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

Mohsen Sadeghi () and Frank Noé ()
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Mohsen Sadeghi: Freie Universität Berlin
Frank Noé: Freie Universität Berlin

Nature Communications, 2020, vol. 11, issue 1, 1-13

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16424-0

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