[{"external_id":{"arxiv":["2603.15170"]},"ec_funded":1,"volume":164,"publisher":"AIP Publishing","file_date_updated":"2026-05-05T12:35:24Z","_id":"21748","year":"2026","language":[{"iso":"eng"}],"PlanS_conform":"1","publication":"Journal of Chemical Physics","corr_author":"1","title":"Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization","day":"14","publication_status":"published","ddc":["540"],"type":"journal_article","abstract":[{"text":"Cells are defined by lipid membranes that differ in their structure across the tree of life. While the membranes of most bacteria and eukaryotes consist of single-headed bilayer lipids, the membranes of archaea are composed of mixtures of single-headed bilayer lipids and double-headed bolalipids. Archaeal bolalipids can adopt straight or u-shaped conformations, enabling them—together with bilayer lipids—to control whether membranes form bilayer or monolayer structures. Yet, the physical principles governing archaeal membranes remain largely unexplored, especially how membrane structure couples to externally imposed curvature during membrane remodeling. Here, we perform coarse-grained molecular dynamics simulations of toroidal vesicles to systematically probe the effects of all relevant combinations of mean and Gaussian curvatures on shape stability and lipid organization. We find that soft bilayer membranes can sustain all curvatures induced, whereas rigid bolalipid monolayer membranes either transition to different vesicle shapes or rupture. Bilayer-mimicking u-shaped bolalipids and bilayer lipids are spatially accumulated in regions of high mean membrane curvature independent of Gaussian curvature. Our work identifies curvature–composition coupling as a physical signature of archaeal membrane remodeling.","lang":"eng"}],"article_number":"144902","publication_identifier":{"issn":[" 0021-9606"],"eissn":["1089-7690"]},"doi":"10.1063/5.0325170","date_updated":"2026-05-05T12:40:41Z","issue":"14","citation":{"mla":"Frey, Felix F., et al. “Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization.” <i>Journal of Chemical Physics</i>, vol. 164, no. 14, 144902, AIP Publishing, 2026, doi:<a href=\"https://doi.org/10.1063/5.0325170\">10.1063/5.0325170</a>.","apa":"Frey, F. F., Santana de Freitas Amaral, M., &#38; Šarić, A. (2026). Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0325170\">https://doi.org/10.1063/5.0325170</a>","short":"F.F. Frey, M. Santana de Freitas Amaral, A. Šarić, Journal of Chemical Physics 164 (2026).","ama":"Frey FF, Santana de Freitas Amaral M, Šarić A. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. <i>Journal of Chemical Physics</i>. 2026;164(14). doi:<a href=\"https://doi.org/10.1063/5.0325170\">10.1063/5.0325170</a>","ieee":"F. F. Frey, M. Santana de Freitas Amaral, and A. Šarić, “Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization,” <i>Journal of Chemical Physics</i>, vol. 164, no. 14. AIP Publishing, 2026.","chicago":"Frey, Felix F, Miguel Santana de Freitas Amaral, and Anđela Šarić. “Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2026. <a href=\"https://doi.org/10.1063/5.0325170\">https://doi.org/10.1063/5.0325170</a>.","ista":"Frey FF, Santana de Freitas Amaral M, Šarić A. 2026. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. Journal of Chemical Physics. 164(14), 144902."},"intvolume":"       164","has_accepted_license":"1","month":"04","OA_type":"hybrid","OA_place":"publisher","quality_controlled":"1","arxiv":1,"oa_version":"Published Version","department":[{"_id":"AnSa"}],"article_type":"original","article_processing_charge":"Yes (in subscription journal)","related_material":{"record":[{"relation":"research_data","status":"public","id":"21800"}]},"file":[{"date_created":"2026-05-05T12:35:24Z","access_level":"open_access","checksum":"2e10c4f4531676e0771ef3730e4b63a9","relation":"main_file","file_id":"21801","file_name":"2026_JourChemPhysics_Frey.pdf","creator":"dernst","content_type":"application/pdf","date_updated":"2026-05-05T12:35:24Z","success":1,"file_size":8764791}],"oa":1,"date_created":"2026-04-19T22:07:45Z","fulldoi":"https://doi.org/10.1063/5.0325170","status":"public","date_published":"2026-04-14T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","last_name":"Frey","first_name":"Felix F"},{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral","first_name":"Miguel"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"}],"scopus_import":"1","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)"},"project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"acknowledgement":"F.F. acknowledges the financial support from the NOMIS foundation. M.A. and A.Š. acknowledge the funding from the Volkswagen Foundation (Grant No. Az 96727). A.Š. acknowledges the funding from ERC Starting Grant “NEPA” (Grant No. 802960) and the Vallee Scholarship."