Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

Astrid F Brandner,Simone Melchionna,Fabio Sterpone,Stepan Timr,Marc Baaden,Philippe Derreumaux

doi:10.1038/s41598-019-52760-y

Abstract

In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.

Highlights

The study of biomembranes based on experimental, theoretical and computational approaches occupies a central place in modern biophysics
We present a coupling of Dry Martini[31], an implicit-solvent coarse-grained lipid model, with the Lattice Boltzmann Molecular Dynamics (LBMD) technique[40,41,42,43] to include hydrodynamic interactions (HI) in the implicit-solvent simulation of membranes
Our finding shows that LBMD is a computationally appealing alternative strategy for using implicit solvent CG lipid models coupled to the hydrodynamic interactions from an embedding fluid

Summary

Introduction

The study of biomembranes based on experimental, theoretical and computational approaches occupies a central place in modern biophysics. A great variety of experimental techniques allows characterising many aspects of the structure and dynamics of biomembranes, e.g. the extension of membrane domains[6], lipid diffusion[7], protein localisation[8], membrane deformation and fusion[9] Membrane constructs such as vesicles are studied experimentally for their transport and content release capabilities[10,11]. We show here that this coupling represents a general tool to treat the impact of HI in a broad range of processes involving lipids, standard bilayer membranes, and, for instance, to investigate the dynamics of a vesicle under the perturbative action of the external fluid flow This technique will allow synergic interactions with experiments where lipidic systems are manipulated in fluid flows[49,50]. This feature, already tested for instance to characterise DNA translocation in pores[52], can be extended to investigate voltage-dependent processes at the proximity of neuronal membrane systems

Methods

Results

Conclusion