Molecular dynamics simulations, Plate

Figure 1 (Plate 1). A molecular view of a small section of a flat lipid bilayer generated by molecular dynamics simulations. The bilayers are composed of l-stearoyl-2-docosa-hexaenoyl-5M-g]ycero-3-phosphatidylcholine lipids, i.e. the sn 1 chain is 18 C atoms long and the sn2 chain has 22 carbons, including six cis double bonds. The hydrophobic core is in the centre of the picture, and the hydrated head-group regions are both on top and bottom of the view graph. The head group is zwitterionic and no salt has been added. From [102], Reproduced by permission of the American Physical Society. Copyright (2003)...

The fundamental theorems needed to make use of a molecular dynamics simulation have now been listed. Applications to other problems such as lubrication by a thin film or the related one of viscous flow between two closely spaced plates or down a narrow cylindrical tube will be discussed below. 

S.-B. Zhu and G. W. Robinson, Structure and Dynamics of Liquid Water between Plates, J. Chem. Phys. 94 (1991) 1403-1410 references to other simulations of this widely studied system are given in this paper see also E. Spohr, Molecular Dynamics Simulation Studies of the Density Profiles of Water between 9-3 Lennard-Jones Walls, J. Chem. Phys. 106 (1997) 388-391. 

To complement H-NMR studies, an extended molecular dynamics simulation of 58 was carried out. The starting geometry for 58 was generated using coordinates taken from the partially helical, C-terminal decapeptide portion (residues 27-36) of the NPY model shown in Plate 13. The residues corresponding to Thr-32 and Gln-34 were replaced with Tyr and Leu, respectively, and subjected to an unconstrained molecular dynamics simulation. The structures obtained from this simulation (a representative structure is shown in Plate 15b) share several important features with those observed by H-NMR, specifically the formation of an Asx turn and close association of the aromatic tyrosine rings. 

In a recent article [5] dealing with the properties of adsorbed water layers and the effect of adsorbed layers on interparticle forces, it was clearly stated that even under common room conditions (relative humidity in the region 40-60%), two or three adsorbed monolayers of water are often present on particles, dominating the interactions, and therefore the physical characteristics of the material. For a two-phase equilibrium system containing hydrophilic silica plates (surface of a-quartz covered by silanol groups) and water molecules, a molecular dynamic simulation expected at least one adsorbed monolayer to be present. Quite different behavior would be expected for less hydrophilic surfaces. The material character and chemical properties of solid materials are of crucial importance in the hydration interaction. Therefore, some common adsorbents which are Irequently used in aqueous electrolyte solutions are discussed separately. 

Figure 24 Potential energy and F order parameter for the methane-water system over the course of the molecular dynamics simulation. The reference value (—0.04) for a fully melted hydrate (horizontal blue line) identifies the beginning of nucleation at 1.2 ps. Snapshots (a) through (f) show the system evolution during the simulation. Adapted from Ref. 119. (For a color version of this figure, please see plate 9 in color plate section.)...

Although one cannot simulate an electrolyte solution, molecular-dynamics studies of an ensemble of water with one or two ions have been performed. The long-range nature of the Coulomb force causes considerable technical difficulties in addition, the interaction potentials are somewhat uncertain. So the results have to be considered with caution. Nevertheless, they seem reasonable, and fit in well with our knowledge of the interface. Figure 17.9 shows the results of a simulation of an ensemble of water molecules with one Li+ and one I"" ion in the presence of a fairly large field between the two metal plates [14]. In... 

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