},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-02-25T00:00:00Z","date_updated":"2026-05-05T12:40:41Z","doi":"10.5281/ZENODO.18772086","fulldoi":"https://doi.org/10.5281/ZENODO.18772086","status":"public","author":[{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017","first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey"},{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić"}],"citation":{"chicago":"Frey, Felix F, Miguel Santana de Freitas Amaral, and Anđela Šarić. “Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization.” Zenodo, 2026. <a href=\"https://doi.org/10.5281/ZENODO.18772086\">https://doi.org/10.5281/ZENODO.18772086</a>.","ista":"Frey FF, Santana de Freitas Amaral M, Šarić A. 2026. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.18772086\">10.5281/ZENODO.18772086</a>.","ieee":"F. F. Frey, M. Santana de Freitas Amaral, and A. Šarić, “Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization.” Zenodo, 2026.","short":"F.F. Frey, M. Santana de Freitas Amaral, A. Šarić, (2026).","ama":"Frey FF, Santana de Freitas Amaral M, Šarić A. Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. 2026. doi:<a href=\"https://doi.org/10.5281/ZENODO.18772086\">10.5281/ZENODO.18772086</a>","apa":"Frey, F. F., Santana de Freitas Amaral, M., &#38; Šarić, A. (2026). Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.18772086\">https://doi.org/10.5281/ZENODO.18772086</a>","mla":"Frey, Felix F., et al. <i>Cracking Donuts and Sorting Lipids: Geometry Controls Archaeal Membrane Stability and Lipid Organization</i>. Zenodo, 2026, doi:<a href=\"https://doi.org/10.5281/ZENODO.18772086\">10.5281/ZENODO.18772086</a>."},"abstract":[{"lang":"eng","text":"LAMMPS input scripts to simulate toroidal vesicles composed of pure bolalipid membranes and archaeal mixture membranes for the following publication: \"Cracking donuts and sorting lipids: geometry controls archaeal membrane stability and lipid organization\" by Felix Frey, Miguel Amaral, and Andela Saric."}],"date_created":"2026-05-05T12:11:52Z","related_material":{"record":[{"id":"21748","status":"public","relation":"used_in_publication"}]},"oa":1,"OA_type":"green","day":"25","OA_place":"repository","oa_version":"Published Version","department":[{"_id":"AnSa"}],"type":"research_data_reference","article_processing_charge":"No","ddc":["540"],"main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.18772086","open_access":"1"}],"publisher":"Zenodo","month":"02","title":"Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization","corr_author":"1","year":"2026","_id":"21800"},{"month":"10","has_accepted_license":"1","article_processing_charge":"Yes","OA_place":"publisher","quality_controlled":"1","OA_type":"gold","oa_version":"Published Version","department":[{"_id":"AnSa"}],"article_type":"original","related_material":{"record":[{"relation":"software","status":"public","id":"21304"}]},"DOAJ_listed":"1","file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2026-02-17T13:02:02Z","success":1,"file_size":10668225,"date_created":"2026-02-17T13:02:02Z","access_level":"open_access","checksum":"4116cd5143558ded995fb9ff5fcbc7e0","relation":"main_file","file_id":"21305","file_name":"2025_elife_Amaral.pdf"}],"oa":1,"date_created":"2026-02-16T15:43:57Z","author":[{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017","first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey"},{"last_name":"Jiang","full_name":"Jiang, Xiuyun","first_name":"Xiuyun"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"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)"},"project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"acknowledgement":"MA, BB, and AŠ acknowledge funding by the Volkswagen Foundation Grant Az 96727. FF acknowledges financial support by the NOMIS foundation. AŠ acknowledges funding by ERC Starting Grant 'NEPA' 802960. We thank Claudia Flandoli for her help with illustrations.","status":"public","fulldoi":"https://doi.org/10.7554/elife.105432","date_published":"2025-10-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","_id":"21251","file_date_updated":"2026-02-17T13:02:02Z","language":[{"iso":"eng"}],"PlanS_conform":"1","publication":"eLife","title":"Balancing stability and flexibility when reshaping archaeal membranes","corr_author":"1","external_id":{"pmid":["41056191 "]},"volume":14,"ec_funded":1,"publisher":"eLife Sciences Publications","ddc":["570"],"type":"journal_article","day":"07","publication_status":"published","article_number":"105432","publication_identifier":{"eissn":["2050-084X"]},"abstract":[{"lang":"eng","text":"Cellular membranes differ across the tree of life. In most bacteria and eukaryotes, single-headed lipids self-assemble into flexible bilayer membranes. By contrast, thermophilic archaea tend to possess bilayer lipids together with double-headed, monolayer spanning bolalipids, which are thought to enable cells to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we explore the trade-offs at play when forming membranes. We find that flexible bolalipids form membranes that resemble bilayer membranes because they are able to assume a U-shaped conformation. Conversely, rigid bolalipids, which resemble the bolalipids with cyclic groups found in thermophilic archaea, take on a straight conformation and form membranes that are stiff and prone to pore formation when they undergo changes in shape. Strikingly, however, the inclusion of small amounts of bilayer lipids in a bolalipid membrane is enough to achieve fluid bolalipid membranes that are both stable and flexible, resolving this trade-off. Our study suggests a mechanism by which archaea can tune the material properties of their membranes as and when required to enable them to survive in harsh environments and to undergo essential membrane remodelling events like cell division."