Decomposition of a Protein Solution into Voronoi Shells and Delaunay Layers: Calculation of the Volumetric Properties

  • Alexandra V. Kim
  • Vladimir P. Voloshin
  • Nikolai N. Medvedev
  • Alfons Geiger
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8110)


A simple formalism is proposed for a quantitative analysis of interatomic voids inside and outside a solute molecule in solution. It can be applied for the interpretation of volumetric data, obtained in studies of protein folding and unfolding in water. In particular, it helps to divide the partial molar volume of the solute into several components. The method is based on the Voronoi-Delaunay tessellation of molecular-dynamic models of solutions. It is suggested to select successive Voronoi shells, starting from the interface between the solute molecule and the solvent, and continuing to the outside (into the solvent) as well as into the inner of the molecule. Similarly, successive Delaunay layers, consisting of Delaunay simplexes, can also be constructed. Geometrical properties of the selected shells and layers are discussed. The temperature behavior of inner, boundary and outer shells is discussed by the example of a molecular-dynamic model of an aqueous solution of the polypeptide hIAPP.


Voronoi diagram solvation shell molecular dynamics of solutions Voronoi cells Delaunay simplexes partial molar volume 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Alexandra V. Kim
    • 1
  • Vladimir P. Voloshin
    • 1
  • Nikolai N. Medvedev
    • 1
    • 2
  • Alfons Geiger
    • 3
  1. 1.Institute of Chemical Kinetics and CombustionSB RASNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia
  3. 3.Physikalische Chemie, Technische Universität DortmundDortmundGermany

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