Rémi Jullien

MOLECULAR-DYNAMICS CALCULATION OF THE THERMAL CONDUCTIVITY OF VITREOUS SILICA

We use extensive classical molecular-dynamics simulations to calculate the thermal conductivity of a model silica glass. Apart from the potential parameters, this is done with no other adjustable quantity and the standard equations of heat transport are used directly in the simulation box. The calculations have been done between 10 and 1000 K and the results are in good agreement with the experimental data at temperatures above 20 K. The plateau observed around 10 K can be accounted for by correcting our results taking into account finite-size effects in a phenomenological way.

Channel diffusion of sodium in a silicate glass

We use classical molecular dynamics simulations to study the dynamics of sodium atoms in amorphous

Simple models for the restructuring of three-dimensional ballistic aggregates

{\mathrm{Na}}_{2}\mathrm{O}\ensuremath{-}4{\mathrm{SiO}}_{2}.

Structural and electronic properties of the sodium tetrasilicate glass Na 2 Si 4 O 9 from classical and ab initio molecular dynamics simulations

We find that the sodium trajectories form a well connected network of pockets and channels. Inside these channels the motion of the atoms is not cooperative, but rather is given by independent thermally activated hops of individual atoms between the pockets. By determining the probability that an atom returns to a given starting site, we show that such events are not important to the dynamics of this system at high temperatures.

Nonatomic Solvent-Driven Voronoi Tessellation of Proteins:An Open Tool to Analyze Protein Folds

Abstract The effects of some simple restructuring processes in which pairs of rigid clusters can readjust their positions with respect to each other after collision have been investigated using the three-dimensional hierarchical cluster-cluster aggregation model. In these models we assume that contacts between pairs of particles once formed cannot be broken but may move on the surface of particles in one cluster which contact particles in a different cluster immediately after contact has been made. Such structural readjustment processes increase the fractal dimensionality from a value of about 1.89 without readjustment by an amount which depends on model details. The highest fractal dimensionality obtained in the models investigated here was about 2.13. For ballistic aggregation with a zero impact parameter the fractal dimensionality can be raised from 2.04 to 2.21.

Sol-gel process simulation by cluster-cluster aggregation

The structure and the electronic properties of a sodium tetrasilicate

SMALL-ANGLE SCATTERING BY FRACTAL AGGREGATES : A NUMERICAL INVESTIGATION OF THE CROSSOVER BETWEEN THE FRACTAL REGIME AND THE POROD REGIME

({\mathrm{Na}}_{2}{\mathrm{Si}}_{4}{\mathrm{O}}_{9})

Classical molecular dynamics simulations of amorphous silica surfaces

glass were studied by combined Car-Parrinello and classical molecular dynamics simulations. The glass sample was prepared using a method recently employed in a study of a silica glass [M. Benoit et al., Euro. Phys. J. B 13, 631 (2000)]. First we generated a NS4 glass by classical molecular dynamics and then we took it as the initial configuration of a first-principles molecular dynamics simulation. In the ab initio molecular dynamics simulation, the electronic structure was computed in the framework of the Kohn\char21{}Sham density functional theory within the generalized gradient approximation using a B-LYP functional. The Car-Parrinello dynamics is remarkably stable during the considered trajectory and, as soon as it is switched on, some significant structural changes occur. The ab initio description improves the comparison of the structural characteristics with experimental data, in particular concerning the Si\char21{}O and Na\char21{}O bond lengths. From an electronic point of view, we find that the introduction of the sodium oxide in the silica network lowers the band gap and leads to a highly nonlocalized effect on the charges of the network atoms.

Structural properties of glassy and liquid sodium tetrasilicate: comparison between ab initio and classical molecular dynamics simulations

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 cells are built, a lot of tools from geometrical analysis can be applied to investigate the protein structure; volume of cells, number of faces per cell, and number of sides per face are the usual signatures of the protein structure. A distinct difference between faces related to primary, secondary, and tertiary structures has been observed. Faces threaded by the main‐chain have on average more than six edges, whereas those related to helical packing of the amino acid chain have less than five edges. The faces on the protein surface have on average five edges within 1% error. The average number of faces on the protein surface for a given type of amino acid brings a new point of view in the characterization of the exposition to the solvent and the classification of amino acid as hydrophilic or hydrophobic. It may be a convenient tool for model validation. Proteins 2002;49:446–456.

FLUCTUATING BOND AGGREGATION : A MODEL FOR CHEMICAL GEL FORMATION

The pair-correlation function, g(r, t), and its Fourier transform, the structure factor, S(q, t), were 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 to the gel time, t g , which depends on the volumic fraction, c. In this model, t g tends to infinity when the box size, L, tends to infinity. For systems of finite sizes it is shown numerically that, when t < t g , the wave vector, q m , at which S(q,t) has a maximum, decreases as S(q m , t) -1/D , where D is an apparent fractal dimension of clusters, as measured from the slope of S(q, t). The time evolution of the mean number of particles per cluster, n, was also investigated. Numerical results are in qualitative agreement with small-angle scattering experiments in several systems.