}],"pmid":1,"citation":{"ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Balancing stability and flexibility when reshaping archaeal membranes,” <i>eLife</i>, vol. 14. eLife Sciences Publications, 2025.","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Balancing Stability and Flexibility When Reshaping Archaeal Membranes.” <i>ELife</i>. eLife Sciences Publications, 2025. <a href=\"https://doi.org/10.7554/elife.105432\">https://doi.org/10.7554/elife.105432</a>.","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. 2025. Balancing stability and flexibility when reshaping archaeal membranes. eLife. 14, 105432.","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Balancing stability and flexibility when reshaping archaeal membranes. <i>eLife</i>. 2025;14. doi:<a href=\"https://doi.org/10.7554/elife.105432\">10.7554/elife.105432</a>","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, ELife 14 (2025).","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (2025). Balancing stability and flexibility when reshaping archaeal membranes. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.105432\">https://doi.org/10.7554/elife.105432</a>","mla":"Santana de Freitas Amaral, Miguel, et al. “Balancing Stability and Flexibility When Reshaping Archaeal Membranes.” <i>ELife</i>, vol. 14, 105432, eLife Sciences Publications, 2025, doi:<a href=\"https://doi.org/10.7554/elife.105432\">10.7554/elife.105432</a>."},"intvolume":"        14","doi":"10.7554/elife.105432","date_updated":"2026-02-23T11:49:05Z"},{"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)"},"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"},{"name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222"}],"scopus_import":"1","author":[{"last_name":"Muñoz Basagoiti","full_name":"Muñoz Basagoiti, Maitane","first_name":"Maitane","orcid":"0000-0003-1483-1457","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607"},{"first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","orcid":"0000-0003-3441-1337","first_name":"Billie","last_name":"Meadowcroft","full_name":"Meadowcroft, Billie"},{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral"},{"first_name":"Adam","full_name":"Prada, Adam","last_name":"Prada","id":"a43ed60a-dd22-11ed-9bf7-b34133792ea9"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"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.","status":"public","fulldoi":"https://doi.org/10.1039/d5sm00148j","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_published":"2025-07-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"590bedad19b6f6d40a7ee036a056a6d9","relation":"main_file","date_created":"2025-12-30T10:16:40Z","access_level":"open_access","file_id":"20912","file_name":"2025_SoftMatter_MunozBasagoiti.pdf","content_type":"application/pdf","creator":"dernst","file_size":4841140,"date_updated":"2025-12-30T10:16:40Z","success":1}],"oa":1,"date_created":"2025-09-10T05:34:36Z","article_processing_charge":"Yes (via OA deal)","isi":1,"department":[{"_id":"AnSa"}],"arxiv":1,"oa_version":"Published Version","OA_place":"publisher","quality_controlled":"1","OA_type":"hybrid","article_type":"original","month":"07","has_accepted_license":"1","intvolume":"        21","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>.","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>","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.","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.","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>.","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."},"doi":"10.1039/d5sm00148j","date_updated":"2025-12-30T10:16:52Z","issue":"40","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"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"}],"ddc":["540"],"type":"journal_article","day":"28","publication_status":"published","language":[{"iso":"eng"}],"page":"7736-7756","_id":"20318","year":"2025","file_date_updated":"2025-12-30T10:16:40Z","title":"A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations","corr_author":"1","publication":"Soft Matter","volume":21,"ec_funded":1,"external_id":{"arxiv":["2502.09798"],"isi":["001562846800001"]},"publisher":"Royal Society of Chemistry"},{"article_processing_charge":"No","type":"research_data_reference","department":[{"_id":"AnSa"}],"oa_version":"Published Version","day":"15","OA_type":"green","OA_place":"repository","_id":"21304","year":"2024","title":"archaeal_membranes : code and examples","corr_author":"1","month":"10","has_accepted_license":"1","publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.13934991","open_access":"1"}],"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)"},"citation":{"apa":"Santana de Freitas Amaral, M. (2024). archaeal_membranes : code and examples. