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• W4300979642 abstract "Lipid membranes are integral building blocks of living cells and perform a multitude of biological functions. Currently, molecular simulations of cellular-scale membrane remodeling processes at atomic resolution are extremely difficult, due to their size, complexity, and the large times-scales on which these processes occur. Instead, elastic membrane models are used to simulate membrane shapes and transitions between them and to infer their properties and functions. Unfortunately, an 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 large and highly curved membrane structures. For validation, we reproduce phase diagrams of vesicles with varying surface-to-volume ratios and area difference. We also compute the density of states to verify correct Boltzmann sampling. The software can be used to tackle a range of large-scale membrane remodeling processes as a step toward cell-scale simulations. Additionally, extensive documentation make the software accessible to the broad biophysics and computational cell biology communities." @default.
• W4300979642 created "2022-10-04" @default.
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• W4300979642 date "2022-11-01" @default.
• W4300979642 modified "2023-09-25" @default.
• W4300979642 title "TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes" @default.
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• W4300979642 doi "https://doi.org/10.1063/5.0101118" @default.
• W4300979642 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36347673" @default.
• W4300979642 hasPublicationYear "2022" @default.
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