Paper Citing NAMD - Abstract
Lechuga, Javier; Drikakis, Dimitris; Pal, Sandip
Molecular dynamics study of the interaction of a shock wave with a biological membrane
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, 57:677-692, JUN 20 2008
This paper presents a computational study of the interaction of a shock wave with a biological membrane. The membrane model comprises 21555 atoms which build 66 dalmitoyloteoylphosphatidylcholine (POPC) lipids forming the bilayer, and 4237 water molecules, with the distance between the layers being set to fit around the actual membrane thickness (54 angstrom), and the lattice period being set to fit the actual surface density of lipid molecules. We have employed a molecular dynamics method for solving the Newton equations of motion numerically thereby providing a strategy to understand the basic physics of the biological structure at atomistic level. A shock wave has been modelled as an impulse of 40 Pa s, and simulations for the interaction of the shock wave with the membrane have been performed for 200 ps to investigate the different effects of the shock wave on different membrane properties including thickness, area, volume, order parameter and lateral diffusion. Copyright (C) 2007 John Wiley & Sons, Ltd.
