TriMem: a parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes

  • Lipid membranes are integral building blocks of living cells and perform a multitude of biological functions. Currently, molecular simulations of cellular-scale membrane structures at atomic resolution are nearly impossible, due to their size, complexity, and the large times-scales required. Instead, elastic membrane models are used to simulate membrane topologies and transitions between them, and to infer their properties and functions. Unfortunately, efficiently parallelized open-source simulation code to do so has been lacking. Here, we present TriMem, a parallel hybrid Monte Carlo simulation engine for triangulated lipid membranes. The kernels are efficiently coded in C++ and wrapped with Python for ease-of-use. The parallel implementation of the energy and gradient calculations and of Monte Carlo flip moves of edges in the triangulated membrane enable us to simulate also large and highly curved sub-cellular structures. For validation, we reproduce phase diagrams of vesicles with varying surface-to-volume ratios and area difference. The software can tackle a range of membrane remodelling processes on sub-cellular and cellular scales. Additionally, extensive documentation make the software accessible to the broad biophysics and computational cell biology communities.

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Author:Marc SiggelORCiDGND, Sebastian KehlORCiD, Klaus ReuterORCiD, Jürgen KöfingerORCiD, Gerhard HummerORCiD
Parent Title (English):bioRxiv
Document Type:Preprint
Date of Publication (online):2022/05/26
Date of first Publication:2022/05/26
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2023/06/14
Page Number:13
Licence (German):License LogoCreative Commons - CC BY-NC - Namensnennung - Nicht kommerziell 4.0 International