Traveling through potential energy landscapes of disordered materials: the activation-relaxation technique

A detailed description of the activation-relaxation technique (ART) is presented. This method defines events in the configurational energy landscape of disordered materials, such as a-Si, glasses and polymers, in a two-step process: first, a configuration is activated from a local minimum to a nearby saddle-point; next, the configuration is relaxed to a new minimum; this allows for jumps over energy barriers much higher than what can be reached with standard techniques. Such events can serve as basic steps in equilibrium and kinetic Monte Carlo schemes.Comment: 7 pages, 2 postscript figure

Atomic layering at the liquid silicon surface: a first- principles simulation

We simulate the liquid silicon surface with first-principles molecular dynamics in a slab geometry. We find that the atom-density profile presents a pronounced layering, similar to those observed in low-temperature liquid metals like Ga and Hg. The depth-dependent pair correlation function shows that the effect originates from directional bonding of Si atoms at the surface, and propagates into the bulk. The layering has no major effects in the electronic and dynamical properties of the system, that are very similar to those of bulk liquid Si. To our knowledge, this is the first study of a liquid surface by first-principles molecular dynamics.Comment: 4 pages, 4 figures, submitted to PR

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press

Tendency to occupy a statistically dominant spatial state of the flow as a driving force for turbulent transition

A simple analytical model for a turbulent flow is proposed, which considers the flow as a collection of localized spatial structures that are composed of elementary "cells" in which the state of the particles (atoms or molecules) is uncertain. The Reynolds number is associated with the ratio between the total phase volume for the system and that for the elementary cell. Calculating the statistical weights of the collections of the localized structures, it is shown that as the Reynolds number increases, the elementary cells group into the localized structures, which successfully explains the onset of turbulence and some other characteristic properties of turbulent flows. It is also shown that the basic assumptions underlying the model are involved in the derivation of the Navier-Stokes equation, which suggests that the driving force for the turbulent transition described with the hydrodynamic equations is essentially the same as in the present model, i.e. the tendency of the system to occupy a statistically dominant state plays a key role. The instability of the flow can then be a mechanism to initiate the structural rearrangement of the flow to find this state.Comment: 7 pages, 4 figures, and Supplementary Material (2 pages, 3 figures), to be submitted to "Foundations of Physics". arXiv admin note: substantial text overlap with arXiv:1102.515

Density Distribution in the Liquid Hg-Sapphire Interface

We present the results of a computer simulation study of the liquid density distribution normal to the interface between liquid Hg and the reconstructed (0001) face of sapphire. The simulations are based on an extension of the self-consistent quantum Monte Carlo scheme previously used to study the structure of the liquid metal-vapor interface. The calculated density distribution is in very good agreement with that inferred from the recent experimental data of Tamam et al (J. Phys. Chem. Lett. 1, 1041-1045 (2010)). We conclude that, to account for the difference in structure between the liquid Hg-vapor and liquid-Hg-reconstructed (0001) Al2O3 interfaces, it is not necessary assume there is charge transfer from the Hg to the Al2O3. Rather, the available experimental data are adequately reproduced when the van der Waals interactions of the Al and O atoms with Hg atoms and the exclusion of electron density from Al2O3 via repulsion of the electrons from the closed shells of the ions in the solid are accounted for.Comment: 26 pages, 11 figure

Structure and outcomes of paracetamol poisoning according to the Sverdlovsk regional center for acute poisoning

The purpose of the study is to analyze the structure of acute poisoning with paracetamol in the Sverdlovsk Regional Center for the treatment of poisoning and toxicological centers of Irkutsk, Tyumen and Izhevsk.Цель исследования – провести анализ структуры острых отравлений парацетамолом в Свердловском областном центре по лечению отравлений и токсикологических центрах г. Иркутска, Тюмени и Ижевска