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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)

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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)

- Philippe Jund, Walter Kob, Rémi Jullien
- 2001

We use classical molecular dynamics simulations to study the dynamics of sodium atoms in amorphous Na 2 O-4SiO 2. We find that the sodium trajec-tories form a well connected network of pockets and channels. Inside these channels the motion of the atoms is not cooperative but rather given by independent thermally activated hops of individual atoms between… (More)

- Anwar Hasmy, Rémi Jullien
- 1995

The pair-correlation function g(r, t) and its Fourier transform, the structure factor S(q, t), are computed during the gelation process of identical spherical particles using the diffusion-limited cluster-cluster aggregation model in a box. This numerical analysis shows that the time evolution of the characteristic cluster size ξ exhibits a crossover close… (More)

- Anwar Hasmy, Isabelle Beurroies, Daniel Bourret, Rémi Jullien
- 2008

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)

- Anwar Hasmy, Rémi Jullien
- 2008

Numerical simulations of Diffusion-Limited and Reaction-Limited Cluster-Cluster Aggregation processes of identical particles are performed in a two-dimensional box. It is shown that, for concentrations larger than a characteristic gel concentration, the morphology of the resulting spanning cluster at the gel time t g exhibits a crossover length L c between… (More)

- P Jund, D Caprion, R Jullien
- 1997

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)

- Rémi Jullien, Nathalie Olivi-Tran, Anwar Hasmy, Thierry Woignier, Jean Phalippou, Daniel Bourret +1 other
- 2008

A simple scaling theory for the sintering of fractal aerogels is presented. The densification at small scales is described by an increase of the lower cutoff length a accompanied by a decrease of the upper cutoff length ξ, in order to conserve the total mass of the system. Scaling laws are derived which predict how a, ξ and the specific pore surface area Σ… (More)