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal_membranes : Code and Examples</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>.","ieee":"M. Santana de Freitas Amaral, “archaeal_membranes : code and examples.” Zenodo, 2024.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal_membranes : Code and Examples.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>.","ista":"Santana de Freitas Amaral M. 2024. archaeal_membranes : code and examples, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>.","ama":"Santana de Freitas Amaral M. archaeal_membranes : code and examples. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>","short":"M. Santana de Freitas Amaral, (2024)."},"author":[{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel"}],"status":"public","fulldoi":"https://doi.org/10.5281/ZENODO.13934991","doi":"10.5281/ZENODO.13934991","date_published":"2024-10-15T00:00:00Z","date_updated":"2026-02-23T11:49:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"id":"21251","status":"public","relation":"used_for_analysis_in"}]},"date_created":"2026-02-17T12:52:26Z","abstract":[{"text":"No description provided.","lang":"eng"}]},{"publication_identifier":{"isbn":["978-3-99078-046-6"],"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n"}],"citation":{"apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes: In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes: In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes: In silico modelling and design,” Institute of Science and Technology Austria, 2024.","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes: In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>.","short":"M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","ama":"Santana de Freitas Amaral M. Archaeal membranes: In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>"},"doi":"10.15479/at:ista:18661","date_updated":"2026-07-29T13:15:48Z","_id":"18661","file_date_updated":"2025-06-18T22:30:03Z","year":"2024","language":[{"iso":"eng"}],"page":"57","title":"Archaeal membranes: In silico modelling and design","corr_author":"1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","ddc":["572","530"],"type":"dissertation","day":"17","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"18670","status":"public"}]},"file":[{"file_name":"2024_msfa_thesis.zip","file_id":"18671","relation":"source_file","checksum":"eca06497a29078558395455c890a32d9","access_level":"closed","date_created":"2024-12-18T12:27:01Z","file_size":19161387,"embargo_to":"open_access","date_updated":"2025-06-18T22:30:03Z","content_type":"application/zip","creator":"mamaral"},{"date_updated":"2025-06-18T22:30:03Z","file_size":16530084,"creator":"mamaral","embargo":"2025-06-18","content_type":"application/pdf","file_id":"18672","file_name":"2024_msfa_thesis.pdf","date_created":"2024-12-18T12:26:30Z","access_level":"open_access","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","relation":"main_file"}],"oa":1,"date_created":"2024-12-16T10:53:39Z","degree_awarded":"PhD","author":[{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral"}],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-sa/4.0/","status":"public","fulldoi":"https://doi.org/10.15479/at:ista:18661","date_published":"2024-12-17T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"12","has_accepted_license":"1","article_processing_charge":"No","doi_confirm":"1","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"oa_version":"Published Version","supervisor":[{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}]},{"abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties."}],"date_updated":"2026-09-22T22:31:07Z","doi":"10.1101/2024.10.18.619072","citation":{"apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>.","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” <i>bioRxiv</i>. .","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.).","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>"},"ec_funded":1,"publication":"bioRxiv","corr_author":"1","title":"Stability vs flexibility: Reshaping archaeal membranes in silico","year":"2024","_id":"18670","language":[{"iso":"eng"}],"publication_status":"draft","day":"27","type":"preprint","date_created":"2024-12-18T10:07:45Z","related_material":{"record":[{"id":"18661","status":"public","relation":"dissertation_contains"}]},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-11-27T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","status":"public","fulldoi":"https://doi.org/10.1101/2024.10.18.619072","acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","author":[{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral"},{"full_name":"Frey, Felix F","last_name":"Frey","first_name":"Felix F","orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"}],"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.10.18.619072"}],"month":"11","OA_place":"repository","oa_version":"Preprint","department":[{"_id":"AnSa"}],"article_processing_charge":"No"}]