Atomistic simulations of rare events using gentlest ascent dynamics

The dynamics of complex systems often involve thermally activated barrier crossing events that allow these systems to move from one basin of attraction on the high dimensional energy surface to another. Such events are ubiquitous, but challenging to simulate using conventional simulation tools, such as molecular dynamics. Recently, E and Zhou [Nonlinearity 24(6), 1831 (2011)] proposed a set of dynamic equations, the gentlest ascent dynamics (GAD), to describe the escape of a system from a basin of attraction and proved that solutions of GAD converge to index-1 saddle points of the underlying energy. In this paper, we extend GAD to enable finite temperature simulations in which the system hops between different saddle points on the energy surface. An effective strategy to use GAD to sample an ensemble of low barrier saddle points located in the vicinity of a locally stable configuration on the high dimensional energy surface is proposed. The utility of the method is demonstrated by studying the low barrier saddle points associated with point defect activity on a surface. This is done for two representative systems, namely, (a) a surface vacancy and ad-atom pair and (b) a heptamer island on the (111) surface of copper.     

Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena

An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.     

Mode coupling behavior of a Lennard-Jones binary mixture: a comparison between bulk and confined phases

We present a quantitative comparison at equivalent thermodynamical conditions of bulk and confined dynamical properties of a Lennard-Jones binary mixture upon supercooling. Both systems had been previously found to display a behavior in agreement with the mode coupling theory of the evolution of glassy dynamics. Differences and analogies of behavior are discussed focusing, in particular, on the role of hopping in reducing spatially correlated dynamics in the confined system with respect to the bulk.     

Effect of Vacancy Defects on the Young's Modulus and Fracture Strength of Graphene: A Molecular Dynamics Study

The Young's modulus of graphene with various rectangular and circular vacancy defects is investigated by molecular dynamics simulation. By comparing with the results calculated from an effective spring model, it is demonstrated that the Young's modulus of graphene is largely correlated to the size of vacancy defects perpendicular to the stretching direction. And a linear reduction of Young's modulus with the increasing concentration of mono‐atomic‐vacancy defects (i.e., the slope of ?0.03) is also observed. The fracture behavior of graphene, including the fracture strength, crack initiation and propagation are then studied by the molecular dynamics simulation, the effective spring model, and the quantized fracture mechanics. The blunting effect of vacancy edges is demonstrated, and the characterized crack tip radius of 4.44 Å is observed.     

Migration of Ag in low-temperature Ag2S from first principles

Using the density-functional theory combined with the nudged elastic band method, we have calculated migration pathways and estimated the activation energy barriers for the diffusion of Ag ions in low-temperature Ag2S. The activation energy barriers for four essential migrations for an Ag ion, namely, from a tetrahedral (T) site to an adjacent T vacancy (VT), from an octahedral (O) site to an adjacent O vacancy (VO), from T to VO, and from O to VT, are estimated as 0.461, 0.668, 0.212, and 0.318 eV, respectively, which are comparable to experimental values. This means that diffusions of Ag ions between nonequivalent sites are preferable to those between equivalent sites, and that direct T-VT and O-VO diffusions are less likely to occur than indirect T-VO-T and O-VT-O diffusions. These diffusion behaviors between nonequivalent sites have also been supported by ab initio molecular dynamics simulations, in which the diffusion pathways are directly observed.     

Molecular dynamics investigation of oxygen vacancy diffusion in rutile

Oxygen vacancy diffusion in rutile was studied by Born-Oppenheimer molecular dynamics techniques in the framework of the semiempirical molecular orbital method MSINDO. Migration of an oxygen vacancy from the rutile (110) surface towards the bulk was simulated. The metadynamics technique was employed to accelerate the diffusion processes. In this way, transition state structures and activation energies for the diffusion processes were obtained. Rate constants and the time scale of diffusion processes were estimated for different temperatures using the calculated activation energy. It was found that the vacancies in the bulk are less stable than on the surface. The feasibility of oxygen vacancy diffusion under experimental conditions is discussed.     

