Treffer: A tutorial for mesoscale computer simulations of lipid membranes: tether pulling, tubulation and fluctuations.
Title:
A tutorial for mesoscale computer simulations of lipid membranes: tether pulling, tubulation and fluctuations.
Authors:
Muñoz-Basagoiti M; Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria. andela.saric@ista.ac.at., Frey F; Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria. andela.saric@ista.ac.at., Meadowcroft B; Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria. andela.saric@ista.ac.at.; University College London, Gower St, London WC1E 6BT, UK., Amaral M; Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria. andela.saric@ista.ac.at., Prada A; Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria. andela.saric@ista.ac.at., Šarić A; Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria. andela.saric@ista.ac.at.
Source:
Soft matter [Soft Matter] 2025 Oct 15; Vol. 21 (40), pp. 7736-7756. Date of Electronic Publication: 2025 Oct 15.
Publication Type:
Journal Article; Review
Language:
English
Journal Info:
Publisher: Royal Society of Chemistry Country of Publication: England NLM ID: 101295070 Publication Model: Electronic Cited Medium: Internet ISSN: 1744-6848 (Electronic) Linking ISSN: 1744683X NLM ISO Abbreviation: Soft Matter Subsets: MEDLINE
Imprint Name(s):
Original Publication: Cambridge, England : Royal Society of Chemistry, 2005-
MeSH Terms:
References:
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Nano Lett. 2023 May 24;23(10):4267-4273. (PMID: 37141427)
J Membr Biol. 2022 Dec;255(6):757-777. (PMID: 36197492)
Soft Matter. 2022 Mar 2;18(9):1747-1756. (PMID: 34994752)
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Curr Opin Cell Biol. 2021 Aug;71:103-111. (PMID: 33721706)
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J Comput Chem. 2005 Dec;26(16):1781-802. (PMID: 16222654)
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Nano Lett. 2011 Dec 14;11(12):5391-5. (PMID: 22047641)
Annu Rev Biophys. 2019 May 6;48:93-119. (PMID: 30811220)
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jun;75(6 Pt 2):066707. (PMID: 17677389)
Macromol Rapid Commun. 2009 May 19;30(9-10):752-71. (PMID: 21706661)
Chem Phys Lipids. 2015 Jan;185:11-45. (PMID: 24835737)
Biomech Model Mechanobiol. 2019 Apr;18(2):425-433. (PMID: 30417230)
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jul;82(1 Pt 1):011905. (PMID: 20866646)
J Comput Chem. 2008 Aug;29(11):1859-65. (PMID: 18351591)
Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14159-64. (PMID: 16186506)
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J Chem Theory Comput. 2018 Nov 13;14(11):6050-6062. (PMID: 30253091)
ACS Synth Biol. 2022 Oct 21;11(10):3120-3133. (PMID: 36164967)
J Chem Phys. 2013 Jul 7;139(1):014702. (PMID: 23822315)
Living J Comput Mol Sci. 2019 Jan 9;1(1):. (PMID: 36204133)
Angew Chem Int Ed Engl. 2021 May 3;60(19):10661-10669. (PMID: 33355974)
Nat Rev Mol Cell Biol. 2017 Nov;18(11):685-701. (PMID: 28875992)
Phys Rev A. 1991 Jul 15;44(2):1182-1202. (PMID: 9906067)
Eur Phys J E Soft Matter. 2003 Aug;11(4):399-408. (PMID: 15011041)
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Proc Natl Acad Sci U S A. 2022 Jan 4;119(1):. (PMID: 34983838)
Int J Mol Sci. 2022 Jul 22;23(15):. (PMID: 35897670)
