Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models

Nat Commun. 2020 Jun 11;11(1):2951. doi: 10.1038/s41467-020-16424-0.

Abstract

Biomembranes are two-dimensional assemblies of phospholipids that are only a few nanometres thick, but form micrometre-sized structures vital to cellular function. Explicit molecular modelling of biologically relevant membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Coarse-grained solvent-free membrane models offer efficient sampling but sacrifice realistic kinetics, thereby limiting the ability to predict pathways and mechanisms of membrane processes. Here, we present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics. This framework facilitates efficient simulation of large biomembrane systems with large timesteps, while achieving realistic equilibrium and non-equilibrium kinetics. It helps to bridge between the nanometer/nanosecond spatiotemporal resolutions of coarse-grained models and biologically relevant time- and lengthscales. As a demonstration, we investigate fluctuations of red blood cells, with varying cytoplasmic viscosities, in 150-milliseconds-long trajectories, and compare kinetic properties against single-cell experimental observations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Membrane / chemistry*
  • Cell Membrane / metabolism*
  • Computer Simulation*
  • Erythrocytes / metabolism
  • Humans
  • Hydrodynamics
  • Kinetics
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Phospholipids / chemistry

Substances

  • Phospholipids