Oxygen vacancy formation for transient structures on the CeO2(110) surface at 300 and 750 K

Ab initio embedded-cluster calculations have been performed for the CeO2(110) surface using temperature induced structures from molecular dynamics (MD) snapshots. As a first step towards understanding how temperature induced distortions of the surface structure influence the surface oxygen reactivity, the energy cost of removing an O atom from the surface was calculated for 41 snapshots from the MD simulation at 300 K. The quantum mechanical embedded-cluster calculations show that already at 300 K the dynamics causes significant fluctuations (root mean square of 0.37 eV) in the O vacancy formation energy (Evac) while the distribution of the two excess electrons associated with the vacancy is virtually unaffected by the surface dynamics and remains localized on the two Ce ions close to the vacancy. It is also found that the quantum mechanical Evac fluctuations can be reproduced by oxygen vacancy calculations using only the relaxed shell-model force field (FF) itself and the MD geometries. Using the FF as the interaction model, the effect of raising the temperature to 750 K and the effect of doping with Ca were investigated for the oxygen vacancy formation.     

Optimized energy landscape exploration using the ab initio based activation-relaxation technique

Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczo?s algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.     

On the Phase Diagram of LiF-KCI-KBr and KF-NaCI-NaBr Systems

The phase diagrams of LiF-KCl-KBr and KF-NaCl-NaBr systems have been de'er-mined by visual polythermal method with the X-ray diffraction analysis of solid phases.The thermodynamical behaviour of the molten salt solutions of these systems are estimated on the basis of the data of phase diagrams.The thermodynamical behaviour of these recipioral-salt-pair containing systems is explained by the results of the computerized simulation using Monte Carlo method.     

The oxygen vacancy in crystal phases of WO(3)

The oxygen vacancy in WO(3) has previously been implicated in the electrochromism mechanism in this material. Previous theoretical calculations on the oxygen vacancy in WO(3) have not considered the full range of crystal structures adopted by the material. Here we report studies of the oxygen vacancy in seven crystal phases. The use of a very accurate tungsten plane-wave pseudopotential means that a byproduct of this study is a more detailed and complete picture of undefected WO(3) than previously available. Electronic structures of the crystal phases in both undefected and defected systems have been calculated and are discussed. The band gap in WO(3) is dependent upon bonding-antibonding interactions, these being dependent upon overlap in each direction. The effect of an oxygen vacancy is dependent upon the availability of both Op and Wd electrons, this being different for the various phases. A variety of behavior is predicted, which may be explained in terms of O2p-W5d mixing, including the formation of long W-W dimer bonds. It is found that the nature of a polaron in this material is dependent upon both the crystal structure and distribution of oxygen vacancies.     

Self-organization process of ordered structures in linear and star poly(styrene)-poly(isoprene) block copolymers: Gaussian models and mesoscopic parameters of polymeric systems

Mesoscopic simulations of linear and 3-arm star poly(styrene)-poly(isoprene) block copolymers was performed using a representation of the polymeric molecular structures by means of Gaussian models. The systems were represented by a group of spherical beads connected by harmonic springs; each bead corresponds to a segment of the block chain. The quantitative estimation for the bead-bead interaction of each system was calculated using a Flory-Huggins modified thermodynamical model. The Gaussian models together with dissipative particle dynamics (DPD) were employed to explore the self-organization process of ordered structures in these polymeric systems. These mesoscopic simulations for linear and 3-arm star block copolymers predict microphase separation, order-disorder transition, and self-assembly of the ordered structures with specific morphologies such as body-centered-cubic (BCC), hexagonal packed cylinders (HPC), hexagonal perforated layers (HPL), alternating lamellar (LAM), and ordered bicontinuous double diamond (OBDD) phases. The agreement between our simulations and experimental results validate the Gaussian chain models and mesoscopic parameters used for these polymers and allow describing complex macromolecular structures of soft condensed matter with large molecular weight at the statistical segment level.     

On the statistics of dense,disordered assemblies: Equilibrium and dynamics

We consider implications of a lattice model which operates with a vacancy fraction h as a measure of structural disorder. Consequences for the configurational thermodynamics of one- and multicomponent systems and their phase equilibria are briefly indicated. The principal topic is the glassy state under steady state conditions, as well as the kinetics of relaxational processes toward equilibrium. The central role of the h-function in its dependence on variables of state is made evident among others by the connection between equation of state and thermo-elastic properties. Moreover, a dynamics of volume relaxation can be treated by means of a corresponding theory for the h-function. Applications of this theory to isothermal annealing below the glass temperature T_g, the response to a constant cooling rate of the melt through the transition zone, and the computation of a complex compression modulus are reviewed. The implications of vacancy cluster distributions for the analysis of positron spectroscopy are pointed out. Finally we indicate the basis for the development of correlations between T_g and structural parameters.     

