An anisotropic coarse-grained model based on Gay-Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model

2015 ◽  
Vol 36 (15) ◽  
pp. 1103-1113 ◽  
Author(s):  
Hujun Shen ◽  
Yan Li ◽  
Peijun Xu ◽  
Xiaofang Li ◽  
Huiying Chu ◽  
...  
Keyword(s):  
Coarse Grained ◽  
Implicit Solvent ◽  
Implicit Solvent Model ◽  
Coarse Grained Model ◽  
Model Based ◽  
Solvent Model ◽  
Dmpc Bilayer

scholarly journals Explicit and implicit modeling of nanobubbles in hydrophobic confinement

2010 ◽  
Vol 82 (1) ◽  
pp. 3-12 ◽  
Author(s):  
Joachim Dzubiella
Keyword(s):  
Large Scale ◽  
Md Simulations ◽  
Energy Functional ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Implicit Solvent Model ◽  
Solvent Model ◽  
Nanofluidic Devices ◽  
Capillary Evaporation ◽  
Hydrophobic Solutes

Water at normal conditions is a fluid thermodynamically close to the liquid-vapor phase coexistence and features a large surface tension. This combination can lead to interesting capillary phenomena on microscopic scales. Explicit water molecular dynamics (MD) computer simulations of hydrophobic solutes, for instance, give evidence of capillary evaporation on nanometer scales, i.e., the formation of nanometer-sized vapor bubbles (nanobubbles) between confining hydrophobic surfaces. This phenomenon has been exemplified for solutes with varying complexity, e.g., paraffin plates, coarse-grained homopolymers, biological and solid-state channels, and atomistically resolved proteins. It has been argued that nanobubbles strongly impact interactions in nanofluidic devices, translocation processes, and even in protein stability, function, and folding. As large-scale MD simulations are computationally expensive, the efficient multiscale modeling of nanobubbles and the prediction of their stability poses a formidable task to the'nanophysical' community. Recently, we have presented a conceptually novel and versatile implicit solvent model, namely, the variational implicit solvent model (VISM), which is based on a geometric energy functional. As reviewed here, first solvation studies of simple hydrophobic solutes using VISM coupled with the numerical level-set scheme show promising results, and, in particular, capture nanobubble formation and its subtle competition to local energetic potentials in hydrophobic confinement.

Stability of membrane-induced self-assemblies of spherical nanoparticles

Soft Matter ◽  
2018 ◽  
Vol 14 (24) ◽  
pp. 5019-5030 ◽  
Author(s):  
Eric J. Spangler ◽  
P. B. Sunil Kumar ◽  
Mohamed Laradji
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Lipid Membranes ◽  
The Self ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Spherical Nanoparticles ◽  
Implicit Solvent Model ◽  
Solvent Model ◽  
Dynamics Simulations

The self-assembly of spherical nanoparticles, resulting from their adhesion on tensionless lipid membranes, is investigated through molecular dynamics simulations of a coarse-grained implicit-solvent model for self-assembled lipid membranes.

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

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Astrid F. Brandner ◽  
Stepan Timr ◽  
Simone Melchionna ◽  
Philippe Derreumaux ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lattice Boltzmann ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Mesoscopic Scale ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Cellular Compartments ◽  
Biological Entities

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.

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