Underpotential deposition of Cu on Au(111) in sulfate-containing electrolytes: a theoretical and experimental study

We study the underpotential deposition of Cu on single-crystal Au(111) electrodes in sulfate-containing electrolytes by a combination of computational statistical-mechanics based lattice-gas modeling and experiments. The experimental methods are in situ cyclic voltammetry and coulometry and ex situ Auger electron spectroscopy and low-energy electron diffraction. The experimentally obtained voltammetric current and charge densities and adsorbate coverages are compared with the predictions of a two-component lattice-gas model for the coadsorption of Cu and sulfate. This model includes effective, lateral interactions out to fourth-nearest neighbors. Using group-theoretical ground-state calculations and Monte Carlo simulations, we estimate effective electrovalences and lateral adsorbate--adsorbate interactions so as to obtain overall agreement with experiments, including both our own and those of other groups. In agreement with earlier work, we find a mixed R3xR3 phase consisting of 2/3 monolayer Cu and 1/3 monolayer sulfate at intermediate electrode potentials, delimited by phase transitions at both higher and lower potentials. Our approach provides estimates of the effective electrovalences and lateral interaction energies, which cannot yet be calculated by first-principles methods.Comment: 36 pages, 14 Postscript figures are in uufiles for

Void Growth in BCC Metals Simulated with Molecular Dynamics using the Finnis-Sinclair Potential

The process of fracture in ductile metals involves the nucleation, growth, and linking of voids. This process takes place both at the low rates involved in typical engineering applications and at the high rates associated with dynamic fracture processes such as spallation. Here we study the growth of a void in a single crystal at high rates using molecular dynamics (MD) based on Finnis-Sinclair interatomic potentials for the body-centred cubic (bcc) metals V, Nb, Mo, Ta, and W. The use of the Finnis-Sinclair potential enables the study of plasticity associated with void growth at the atomic level at room temperature and strain rates from 10^9/s down to 10^6/s and systems as large as 128 million atoms. The atomistic systems are observed to undergo a transition from twinning at the higher end of this range to dislocation flow at the lower end. We analyze the simulations for the specific mechanisms of plasticity associated with void growth as dislocation loops are punched out to accommodate the growing void. We also analyse the process of nucleation and growth of voids in simulations of nanocrystalline Ta expanding at different strain rates. We comment on differences in the plasticity associated with void growth in the bcc metals compared to earlier studies in face-centred cubic (fcc) metals.Comment: 24 pages, 12 figure

Time-dependent energy absorption changes during ultrafast lattice deformation

The ultrafast time-dependence of the energy absorption of covalent solids upon excitation with femtosecond laser pulses is theoretically analyzed. We use a microscopic theory to describe laser induced structural changes and their influence on the electronic properties. We show that from the time evolution of the energy absorbed by the system important information on the electronic and atomic structure during ultrafast phase transitions can be gained. Our results reflect how structural changes affect the capability of the system to absorb external energy.Comment: 7 pages RevTeX, 8 ps figures, submitted to Journal of Appl. Physic

Molecular dynamics modeling of ultrathin amorphous carbon films

Amorphous carbon films about 20 mn thick are used by the computer industry as protective coatings on magnetic disks. The structure and function of this family of materials at the atomic level is poorly understood. The growth and properties of a:C and a:CH films 1 to 5 nm thick has been simulated using classical molecular dynamics and a bond-order potential with torsional terms. Studies of quenched melts that verify the ability of this potential to reproduce known features of extended structures of carbon in two and three dimensions are briefly described. In molecular dynamics calculations the incident species were neutral atoms C, or C and H with energies up to 100 eV. The stoichiometry, chemical bonding and distribution functions within the films were analyzed using IBM`s Power Visualization System for different incident gas energies. Microscopic features such as multiple ring structures, including planar graphitic structures, were easily identified. Some preliminary studies of the nanotribology of the a:C films are described, including nano-indentation and sliding in contact with a rigid probe

High pressure diamond-like liquid carbon

We report density-functional based molecular dynamics simulations, that show that, with increasing pressure, liquid carbon undergoes a gradual transformation from a liquid with local three-fold coordination to a 'diamond-like' liquid. We demonstrate that this unusual structural change is well reproduced by an empirical bond order potential with isotropic long range interactions, supplemented by torsional terms. In contrast, state-of-the-art short-range bond-order potentials do not reproduce this diamond structure. This suggests that a correct description of long-range interactions is crucial for a unified description of the solid and liquid phases of carbon.Comment: 4 pages, 5 figure

Structural transitions and nonmonotonic relaxation processes in liquid metals

Structural transitions in melts as well as their dynamics are considered. It is supposed that liquid represents the solution of relatively stable solid-like locally favored structures (LFS) in the surrounding of disordered normal-liquid structures. Within the framework of this approach the step changes of liquid Co viscosity are considered as liquid-liquid transitions. It is supposed that this sort of transitions represents the cooperative medium-range bond ordering, and corresponds to the transition of the "Newtonian fluid" to the "structured fluid". It is shown that relaxation processes with oscillating-like time behavior ($\omega \sim 10^{-2}$~$s^{-1}$) of viscosity are possibly close to this point

Nature of phase transition(s) in striped phase of triangular-lattice Ising antiferromagnet

Different scenarios of the fluctuation-induced disordering of the striped phase which is formed at low temperatures in the triangular-lattice Ising model with the antiferromagnetic interaction of nearest and next-to-nearest neighbors are analyzed and compared. The dominant mechanism of the disordering is related to the formation of a network of domain walls, which is characterized by an extensive number of zero modes and has to appear via the first-order phase transition. In principle, this first-order transition can be preceded by a continuous one, related to the spontaneous formation of double domain walls and a partial restoration of the broken symmetry, but the realization of such a scenario requires the fulfillment of rather special relations between the coupling constants.Comment: 10 pages, 7 figures, ReVTeX

Identifying Orientation-specific Lipid-protein Fingerprints using Deep Learning

Improved understanding of the relation between the behavior of RAS and RAF proteins and the local lipid environment in the cell membrane is critical for getting insights into the mechanisms underlying cancer formation. In this work, we employ deep learning (DL) to learn this relationship by predicting protein orientational states of RAS and RAS-RAF protein complexes with respect to the lipid membrane based on the lipid densities around the protein domains from coarse-grained (CG) molecular dynamics (MD) simulations. Our DL model can predict six protein states with an overall accuracy of over 80%. The findings of this work offer new insights into how the proteins modulate the lipid environment, which in turn may assist designing novel therapies to regulate such interactions in the mechanisms associated with cancer development

Dynamic Density Functional Theory of Multicomponent Cellular Membranes

We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be extended to include features such as the presence of proteins and membrane deformations. This framework represents a paradigm shift by enabling simulations that can access cellular length-scales ($\mu$m) and time-scales on the order of seconds, all while maintaining near-fidelity to the underlying MD models. Membrane interactions with RAS, a potentially oncogenic protein, are considered as an application. Simulation results are presented and verified with MD simulations, and implications of this new capability are discussed