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Profiles of various membrane characteristics are traditionally calculated from the middle plane of the membrane towards the surface. In this approach, atomic positions near the membrane surface are determined inaccurately because, strictly speaking, the membrane is nonplanar and can have unevennesses or a variable thickness. However, the profile can also be calculated from the membrane surface. We propose to use the Voronoi boundary surface (a set of adjacent faces of Voronoi regions of membrane atoms and surrounding water) as this surface. It naturally divides the space between the membrane and water. Atomic density and empty intermolecular space profiles calculated relative to this surface reveal new features not seen when the middle plane is used. [ABSTRACT FROM AUTHOR]

Mechanisms of radiation damages in minerals promising for the utilization of highly active radioactive waste (zircon ZrSiO, monazite LaPO, orthophosphate YbPO, lakargiite CaZrSnTi, and GdZrO and GdTiO compounds with the pyrochlore structure) are studied by the computer simulation using the molecular dynamics method. The formation of a damaged region in the structures under study is considered along with the recovery (relaxation) processes in these structures. The number of Frenkel pairs and antistructural defects that form in the structure of these minerals after the pass of the knocked out thorium atom is calculated by the molecular dynamics method. A parameter is proposed that characterizes the mineral tendency to amorphization under the effect of the radiation damage. The obtained results show that one of the main factors determining the radiation stability of minerals is the crystal structure type, compounds with the monazite structure being more radiationally stable than compounds with the zircon structure. It is found that the GdZrO compound and lakargiite have a weaker tendency to amorphization than other minerals such as zircon, monazite, and orthophosphate YbPO. A high radiation stability of the studied GdZrO compound as well as a solid solution of the composition CaZrSnTiO makes it possible to propose them as a possible matrix for the utilization of highly active radioactive waste. [ABSTRACT FROM AUTHOR]

By classical molecular dynamics, a series of solutions in the ternary water-lithium nitrate-calcium nitrate system is simulated. The radial distribution functions for different atom pairs are calculated, the coordination numbers are estimated, and the pattern of change of their first solvation shell composition with a change in the component ratio in the model system is examined. The first sphere of water molecule in the solutions with different concentration is considered in detail. Eight main structural types of the nearest-neighbor water molecule surrounding and their major features are identified, the probabilities of the occurrence of these structures in the ternary system are estimated. [ABSTRACT FROM AUTHOR]

The behavior of structures of H2O crystalline ices Ih, Ic, XI, VII, VIII, VI is studied in molecular dynamics experiment using the potential offered by Poltev and Malenkov. The behavior of the system consisting of one of the two identical interpenetrating, but without any common hydrogen bonds, water frameworks comprising the ice VI structure is also simulated. As a result of simulations, the ice VII structure has collapsed, whereas other systems proved to be stable. The reasons of instability of the ice VII and previously studied ice IV structures in molecular dynamics experiments are discussed. Based on the simulation results of the above-mentioned ices and previous simulation of ices II, III, IX, IV, and XII, the general regularities of dynamic properties of water molecules in crystalline water ices are formulated. Unreliability of results obtained by molecular dynamics in the investigation of self-organizing processes in aqueous systems is shown. [ABSTRACT FROM AUTHOR]

A molecular dynamics simulation was performed for silver clusters of 147, 309, and 561 atoms with the initial cuboctahedral habit in the temperature range 0–1000 K with an embedded atom potential for silver. Structural transitions of the silver clusters to complex twins (icosahedral habit) with coherent (111)/(111) boundaries over all edges of icosahedra were found, which started at temperatures of 50 K, 350 K, and 700 K, respectively. To analyze the structural transformations in nanoparticles, an algorithm is proposed based on a simplicial Delaunay decomposition (Delaunay triangulation). It was found that after the transition of silver nanoparticles to complex twins, the atomic motion becomes vibrational; the atoms vibrate around the sites that correspond to the vertices of the regular polyhedra. In the case of the 147-atom silver nanoparticle, the polyhedra are arranged in the following sequence, starting from the center of mass: icosahedron (12 atoms), icosododecahedron (30 atoms), icosahedron (12 atoms), dodecahedron (20 atoms), truncated icosahedron (60 atoms, isostructural with fullerene C60), icosahedron (12 atoms), and one atom at the center of mass. [ABSTRACT FROM AUTHOR]

This review is an attempt to analyze some of the experimental problems arising in the course of growth of orientated molecular films using metal monophthalocyanine (MPc) films as an example and to demonstrate the possibilities of molecular dynamics simulation of these processes for solving experimental problems. Examples of theoretical simulation of adsorption processes are given; formation of a molecular monolayer is considered for copper phthalocyanine films as an example. [ABSTRACT FROM AUTHOR]