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Approach for the structure analysis of complex molecular systems at computer simulation

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  • Medvedev, N.N

Abstract

The structure of complex inhomogeneous systems is a current problem in the physics of liquids, glasses, polymers, molecular biology, and material science. To understand the physical properties of such materials, one should study the structure in “micro” and “macro” levels, which demands a unified rigorous approach for structure investigations. We demonstrate that the Voronoi–Delaunay technique, which is well known in mathematics and in computer simulations, can be used for this purpose. The Voronoi–Delaunay tessellation contains complete information about the structure of a computer model. The method is applied for studying the intermediate range order to show that the behavior of the so-called prepeak in the structure factor is defined by a motif of spatial distribution of voids in the model. A large model of dense packing of spherical atoms in the process of crystallization from non-crystalline phase is analyzed. The extended linear defects of the diverse types are revealed. Investigation of the free volume distribution in the lipid bilayer in water is carried out. The results obtained can help for understanding a mechanism of diffusion of small molecules across lipid membranes.

Suggested Citation

  • Medvedev, N.N, 2002. "Approach for the structure analysis of complex molecular systems at computer simulation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 314(1), pages 678-685.
    • Handle: RePEc:eee:phsmap:v:314:y:2002:i:1:p:678-685
    DOI: 10.1016/S0378-4371(02)01179-2
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