TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes
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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.
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Since the membrane surface did not undergo any topological changes, the second term of the Helfrich Hamiltonian was safely ignored based on the Gauss-Bonnet theorem, as total Gaussian curvature remains constant under pure deformations.
“Since the membrane surface did not undergo any topological changes, we safely ignored the second term, based on the Gauss-Bonnet theorem, as the total Gaussian curvature remains constant under pure deformations.109”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [109]
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Self-citation
- Authors
- Siggel, M., Kehl, S., Reuter, K., Köfinger, J., & Hummer, G.
- Affiliations
- Max Planck Institute of Biophysics (DE)
- Max Planck Computing and Data Facility (DE)
- Goethe University Frankfurt (DE)
- Corresponding author
- Hummer, Gerhard
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2022-11-01
- Volume
- 157
- Issue
- 17
- Pages
- 174801-174801
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W4300979642
- Cited by
- 22
- References
- 56
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 10 · 2023: 2 · 2022: 1
- FWCI
- 1.55
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- The Journal of Chemical Physics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) (submittedVersion, cc-by-nc)
- Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) (submittedVersion, cc-by)
- Funders
- Max-Planck-Gesellschaft
- Hessisches Ministerium für Wissenschaft und Kunst (LOEWE DynaMem)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- lipid membranes, elastic membrane model, Hamiltonian Monte Carlo, parallel simulation, membrane remodeling, surface-to-volume ratio, density of states, Boltzmann sampling
- MeSH terms
- Computer Simulation, Lipids, Monte Carlo Method, Software
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