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: Contribution to journalArticle

22 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
Pages (from-to)217-226
Number of pages10
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3045
Publication statusPublished - 2004

Fingerprint

Lipid bilayers
Delaunay
Voronoi
Biological systems
Voids
Structural analysis
Navigation
Glass
Molecules
Computer simulation
Lipid Bilayers
Liquids
Computer Simulation
Lipid Bilayer
Tessellation
Voronoi Diagram
Structural Analysis
Biological Systems
Building Blocks
Cavity

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Implementation of the Voronoi-Delaunay method for analysis of intermolecular voids. / Anikeenko, A. V.; Alinchenko, M. G.; Voloshin, V. P.; Medvedev, N. N.; Gavrilova, M. L.; Jedlovszky, P.

In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 3045, 2004, p. 217-226.

Research output: Contribution to journalArticle

@article{6aef7607503e4062b0f460908fbbbe40,
title = "Implementation of the Voronoi-Delaunay method for analysis of intermolecular voids",
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.",
author = "Anikeenko, {A. V.} and Alinchenko, {M. G.} and Voloshin, {V. P.} and Medvedev, {N. N.} and Gavrilova, {M. L.} and P. Jedlovszky",
year = "2004",
language = "English",
volume = "3045",
pages = "217--226",
journal = "Lecture Notes in Computer Science",
issn = "0302-9743",
publisher = "Springer Verlag",

}

TY - JOUR

T1 - Implementation of the Voronoi-Delaunay method for analysis of intermolecular voids

AU - Anikeenko, A. V.

AU - Alinchenko, M. G.

AU - Voloshin, V. P.

AU - Medvedev, N. N.

AU - Gavrilova, M. L.

AU - Jedlovszky, P.

PY - 2004

Y1 - 2004

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=35048863957&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35048863957&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:35048863957

VL - 3045

SP - 217

EP - 226

JO - Lecture Notes in Computer Science

JF - Lecture Notes in Computer Science

SN - 0302-9743

ER -