Saddle Points and Dynamics of Lennard-Jones Clusters, Solids and Supercooled Liquids

The properties of higher-index saddle points have been invoked in recent theories of the dynamics of supercooled liquids. Here we examine in detail a mapping of configurations to saddle points using minimization of $|\nabla E|^2$, which has been used in previous work to support these theories. The examples we consider are a two-dimensional model energy surface and binary Lennard-Jones liquids and solids. A shortcoming of the mapping is its failure to divide the potential energy surface into basins of attraction surrounding saddle points, because there are many minima of $|\nabla E|^2$ that do not correspond to stationary points of the potential energy. In fact, most liquid configurations are mapped to such points for the system we consider. We therefore develop an alternative route to investigate higher-index saddle points and obtain near complete distributions of saddles for small Lennard-Jones clusters. The distribution of the number of stationary points as a function of the index is found to be Gaussian, and the average energy increases linearly with saddle point index in agreement with previous results for bulk systems.Comment: 14 pages, 7 figure

Surface structure in simple liquid metals. An orbital free first principles study

Molecular dynamics simulations of the liquid-vapour interfaces in simple sp-bonded liquid metals have been performed using first principles methods. Results are presented for liquid Li, Na, K, Rb, Cs, Mg, Ba, Al, Tl, and Si at thermodynamic conditions near their respective triple points, for samples of 2000 particles in a slab geometry. The longitudinal ionic density profiles exhibit a pronounced stratification extending several atomic diameters into the bulk, which is a feature already experimentally observed in liquid K, Ga, In, Sn and Hg. The wavelength of the ionic oscillations shows a good scaling with the radii of the associated Wigner-Seitz spheres. The structural rearrangements at the interface are analyzed in terms of the transverse pair correlation function, the coordination number and the bond-angle distribution between nearest neighbors. The valence electronic density profile also shows (weaker) oscillations whose phase, with respect to those of the ionic profile, changes from opposite phase in the alkalis to almost in-phase for Si.Comment: 16 pages, 18 figures, 5 tables. Submitted to Phys. Rev.

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

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

Two-pulse stimulated echo in magnets

The results of experimental study of two-pulse stimulated echo in ferromagnets of two types are presented. Ferromagnet Co and half-metal Co MnSi 2, in which a single-pulse echo formed by the distortion mechanism of the fronts of exciting pulse is also observed, are classified among the first type. Lithium ferrite and intermetal compound MnSb characterized by the absence of single-pulse echo in them - belong to the second type. For signals of two-pulse stimulated echo in the materials of the first type a short time and a long time of relaxations are observed. The short time is about the order of value shorter less than the spin-spin relaxation time. The long time is close to the transverse relaxation time of single-pulse echo formed by the distortion mechanism. The mechanisms that provide the possible interpretations of the peculiarities of the processes of nuclear magnetic relaxation are discussed.Comment: 10 pages, 7 figure

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

Application of 3D Zernike descriptors to shape-based ligand similarity searching

Background: The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. Results: In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability