Paper Citing NAMD - Abstract
Raczynski, Przemyslaw; Raczynska, Violetta; Gorny, Krzysztof; Gburski, Zygmunt
Properties of ultrathin cholesterol and phospholipid layers surrounding silicon-carbide nanotube: MD simulations
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 580:22-30, AUG 15 2015
Computer simulation technique was used to study the dynamics of cholesterol and POPC phospholipid molecules forming a thin layer on the surface of the carbon and silicon-carbide nanotubes. Each nanotube was surrounded by an ultra-thin film formed by n lipid molecules, where n varies from 15 to 50. All studies were done for five temperatures, including physiological one (T = 260, 285, 310, 335 and 360 K). The influence of a nanotube on the dynamics of cholesterol or phospholipid molecules in a layer is presented and discussed. The water is ubiquitous in all biological milieus, where the cholesterol or lipids occur. Thus, simulations were performed in a water environment. Moreover, to show different behavior of lipids in systems with water the results were compared with the samples without it. The dynamical and structural observables, such as the mean square displacement, diffusion coefficient, radial distribution function, and activation energy were calculated to qualitatively investigate the behavior of cholesterol and phospholipid molecules in the layers. We observed remarkable differences between the cholesterol dynamics depending whether the ultrathin film surrounds carbon or silicon-carbide nanotube and whether the water environment appeared. (C) 2015 Elsevier Inc. All rights reserved.
