Percolation transitions in compressed SiO glasses.

Amorphous-amorphous transformations under pressure are generally explained by changes in the local structure from low- to higher-fold coordinated polyhedra. 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 (SiO) glasses, showing that the structural changes from low- to high-density amorphous structures occur through a sequence of percolation transitions.

The sigma delocalization in planar boron clusters.

The sigma delocalization plays an important role in the stability of small boron clusters; therefore, it is important to establish under which circumstances this delocalization contributes to the aromaticity of these molecules. In this work, using electron localization function (ELF) calculations, we show that sigma and pi electrons follow different patterns of delocalization. For sigma electrons the delocalization is mainly due to the p(sigma) radial overlapping which decreases with ring size, thus, considerable delocalization is expected for small rings, while for the pi subsystem, the Hückel rule of organic chemistry works successfully regardless of the cluster size.

Extended Hückel tight-binding approach to electronic excitations.

In this work, we propose the application of a self-consistent extended Huckel tight-binding (EHTB) method in the computation of the absorption optical spectrum of molecules within the linear response time dependent density functional formalism. The EHTB approach is presented as an approximation to the Kohn-Sham energy functional. The method is applied to the computation of excitation energies and oscillator strengths of benzene, pyridine, naphthalene, diazines, and the fullerenes: C(60)(I(h)), C(70)(D(5h)), and C(80)(D(2)).

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.

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.

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.

Thickness induced structural transition in suspended fcc metal nanofilms.

Recent experiments show that at a critical thickness, surface forces can dominate the bulk coercing suspended Au nanofilms to globally reconstruct from the (001) to the (111) orientation. Here we perform molecular dynamics simulations demonstrating that such transformations are generic to other fcc metals. This contrasts with surface reconstruction on the bulk occurring only in 5d metals.

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.

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.

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.

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).