Literature DB >> 19026076

Molecular dynamics simulation of confined fluids in isosurface-isothermal-isobaric ensemble.

Hossein Eslami1, Farkhondeh Mozaffari, Jalil Moghadasi, Florian Müller-Plathe.   

Abstract

A method for the simulation of fluids confined between surfaces is developed. The molecular dynamics, with coupling to an external bath, simulation method of Berendsen et al. [J. Chem. Phys. 81, 3684 (1984)] is extended for this purpose. We keep the temperature and the parallel component of pressure fixed and change the box length in the perpendicular direction with respect to the confining surfaces to archive equilibrium. The simulation is easy to perform, especially in the case of solvation force computation. Employing this method, the simulation results on the confined Lennard-Jones and water are presented and are compared to previous grand canonical ensemble Monte Carlo and molecular dynamics simulation results. While consistent with other methods, our results show that spherical Lennard-Jones particles and water form layered structures parallel to the confining surfaces with enhanced layering with increasing pressure. Also we studied the oscillatory behaviors of solvation force and number density of confined particles as well as the stepwise variation of particle numbers as a function of separation between confining surfaces.

Entities:  

Year:  2008        PMID: 19026076     DOI: 10.1063/1.3009844

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  4 in total

1.  Physical characterization and in silico modeling of inulin polymer conformation during vaccine adjuvant particle formation.

Authors:  Thomas G Barclay; Harinda Rajapaksha; Alagu Thilagam; Gujie Qian; Milena Ginic-Markovic; Peter D Cooper; Andrea Gerson; Nikolai Petrovsky
Journal:  Carbohydr Polym       Date:  2016-01-29       Impact factor: 9.381

2.  Effect of salt valency and concentration on structure and thermodynamic behavior of anionic polyelectrolyte Na+-polyethacrylate aqueous solution.

Authors:  Praveenkumar Sappidi; Upendra Natarajan
Journal:  J Mol Model       Date:  2016-10-26       Impact factor: 1.810

3.  Molecular dynamics study of the behavior of nitromethanes enclosed inside carbon nanotube containers.

Authors:  Se Won Bae; Soo Gyeong Cho
Journal:  J Mol Model       Date:  2016-06-04       Impact factor: 1.810

4.  Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors.

Authors:  Jordana K Thibado; Jean-Yves Tano; Joon Lee; Leslie Salas-Estrada; Davide Provasi; Alexa Strauss; Joao Marcelo Lamim Ribeiro; Guoqing Xiang; Johannes Broichhagen; Marta Filizola; Martin J Lohse; Joshua Levitz
Journal:  Elife       Date:  2021-04-21       Impact factor: 8.713

  4 in total

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