scholarly journals Coarse-grained, density dependent implicit solvent model reliably reproduces behavior of a model surfactant system

2009 ◽  
Vol 130 (20) ◽  
pp. 204903 ◽  
Author(s):  
Erik C. Allen ◽  
Gregory C. Rutledge
Keyword(s):  
Coarse Grained ◽  
Implicit Solvent ◽  
Implicit Solvent Model ◽  
Density Dependent ◽  
Surfactant System ◽  
Solvent Model

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 Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

2008 ◽  
Vol 4 (5) ◽  
pp. 855-868 ◽  
Author(s):  
Anthony K. Felts ◽  
Emilio Gallicchio ◽  
Dmitriy Chekmarev ◽  
Kristina A. Paris ◽  
Richard A. Friesner ◽  
...  
Keyword(s):  
Torsion Angle ◽  
Implicit Solvent ◽  
Implicit Solvent Model ◽  
Solvent Model ◽  
Loop Conformations
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