Biophys J. 2021 Aug 3;120(15):3211-3221. (PMID: 34197798)
Sci Adv. 2021 Feb 5;7(6):. (PMID: 33547068)
Nano Lett. 2014 Feb 12;14(2):687-93. (PMID: 24383757)
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Nano Lett. 2013 Sep 11;13(9):4546-50. (PMID: 23972158)
Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Apr;65(4 Pt 1):041901. (PMID: 12005867)
Nat Comput Sci. 2023 Apr;3(4):334-345. (PMID: 38177937)
Nat Commun. 2024 Jan 16;15(1):548. (PMID: 38228588)
Adv Biol (Weinh). 2022 Jan;6(1):e2101020. (PMID: 34859961)
Biophys J. 2010 May 19;98(10):2215-25. (PMID: 20483330)
Soft Matter. 2021 Jan 22;17(2):319-330. (PMID: 32914814)
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J Chem Theory Comput. 2015 May 12;11(5):2144-55. (PMID: 26574417)
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Biophys J. 2024 Feb 6;123(3):307-316. (PMID: 38158654)
Phys Rev Lett. 2002 Jun 10;88(23):238101. (PMID: 12059401)
RSC Adv. 2019 Feb 6;9(8):4644-4658. (PMID: 35520151)
J Chem Phys. 2013 Jan 14;138(2):024907. (PMID: 23320721)
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J Chem Phys. 2019 Oct 28;151(16):164108. (PMID: 31675861)
Cell. 2020 Sep 3;182(5):1140-1155.e18. (PMID: 32814015)
Phys Rev Lett. 2012 Mar 16;108(11):118101. (PMID: 22540513)
J Phys Chem B. 2021 Sep 30;125(38):10710-10719. (PMID: 34461720)
Soft Matter. 2021 Apr 14;17(14):3798-3806. (PMID: 33629089)
Eur Phys J E Soft Matter. 2014 May;37(5):42. (PMID: 24859281)
J Chem Phys. 2008 Jan 21;128(3):035102. (PMID: 18205524)
J Chem Phys. 2005 Jun 15;122(23):234711. (PMID: 16008477)
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Curr Opin Struct Biol. 2009 Apr;19(2):128-37. (PMID: 19345092)
J Chem Phys. 2022 Nov 7;157(17):174801. (PMID: 36347673)
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jul;72(1 Pt 1):011915. (PMID: 16090009)
Nat Methods. 2021 Sep;18(9):1013-1026. (PMID: 34446922)
Chem Rev. 2019 May 8;119(9):6086-6161. (PMID: 30978005)
Nature. 2005 Dec 1;438(7068):590-6. (PMID: 16319878)
J Phys Condens Matter. 2006 Jul 19;18(28):S1191-219. (PMID: 21690837)
Proc Natl Acad Sci U S A. 2015 May 12;112(19):6068-73. (PMID: 25918423)
J Chem Phys. 2008 May 14;128(18):184105. (PMID: 18532797)
Science. 2008 May 9;320(5877):789-92. (PMID: 18467587)
Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Sep;66(3 Pt 2B):036304. (PMID: 12366250)
J Chem Phys. 2016 Feb 28;144(8):084102. (PMID: 26931676)
J Phys Chem Lett. 2021 Nov 4;12(43):10497-10504. (PMID: 34677984)
Science. 2014 Mar 28;343(6178):1443-4. (PMID: 24675944)
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Mar;69(3 Pt 1):031903. (PMID: 15089318)
Nature. 1991 Feb 7;349(6309):475-81. (PMID: 1992351)
Nature. 2020 Oct;586(7827):52-56. (PMID: 32999485)
Phys Rev Lett. 2019 Mar 1;122(8):088102. (PMID: 30932591)
Phys Rev Lett. 2004 Nov 5;93(19):198105. (PMID: 15600888)
Biochim Biophys Acta Biomembr. 2022 Jul 1;1864(7):183897. (PMID: 35231438)
Cell. 2024 Feb 1;187(3):545-562. (PMID: 38306981)
Substance Nomenclature:
0 (Lipid Bilayers)
0 (Membrane Lipids)
0 (Membrane Lipids)
Entry Date(s):
Date Created: 20250904 Date Completed: 20251015 Latest Revision: 20251016
Update Code:
20251016
PubMed Central ID:
PMC12409609
DOI:
10.1039/d5sm00148j
PMID:
40905106
Database:
MEDLINE
Weitere Informationen
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.