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A three-dimensional Voronoi tessellation of folded proteins is used to analyze geometrical and topological properties of a set of proteins. To each amino acid is associated a central point surrounded by a Voronoi cell. Voronoi cells describe the packing of the amino acids. Special attention is given to reproduction of the protein surface. Once the Voronoi(More)
The packing geometry of amino acids in folded proteins is analyzed via a modified Voronoï tessellation method which distinguishes bulk and surface. From a statistical analysis of the Voronoï cells over 40 representative proteins, it appears that the packings are in average similar to random packings of hard spheres encountered in condensed matter physics,(More)
UNLABELLED Voro3D is an original easy-to-use tool, which provides a brand new point of view on protein structures through the three-dimensional (3D) Voronoi tessellations. To construct the Voronoi cells associated with each amino acid by a number of different tessellation methods, Voro3D uses a protein structure file in the PDB format as an input. After(More)
An extension of the Voronoi tessellation, the Laguerre polyhedral decomposition, is introduced and applied to the analysis of the packing geometry of amino-acids in folded proteins. This method considers an ensemble of points with different weights and therefore it is well suited for a geometrical analysis of a set of objects with a wide size distribution.(More)
The experimental density dependence of gas (argon and nitrogen) permeabil-ity of partially densified silica aerogels in the Knudsen regime is quantitatively accounted for by a computer model. The model simulates both the structure of the sintered material and the random ballistic motion of a point particle inside its voids. The same model is also able to(More)
Stretched exponential relaxation [exp-(t/tau)(beta(K))] is observed in a large variety of systems but has not been explained so far. Studying random walks on percolation clusters in curved spaces whose dimensions range from 2 to 7, we show that the relaxation is accurately a stretched exponential and is directly connected to the fractal nature of these(More)
In order to improve our understanding of the glass transition we performed constant-energy molecular dynamics simulations on a soft-sphere system quenched from the liquid state to zero temperature. The temperature dependence of static (radial pair distribution function) and dynamic quantities (self-diiusion constant) has been investigated together with the(More)