Implementation of the Voronoi-Delaunay method for analysis of intermolecular voids

A. V. Anikeenko, M. G. Alinchenko, V. P. Voloshin, N. N. Medvedev, M. L. Gavrilova, P. Jedlovszky

Research output: Chapter in Book/Report/Conference proceedingChapter

25 Citations (Scopus)

Abstract

Voronoi diagram and Delaunay tessellation have been used for a long time for structural analysis of computer simulation of simple liquids and glasses. However the method needs a generalization to be applicable to molecular and biological systems. Crucial points of implementation of the method for analysis of intermolecular voids in 3D are discussed in this paper. The main geometrical constructions - the Voronoi S-network and Delaunay S-simplexes, are discussed. The Voronoi network "lies" in the empty spaces between molecules and represents a "navigation map" for intermolecular voids. The Delaunay S-simplexes determine the simplest interatomic cavities and serve as building blocks for composing complex voids. An algorithm for the Voronoi S-network calculation is illustrated on example of lipid bilayer model.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
EditorsAntonio Lagan`a, Marina L. Gavrilova, Vipin Kumar, Youngsong Mun, C.J. Kenneth Tan, Osvaldo Gervasi
PublisherSpringer Verlag
Pages217-226
Number of pages10
ISBN (Print)3540220577, 9783540220572
DOIs
Publication statusPublished - Jan 1 2004

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3045
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Anikeenko, A. V., Alinchenko, M. G., Voloshin, V. P., Medvedev, N. N., Gavrilova, M. L., & Jedlovszky, P. (2004). Implementation of the Voronoi-Delaunay method for analysis of intermolecular voids. In A. Lagan`a, M. L. Gavrilova, V. Kumar, Y. Mun, C. J. Kenneth Tan, & O. Gervasi (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pp. 217-226). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3045). Springer Verlag. https://doi.org/10.1007/978-3-540-24767-8_23