Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-...
For two models of water, the profiles for atomic density, the local energy per molecule, the normal component of the pressure tensor, the polarization vector, the volume and molecular polarizabilities, the local electric potential and the electric field affecting a water molecule are obtained. The...
The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes ...
We named the models SW, or shell water models: To account for anisotropic polarization, the spring force on the shell particle has been modified to depend on the displacement of the shell particle in the molecular coordinate frame. The model is constructed so as to reproduce the vacuum dipole...
Joseph, S., Aluru, N.R.: Pumping of confined water in carbon nanotubes by rotation-translation coupling. Phys. Rev. Lett.101(6), 064502 (2008) ArticleADSGoogle Scholar Tieleman, D.P., Hess, B., Sansom, M.S.P.: Analysis and evaluation of channel models: simulations of alamethicin. Bi...
The models used in each simulation were generated with the PACKMOL [28] software, where periodic boxes of 15.64653Å3and 15.64893Å3were used for single ion solutions and diluted CsI solution respectively. For single ion solutions, the periodic boxes contain 128 water molecules each, which corres...
The combination of molecular dynamics computations with NMR relaxation techniques will hopefully stimulate novel technological developments in food engineering based on such fundamental studies. 展开 关键词: Water Carbohydrates Proteins Magnetic Resonance Spectroscopy Chemistry, Physical Models, Molecular Food ...
Molecular dynamics study of water and Na+ ions in models of the pore region of the nicotinic acetylcholine receptor The nicotinic acetylcholine receptor (nAChR) is an integral membrane protein that forms ligand-gated and cation-selective channels. The central pore is lin... GRSS Sansom - 《Biophy...
Many models have been proposed to represent water, but mainly four are repeatedly used in clay–water and clay–water–inhibitor system interactions: SPC (simple point charge) (Berendsen et al. 1981), TIP4P (four-point transferable intermolecular potentials) (Jorgensen and Madura 1983), MCY (O....
The latter, especially the hydrogen bonding interaction between water molecules and cellulose, plays a predominant role in the diffusion behavior of water molecules in the models of which the free volume rarely varies. The diffusion coefficient of water molecules has an excellent correlation with water...