Heterogeneity of the local structure in sub- and supercritical ammonia: a Voronoi polyhedra analysis.

We report results of molecular dynamics simulations and detailed analysis of the local structure of sub- and supercritical ammonia in the range of temperature between 250 and 500 K along the 135 bar isobar. This analysis is based on the behavior of distributions of metric and topological properties of the Voronoi polyhedra (VP). We show that by increasing the temperature, the volume, surface, and face area distributions of the Voronoi polyhedra as well as the vacancy radius distribution broaden, particularly near the temperature T(α), where the calculated thermal expansion coefficient has its maximum. Furthermore, the rate of increase of the corresponding mean values and fluctuations increases drastically when approaching T(α). This behavior clearly indicates that the local structure, as described by the VP, becomes increasingly heterogeneous upon approaching this temperature. This heterogeneous distribution of ammonia molecules is traced back to the increase of the large voids with increasing temperature, and is also clearly seen in the behavior of the fluctuation of the local density, as measured by the VP. More interestingly, the maximum in the heterogeneity coincides with the maximum of the fluctuation in the density of the VP.

Grand canonical Monte Carlo simulation of the adsorption isotherms of water molecules on model soot particles.

The grand canonical Monte Carlo method is used to simulate the adsorption isotherms of water molecules on different types of model soot particles. The soot particles are modeled by graphite-type layers arranged in an onionlike structure that contains randomly distributed hydrophilic sites, such as OH and COOH groups. The calculated water adsorption isotherm at 298 K exhibits different characteristic shapes depending both on the type and the location of the hydrophilic sites and also on the size of the pores inside the soot particle. The different shapes of the adsorption isotherms result from different ways of water aggregation in or/and around the soot particle. The present results show the very weak influence of the OH sites on the water adsorption process when compared to the COOH sites. The results of these simulations can help in interpreting the experimental isotherms of water adsorbed on aircraft soot.

Computer simulation study of intermolecular voids in unsaturated phosphatidylcholine lipid bilayers.

Computer simulation of the liquid crystalline phase of five different hydrated unsaturated phosphadidylcholine (PC) lipid bilayers, i.e., membranes built up by 18:0/18:1omega9cis PC, 18:0/18:2omega6cis PC, 18:0/18:3omega3cis PC, 18:0/20:4omega6cis PC, and 18:0/22:6omega3cis PC molecules have been performed on the isothermal-isobaric ensemble at 1 atm and 303 K. (The notation n:domegapcis specifies the lipid tails: n refers to the total number of carbon atoms in the chain, d is the number of the methylene-interrupted double bonds, p denotes the number of carbons between the chain terminal CH(3) group and the nearest double bond, and cis refers to the conformation around the double bonds.) The characteristics of the free volume in these systems have been analyzed by means of a generalized version of the Voronoi-Delaunay method [M. G. Alinchenko et al., J. Phys. Chem. B 108, 19056 (2004)]. As a reference system, the hydrated bilayer of the saturated 14:014:0 PC molecules (dimyristoylphosphatidylcholine) has also been analyzed. It has been found that the profiles of the fraction of the free volume across the membrane exhibit a rather complex pattern. This fine structure of the free volume fraction profiles can be interpreted by dividing the membrane into three separate major zones (i.e., zones of the aqueous, polar, and apolar parts of the membrane) and defining five subzones within these zones according to the average position of various atomic groups in the membrane. The fraction of the free volume in the middle of the membrane is found to increase with increasing unsaturation of the sn-2 chain of the lipid molecule. This is due to the fact that with increasing number of methylene-interrupted double bonds the lipid tails become more flexible, and hence they do not extend to the middle of the membrane. It is found that there are no broad enough preformed channels in the bilayers through which small penetrants, such as water molecules, can readily go through; however, the existing channels can largely facilitate the permeation of these molecules.

Viscosity of liquid water from computer simulations with a polarizable potential model

The longitudinal and shear viscosity of water are calculated by molecular dynamics simulation with a polarizable potential model at room temperature. To overcome the difficulty of evaluating directly the stress autocorrelation function of a system with intrinsically many-body forces, we have resorted to the analysis of the wave-vector-dependent longitudinal and transverse-current correlation functions. In a memory function formalism, the generalized viscosity can be evaluated as a function of the wave vector k. By extrapolating to k=0, we find longitudinal and shear viscosity values in better agreement with the experimental value than the corresponding quantities evaluated by making use of a nonpolarizable potential model. This result points out that for a realistic reproduction of transport quantities, it is crucial to take into account many-body contributions to the interaction potential.