A tutorial for mesoscale computer simulations of lipid membranes: tether pulling, tubulation and fluctuation
arXiv:2502.09798 · doi:10.1039/D5SM00148J
Abstract
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 (CGMS) 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 CGMS. Lastly, we construct a hands-on tutorial on how to apply CGMS, by providing a pedagogical examination of tether pulling, tubulation and 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.
References in corpus (29)
- Formation and Interaction of Membrane Tubes
- Efficient tunable generic model for fluid bilayer membranes
- Elastic deformation of a fluid membrane upon colloid binding
- Fluid Vesicles with Viscous Membranes in Shear Flow
- Solvent free model for self-assembling fluid bilayer membranes: Stabilization of the fluid phase based on broad attractive tail potentials
- Dynamics of Domain Growth in Self-Assembled Fluid Vesicles
- Sculpting vesicles with active particles: Less is more
- Fluid-membrane tethers: minimal surfaces and elastic boundary layers
- "Water-free" computer model for fluid bilayer membranes
- A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers
- Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles
- Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments
- Wrapping of ellipsoidal nano-particles by fluid membranes
- Flexible Lipid Bilayers in Implicit Solvent
- Membrane simulation models from nm to m scale
- A Simple Computer Model for Liquid Lipid Bilayers
- Bending models of lipid bilayer membranes: spontaneous curvature and area-difference elasticity
- Stochastic Dynamics of Nanoparticle and Virus Uptake
- The Effect of Thermal Fluctuations on Schulman Area Elasticity
- Are stress-free membranes really 'tensionless'?
- Mode excitation Monte Carlo simulations of mesoscopically large membranes
- Dynamic shapes of floppy vesicles enclosing active Brownian particles with membrane adhesion
- Dynamics of particle uptake at cell membranes
- On the connection between dissipative particle dynamics and the Itô-Stratonovich dilemma
- Wrapping pathways of anisotropic dumbbell particles by giant unilamellar vesicles
- Structure formation in binary mixtures of lipids and detergents: Self-assembly and vesicle division
- Structure formation of surfactant membranes under shear flow
- PyMembrane: A flexible framework for efficient simulations of elastic and liquid membranes
- flippy: User friendly and open source framework for lipid membrane simulations