Study of the structural and atomic diffusive properties of the ordered Cu3Au (110) surface

The structural properties, the formation and migration energies of a single vacancy migrating intralayer and interlayer in the CuAu‐terminated (110) surface of Cu₃Au ordered alloy have been calculated and discussed by using the modified analytical embedded‐atom method (MAEAM) and molecular dynamics (MD) methods. The surface layer exhibits rippling that the Au atoms are raised above Cu atoms about 0.117 Å in the topmost layer. The displacements of the topmost two layers are comparatively larger, while the third layer relaxes slightly and there are no changes in the nether layers. From energy minimization, the vacancy is most likely to be formed in the first layer (1L), especially on the Au site. The surface vacancy shows the smallest formation energy compared to the interlayer and bulk vacancies, while the corresponding value converges after the fifth layer (5L). For Cu vacancy originally sited in the second layer (2L) and migrated intralayer and interlayer, the diffusion without causing the local disorder is the most favorable, and the vacancy tends to migrate to the topmost layer. In the topmost layer of the CuAu‐terminated (110) surface, the circularity path is preferred over the beeline path. Copyright © 2011 John Wiley & Sons, Ltd.     

Coadsorbate‐Induced Reversal of Solid–Liquid Interface Dynamics

Coadsorbed anions are well‐known to influence surface reactivity and dynamics at solid–liquid interfaces. Here we demonstrate that the chemical nature of these spectator species can entirely determine the microscopic dynamic behavior. Quantitative in situ video‐STM data on the surface diffusion of adsorbed sulfur atoms on Cu(100) electrodes in aqueous solution covered by bromide and chloride spectators, respectively, reveal in both cases a strong exponential potential dependence, but with opposite sign. This reversal is highly surprising in view of the isostructural adsorbate arrangement in the two systems. Detailed DFT studies suggest an anion‐induced difference in the sulfur diffusion mechanism, specifically an exchange diffusion on the Br‐covered surface. Experimental evidence for the latter is provided by the observation of Cu vacancy formation in the Br system, which can be rationalized by a side reaction of the sulfur exchange diffusion.     

A Review on Microfluidics: An Aid to Assisted Reproductive Technology

Infertility is a state of the male or female reproductive system that is defined as the failure to achieve pregnancy even after 12 or more months of regular unprotected sexual intercourse. Assisted reproductive technology (ART) plays a crucial role in addressing infertility. Various ART are now available for infertile couples. Fertilization in vitro (IVF), intracytoplasmic sperm injection (ICSI) and intrauterine insemination (IUI) are the most common techniques in this regard. Various microfluidic technologies can incorporate various ART procedures such as embryo and gamete (sperm and oocyte) analysis, sorting, manipulation, culture and monitoring. Hence, this review intends to summarize the current knowledge about the application of this approach towards cell biology to enhance ART.     

Structural,Vibrational and Electronic Properties of Defective Single‐Walled Carbon Nanotubes Functionalised with Carboxyl Groups: Theoretical Studies

Covalent sidewall functionalisation of defective zigzag single‐walled carbon nanotubes [SWCNTs(10,0)] with COOH groups is investigated by using DFT. Four types of point defects are considered: vacancy (V), divacancy [V₂(5‐8‐5), V₂(555‐777)], adatom (AA) and Stone–Wales (SW). The energetic, structural, electronic and vibrational properties of these systems are analysed. Decreasing reactivity is observed in the following order: AA>V>V₂(555‐777)>V₂(5‐8‐5)>SW. These studies also demonstrate that the position in which a carboxyl group is attached to a defective SWCNT is of primary importance. Saturation of two‐coordinate carbon atoms in systems with the vacancy V‐7 and with the adatom AA‐1(2) is 3.5–4 times more energetically favourable than saturation of three‐coordinate carbon atoms for all studied systems. Vibrational analysis for these two systems shows significant redshifts of the ν(C?O) stretching vibration of 96 and 123 cm^?1 compared to that for carboxylated pristine systems. Detailed electronic‐structure analysis of the most stable carboxylated systems is also presented.