scholarly journals Explicit and implicit modeling of nanobubbles in hydrophobic confinement

2010 ◽  
Vol 82 (1) ◽  
pp. 3-12 ◽  
Author(s):  
Joachim Dzubiella

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.

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Ifat Shub ◽  
Ehud Schreiber ◽  
Yossef Kliger

Molecular dynamic simulations are used for investigating various aspects of biological processes. Such simulations often require intensive computer power; therefore several solutions were developed to minimize the computer power needed, including the usage of elevated temperatures. Yet, such simulations are still not commonly used by the wide scientific community of chemists and biochemists. For about two years now, the molecular simulations suite GROMACS enables conducting simulations using implicit solvent models to further decrease runtimes. In order to quantify the saving in computer power, and to confirm the validity of the models, we followed the simple dissolution process of a single NaCl molecule. The results reveal approximately 350-fold decrease in real-world runtime when using an implicit solvent model and an elevated temperature, compared to using explicit water molecules and simulating at room temperature. In addition, in a wide range of temperatures, the dissolution times of NaCl are distributed, as expected, exponentially, both in explicit and in implicit solvent models, hence confirming the validity of the simulation approach. Hopefully, our findings will encourage many scientists to take advantage of the recent progress in the molecular dynamics field for various applications.


Soft Matter ◽  
2018 ◽  
Vol 14 (24) ◽  
pp. 5019-5030 ◽  
Author(s):  
Eric J. Spangler ◽  
P. B. Sunil Kumar ◽  
Mohamed Laradji

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.


Soft Matter ◽  
2018 ◽  
Vol 14 (15) ◽  
pp. 2796-2807 ◽  
Author(s):  
Andrea Catte ◽  
Mark R. Wilson ◽  
Martin Walker ◽  
Vasily S. Oganesyan

Antimicrobial action of a cationic peptide is modelled by large scale MD simulations.


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