arxiv":["2502.09798"]},"page":"7736-7756","oa":1,"OA_place":"publisher","volume":21,"publication_status":"published","issue":"40","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","department":[{"_id":"AnSa"}],"date_created":"2025-09-10T05:34:36Z","day":"28","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","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":"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"}],"date_updated":"2025-12-30T10:16:52Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","isi":1,"arxiv":1,"type":"journal_article"},{"status":"public","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.15940","open_access":"1"}],"intvolume":"       127","citation":{"chicago":"Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>.","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959.","ista":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 127(51), 10950–10959.","ieee":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.","apa":"Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., &#38; Rivoire, O. (2023). On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>","mla":"Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>.","ama":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. 2023;127(51):10950-10959. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>"},"author":[{"first_name":"Yann","last_name":"Sakref","full_name":"Sakref, Yann"},{"last_name":"Muñoz Basagoiti","full_name":"Muñoz Basagoiti, Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","orcid":"0000-0003-1483-1457","first_name":"Maitane"},{"first_name":"Zorana","last_name":"Zeravcic","full_name":"Zeravcic, Zorana"},{"first_name":"Olivier","full_name":"Rivoire, Olivier","last_name":"Rivoire"}],"date_published":"2023-12-13T00:00:00Z","year":"2023","pmid":1,"abstract":[{"lang":"eng","text":"Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis."}],"doi":"10.1021/acs.jpcb.3c04627","oa_version":"Preprint","publisher":"American Chemical Society","article_processing_charge":"No","isi":1,"arxiv":1,"type":"journal_article","date_updated":"2025-04-23T13:15:17Z","date_created":"2024-01-18T07:47:11Z","day":"13","issue":"51","publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"AnSa"}],"oa":1,"page":"10950-10959","volume":127,"quality_controlled":"1","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"acknowledgement":"We acknowledge funding from ANR-22-CE06-0037-02. This work has received funding from the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754387.","external_id":{"pmid":["38091487"],"arxiv":["2312.15940"],"isi":["001134068000001"]},"month":"12","scopus_import":"1","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"_id":"14831","publication":"The Journal of Physical Chemistry B","title":"On kinetic constraints that catalysis imposes on elementary processes"}]