Literature DB >> 24032960

Dynamic implicit-solvent coarse-grained models of lipid bilayer membranes: fluctuating hydrodynamics thermostat.

Yaohong Wang1, Jon Karl Sigurdsson, Erik Brandt, Paul J Atzberger.   

Abstract

We introduce a thermostat based on fluctuating hydrodynamics for dynamic simulations of implicit-solvent coarse-grained models of lipid bilayer membranes. We show our fluctuating hydrodynamics approach captures interesting correlations in the dynamics of lipid bilayer membranes that are missing in simulations performed using standard Langevin dynamics. Our momentum conserving thermostat accounts for solvent-mediated momentum transfer by coupling coarse-grained degrees of freedom to stochastic continuum fields that account for both the solvent hydrodynamics and thermal fluctuations. We present both a general framework and specific methods to couple the particle and continuum degrees of freedom in a manner consistent with statistical mechanics and amenable to efficient computational simulation. For self-assembled vesicles, we study the diffusivity of lipids and their spatial correlations. We find the hydrodynamic coupling yields within the bilayer interesting correlations between diffusing lipids that manifest as a vortex-like structure similar to those observed in explicit-solvent simulations. We expect the introduced fluctuating hydrodynamics methods to provide a way to extend implicit-solvent models for use in a wide variety of dynamic studies.

Entities:  

Year:  2013        PMID: 24032960     DOI: 10.1103/PhysRevE.88.023301

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  3 in total

1.  Formation and Properties of a Self-Assembled Nanoparticle-Supported Lipid Bilayer Probed through Molecular Dynamics Simulations.

Authors:  Haoyuan Jing; Yanbin Wang; Parth Rakesh Desai; Kumaran S Ramamurthi; Siddhartha Das
Journal:  Langmuir       Date:  2020-05-12       Impact factor: 3.882

2.  Simulation Best Practices for Lipid Membranes [Article v1.0].

Authors:  David J Smith; Jeffery B Klauda; Alexander J Sodt
Journal:  Living J Comput Mol Sci       Date:  2019-01-09

3.  Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.

Authors:  Matthieu Chavent; Tyler Reddy; Joseph Goose; Anna Caroline E Dahl; John E Stone; Bruno Jobard; Mark S P Sansom
Journal:  Faraday Discuss       Date:  2014-06-17       Impact factor: 4.394

  3 in total

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