Percolation transitions in compressed SiO2 glasses.

Amorphous-amorphous transformations under pressure are generally explained by changes in the local structure from low- to higher-fold coordinated polyhedra1-4. However, as the notion of scale invariance at the critical thresholds has not been addressed, it is still unclear whether these transformations behave similarly to true phase transitions in related crystals and liquids. Here we report ab initio-based calculations of compressed silica (SiO2) glasses, showing that the structural changes from low- to high-density amorphous structures occur through a sequence of percolation transitions. When the pressure is increased to 82 GPa, a series of long-range ('infinite') percolating clusters composed of corner- or edge-shared tetrahedra, pentahedra and eventually octahedra emerge at critical pressures and replace the previous 'phase' of lower-fold coordinated polyhedra and lower connectivity. This mechanism provides a natural explanation for the well-known mechanical anomaly around 3 GPa, as well as the structural irreversibility beyond 10 GPa, among other features. Some of the amorphous structures that have been discovered mimic those of coesite IV and V crystals reported recently5,6, highlighting the major role of SiO5 pentahedron-based polyamorphs in the densification process of vitreous silica. Our results demonstrate that percolation theory provides a robust framework to understand the nature and pathway of amorphous-amorphous transformations and open a new avenue to predict unravelled amorphous solid states and related liquid phases7,8.

Correlation between strand asymmetry and phylogeny in mitochondrial DNA.

An evolutionary distance is introduced in order to propose an efficient and feasible procedure for phylogeny studies. Our analysis are based on the strand asymmetry property of mitochondrial DNA, but can be applied to other genomes. Comparison of our results with those reported in conventional phylogenetic trees, gives confidence about our approximation. Our findings support the hypotheses about the origin of the skew and its dependence upon evolutionary pressures, and improves previous efforts on using the strand asymmetry property of genomes for phylogeny inference. For the evolutionary distance introduced here, we observe that the more adequate technique for tree reconstructions correspond to an average link method which employs a sequential clustering algorithm.

Ionic shell and subshell structures in aluminum and gold nanocontacts.

Conductance histograms of aluminum and gold nanocontact rupture are studied experimentally and simulated using embedded atom potentials to assess the interplay between electronic and structural properties at room temperature. Our results reveal a crossover from quantized conductance structures to crystalline faceting or geometric shell/subshell structures at 300 K. The absence of electronic shell structure in gold and aluminum is in stark contrast with the behavior of alkaline metal nanowires which emulate their cluster counterparts. Semiclassical arguments suggest why rapid dominance of ionic structures takes place, and possible nanowire architectures are proposed in consistency with both the experimental and simulated nanocontact data.

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. These changes are explained in terms of hidden long-range correlations within disorder distributions.

From favorable atomic configurations to supershell structures: a new interpretation of conductance histograms.

Simulated minimum cross-section histograms of breaking Al nanocontacts are produced using molecular dynamics. The results allow a new interpretation of the controverted conductance histogram peaks based on preferential geometrical arrangements of nanocontact necks. As temperature increases, lower conductance peaks decrease in favor of broader and higher conductance structures. This reveals the existence of shell and supershell structures favored by the increased mobility of Al atoms.

Three-dimensional rotational Langevin dynamics and the Lebwohl-Lasher model.

We introduce a new scheme for molecular-dynamics simulation of three-dimensional systems exhibiting rotational motions. The procedure is based on the Langevin dynamics method. Our paper is focused on the Lebwohl-Lasher model in order to simulate the isotropic-nematic transition of liquid crystals. In contrast to previous dynamic approximations, our approach allows one to reproduce well the isotropic phase of these systems.

Molecular-dynamics simulation of two-dimensional thermophoresis

A numerical technique is presented for the thermal force exerted on a solid particle by a gaseous medium between two flat plates at different temperatures, in the free molecular or transition flow. This is a two-dimensional molecular-dynamics simulation of hard disks in a inhomogeneous thermal environment. All steady-state features exhibited by the compressible hard-disk gas are shown to be consistent with the expected behaviors. Moreover the thermal force experienced by a large solid disk is investigated, and compared to the analytical case of cylinders moving perpendicularly to the constant temperature gradient for an infinite Knudsen number and in an infinite medium. We show precise examples of how this technique can be used simply to investigate more difficult practical problems, in particluar the influence of nonlinear gradients for large applied differences of temperature, of proximity of the walls, and of smaller Knudsen numbers.

Nonlinear modeling technique for the analysis of DNA chains.

Using a simple computational procedure, we examine DNA chains from different species in order to prove their nonlinear deterministic structures. This procedure applies a nonlinear modeling technique based upon quantitative comparison of the neighborhoods from similar DNA subsegments of size d. Our results reveal that noncoding regions exhibit a deterministic signature at sizes larger than a characteristic dimension d(c). Applications to evolutionary categories and recognition of different DNA regions are discussed.