V. P. Voloshin

Geometrical analysis of the structure of simple liquids: percolation approach

The problem of searching for quantitative laws governing the structure of simple liquids is formulated as a site percolation problem on the Voronoi network. The sites of this four-coordinated network correspond to the figures formed by the four neighbouring atoms (Delaunay simplices). Three quantitative characteristics of the form of the Delaunay simplices are introduced to enable one to colour the sites of the Voronoi network corresponding to the simplices of a specific form and to study the percolation of colouring through the network sites. The clusters of contiguous Delaunay simplices of the specific form have been studied and the percolation thresholds for various colouring types have been obtained for instantaneous configurations of the Lennard-Jones liquid (obtained by the Monte Carlo procedure) as well as for the configurations with removed thermal excitations (F structure). Percolation of all the types of colouring introduced turns out to be correlated, i.e., the Delaunay simplices of a given for...

Can Various Classes of Atomic Configurations (Delaunay Simplices) be Distinguished in Random Dense Packings of Spherical Particles

Abstract One-dimensional and two-dimensional distributions of the characteristics introduced previously for the forms of Delaunay simplices - tetrahedricity and octahedricity - have been investigated in computer models of a crystal, a liquid and an amorphous solid. It has been established that in the absence of thermal perturbations (in the proper structure of the liquid and in an amorphous substance) there exists a distinguishable class of simplices with five almost equal edges and the sixth being longer. This class of simplices named isopentacmons, in turn includes the types of good tetrahedra and good quartoctahedra (a quarter of octahedron). In disordered systems the fraction of tetrahedra relative to quartoctahedra exceeds substantially that in the FCC crystal.

Water adsorption isotherms on porous onionlike carbonaceous particles. Simulations with the grand canonical Monte Carlo method.

The grand canonical Monte Carlo method is used to simulate the adsorption isotherms of water molecules on different types of model soot particles. These soot models are constructed by first removing atoms from onion-fullerene structures in order to create randomly distributed pores inside the soot, and then performing molecular dynamics simulations, based on the reactive adaptive intermolecular reactive empirical bond order (AIREBO) description of the interaction between carbon atoms, to optimize the resulting structures. The obtained results clearly show that the main driving force of water adsorption on soot is the possibility of the formation of new water-water hydrogen bonds with the already adsorbed water molecules. The shape of the calculated water adsorption isotherms at 298 K strongly depends on the possible confinement of the water molecules in pores of the carbonaceous structure. We found that there are two important factors influencing the adsorption ability of soot. The first of these factors, dominating at low pressures, is the ability of the soot of accommodating the first adsorbed water molecules at strongly hydrophilic sites. The second factor concerns the size and shape of the pores, which should be such that the hydrogen bonding network of the water molecules filling them should be optimal. This second factor determines the adsorption properties at higher pressures.

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.

Investigation of free volume percolation under the liquid-glass phase transition

Mutual arrangement of large volume atomic cells (defined as the Voronoi polyhedra) is investigated in molecular dynamics models of Lennard‐Jones liquid, crystal and amorphous solid by the percolation theory methods on the Delaunay network. In addition to ordinary percolation some extended formulations of the percolation problem are realized. All variants of the percolation analysis lead to characteristics of percolating clusters and to the percolation threshold values which do not practically differ for all the three phases. This provides evidence that the phase transition liquid–amorphous solid is not associated with percolation through regions with a large free volume.

Collective motions in computer models of water. Large-scale and long-time correlations

Two-particle correlation functions describing the simultaneous motion of a pair of molecules initially separated by a given distance R0 are calculated to study collective effects in the diffusive motion of water molecules in molecular dynamics models. Various types of such functions and their dependences on the interaction potential, temperature, and the number of particles in the model are considered. At short times (of the order of ten picoseconds), these functions exhibit irregular behavior depending on R0. The most nontrivial and unexpected result was the detection of correlations in the displacements of pairs of particles that extend for tens of angstroms and last for hundreds of picoseconds. Such correlations are not observed in the random walk models of noninteracting particles. It is suggested that the observed large-scale correlations reveal the vortex-like motions of the molecules.

Distributions of Hydrogen Bond Lifetimes in Instantaneous and Inherent Structures of Water

Abstract Various distribution functions of hydrogen bond lifetimes, used to describe the dynamics of breakage and formation of these bonds are calculated for a molecular dynamics model of water of 3456 molecules at 310 K. Quenched (inherent) structures are derived from instantaneous MD structures. Comparing the distribution functions from I and Q structures allows interpreting their characteristic features. The sharp peak at ~15 fs, which prevails in the most frequently used distributions, is ascribed to short-lived “false” H bonds which results from violations of hydrogen bonding criteria induced by dynamic intermolecular vibrations of molecules. A special type of distribution, proposed earlier [34], contains information not only on dynamics, but on true, or random, breaking of hydrogen bonds. The distributions reveal four different types of characteristic times which reflect different sides of H bond dynamics.

Local environmental geometry of atoms in the Lennard-Jones systems

Abstract The distributions of topological and metrical characteristics of the Voronoi polyhedra have been obtained for the Lennard-Jones systems of atoms modelling a crystal, a liquid and a fluid. The distributions of the number of faces, the number of edges per face, the number of pentagonal faces, the histograms of topological types, the radial distributions of the Voronoi polyhedron neighbours, the distribution of edge lengths, face areas and the sphericity factor have been investigated for the Voronoi polyhedra. The local atomic structure is discussed for various phase states and various temperatures and densities. The importance is noted of a simultaneous analysis of topological and metrical characteristics of the Voronoi polyhedra.

Culation of partial molar volume and its components for molecular dynamics models of dilute solutions

This paper is a review of our recent computational studies of volumetric characteristics using computer models of dilute solutions. Partial molar volume (PMV) and its components are calculated for simple and complex molecules in water (methane, noble gases, surfactants, polypeptides). Advantages and disadvantages of various computational methods are discussed. It is proposed to use the Voronoi-Delaunay technique to determine the reasonable boundary between a solute molecule and solvent molecules and to identify the PMV components related to the molecule, the boundary layer, and the solvent. It is noted that the observed increase in PMV with temperature for large molecules is due to an increase in the volume of voids in the boundary layer, i.e., due to the “thermal volume.” In this case, the solvent gives a negative contribution to the PMV. In contrast, for simple molecules (methane), the contribution from the solvent is positive and is the main factor in the increase in the PMV, which is associated with a specific change in water structure around a spherical hydrophobic particle outside the boundary layer. For surfactant molecules, the contribution from the solvent changes sign (from negative to positive) with increasing temperature.

Homogeneity loss phase transition in packings of Lennard-Jones atoms under density decreasing

Abstract Computer models of crystalline and amorphous Lennard-Jones systems show a stability threshold at the density 0.8–0.85. Below that the system loses its stability and becomes inhomogeneous. The characteristic size of regions with higher density is about 10 atomic diameters. Regions of lower density represent branched channels with a diameter exceeding that of atoms which percolate through the whole model space.