Sodium diffusion through amorphous silica surfaces: a molecular dynamics study.

We have studied the diffusion inside the silica network of sodium atoms initially located outside the surfaces of an amorphous silica film. We have focused our attention on structural and dynamical quantities, and we have found that the local environment of the sodium atoms is close to the local environment of the sodium atoms inside bulk sodo-silicate glasses obtained by quench. This is in agreement with recent experimental results.

Voro3D: 3D Voronoi tessellations applied to protein structures.

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 calculation, different structural properties of interest like secondary structures assignment, environment accessibility and exact contact matrices can be derived without any geometrical cut-off.

New universality class for the three-dimensional XY model with correlated impurities: application to 4He in aerogels.

Encouraged by experiments on 4He in aerogels, we confine planar spins in the pores of simulated aerogels (diffusion limited cluster-cluster aggregation) in order to study the effect of quenched disorder on the critical behavior of the three-dimensional XY model. Monte Carlo simulations and finite-size scaling are used to determine critical couplings K(c) and exponents. In agreement with experiments, clear evidence of change in the thermal critical exponents nu and alpha is found at nonzero volume fractions of impurities.

Anomalous low-field classical magnetoresistance in two dimensions.

The magnetoresistance of classical two-dimensional electrons scattered by randomly distributed impurities is investigated by numerical simulation. At low magnetic fields, we find for the first time a negative magnetoresistance proportional to |B|. This unexpected behavior is shown to be due to a memory effect specific for backscattering events, which was not considered previously.

Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds.

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.

Dangling bond deflection model: growth of gel network with loop structure.

It has been shown that the closed-loop structure in the model gel networks is responsible for their stiffness. However, the creation of loops has been underestimated in most of the existing kinetic aggregation models [e.g.

Random walks on fractals and stretched exponential relaxation.

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 clusters. Thus we find that in each dimension the decay exponent beta(K) is related to well-known exponents of the percolation theory in the corresponding flat space.

Voronoï tessellation reveals the condensed matter character of folded proteins.

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, with a quite strong fivefold local symmetry. Moreover, the statistics permits one to establish a classification of amino acids in terms of increasing propensity to be buried in agreement with what is known from chemical considerations.