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Sample records for atomistic kinetic monte

  1. Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

    Science.gov (United States)

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

    Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

  2. Kinetic Activation-Relaxation Technique and Self-Evolving Atomistic Kinetic Monte Carlo: Comparison of on-the-fly kinetic Monte Carlo algorithms

    CERN Document Server

    Béland, Laurent K; Stoller, Roger; Xu, Haixuan

    2014-01-01

    We present a comparison of the kinetic Activation-Relaxation Technique (k-ART) and the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC), two off-lattice, on-the-fly kinetic Monte Carlo (KMC) techniques that were recently used to solve several materials science problems. We show that if the initial displacements are localized the dimer method and the Activation-Relaxation Technique \\emph{nouveau} provide similar performance. We also show that k-ART and SEAKMC, although based on different approximations, are in agreement with each other, as demonstrated by the examples of 50 vacancies in a 1950-atom Fe box and of interstitial loops in 16000-atom boxes. Generally speaking, k-ART's treatment of geometry and flickers is more flexible, e.g. it can handle amorphous systems, and rigorous than SEAKMC's, while the later's concept of active volumes permits a significant speedup of simulations for the systems under consideration and therefore allows investigations of processes requiring large systems that are not acc...

  3. Atomistic kinetic Monte Carlo study of atomic layer deposition derived from density functional theory.

    Science.gov (United States)

    Shirazi, Mahdi; Elliott, Simon D

    2014-01-30

    To describe the atomic layer deposition (ALD) reactions of HfO2 from Hf(N(CH3)2)4 and H2O, a three-dimensional on-lattice kinetic Monte-Carlo model is developed. In this model, all atomistic reaction pathways in density functional theory (DFT) are implemented as reaction events on the lattice. This contains all steps, from the early stage of adsorption of each ALD precursor, kinetics of the surface protons, interaction between the remaining precursors (steric effect), influence of remaining fragments on adsorption sites (blocking), densification of each ALD precursor, migration of each ALD precursors, and cooperation between the remaining precursors to adsorb H2O (cooperative effect). The essential chemistry of the ALD reactions depends on the local environment at the surface. The coordination number and a neighbor list are used to implement the dependencies. The validity and necessity of the proposed reaction pathways are statistically established at the mesoscale. The formation of one monolayer of precursor fragments is shown at the end of the metal pulse. Adsorption and dissociation of the H2O precursor onto that layer is described, leading to the delivery of oxygen and protons to the surface during the H2O pulse. Through these processes, the remaining precursor fragments desorb from the surface, leaving the surface with bulk-like and OH-terminated HfO2, ready for the next cycle. The migration of the low coordinated remaining precursor fragments is also proposed. This process introduces a slow reordering motion (crawling) at the mesoscale, leading to the smooth and conformal thin film that is characteristic of ALD.

  4. Database of atomistic reaction mechanisms with application to kinetic Monte Carlo.

    Science.gov (United States)

    Terrell, Rye; Welborn, Matthew; Chill, Samuel T; Henkelman, Graeme

    2012-07-07

    Kinetic Monte Carlo is a method used to model the state-to-state kinetics of atomic systems when all reaction mechanisms and rates are known a priori. Adaptive versions of this algorithm use saddle searches from each visited state so that unexpected and complex reaction mechanisms can also be included. Here, we describe how calculated reaction mechanisms can be stored concisely in a kinetic database and subsequently reused to reduce the computational cost of such simulations. As all accessible reaction mechanisms available in a system are contained in the database, the cost of the adaptive algorithm is reduced towards that of standard kinetic Monte Carlo.

  5. Atomistic Monte Carlo Simulation of Lipid Membranes

    Directory of Open Access Journals (Sweden)

    Daniel Wüstner

    2014-01-01

    Full Text Available Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA for the phospholipid dipalmitoylphosphatidylcholine (DPPC. We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.

  6. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction......, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential...... of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol....

  7. Efficient kinetic Monte Carlo simulation

    Science.gov (United States)

    Schulze, Tim P.

    2008-02-01

    This paper concerns kinetic Monte Carlo (KMC) algorithms that have a single-event execution time independent of the system size. Two methods are presented—one that combines the use of inverted-list data structures with rejection Monte Carlo and a second that combines inverted lists with the Marsaglia-Norman-Cannon algorithm. The resulting algorithms apply to models with rates that are determined by the local environment but are otherwise arbitrary, time-dependent and spatially heterogeneous. While especially useful for crystal growth simulation, the algorithms are presented from the point of view that KMC is the numerical task of simulating a single realization of a Markov process, allowing application to a broad range of areas where heterogeneous random walks are the dominate simulation cost.

  8. Self-consistent kinetic lattice Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Horsfield, A.; Dunham, S.; Fujitani, Hideaki

    1999-07-01

    The authors present a brief description of a formalism for modeling point defect diffusion in crystalline systems using a Monte Carlo technique. The main approximations required to construct a practical scheme are briefly discussed, with special emphasis on the proper treatment of charged dopants and defects. This is followed by tight binding calculations of the diffusion barrier heights for charged vacancies. Finally, an application of the kinetic lattice Monte Carlo method to vacancy diffusion is presented.

  9. The Role of Temperature on Morphological Properties of Gallium Nanowires: A Kinetic Monte Carlo Study

    Directory of Open Access Journals (Sweden)

    Darwin B. Putungan

    2010-06-01

    Full Text Available In this work, we investigated the effects of temperature on the morphological properties, specifically homogeneous to heterogeneous island ratio R and mean island size, of Ga one-dimensional nanowires through Kinetic Monte Carlo (KMC simulations. Relevant simulation parameters and inputs were first calculated using Density Functional Theory (DFT methods. The system was treated via an atomistic-lattice gas model which includes necessary atomistic processes. KMC implementation of the model was carried out to simulate the growth and evolution of Ga nanowires. The ratio R was found to increase as the temperature was increased, whereas the mean island size decreases for the same temperature trend. These observations were explained by taking note that the increase in thermal energy effected enhanced homogeneous nucleation, outnumbering heterogeneous islands, due to the increased frequency of adatom collisions. On the other hand, enhanced homogenous nucleation impacts the mean island size by favoring creation of new islands rather than making existing islands grow in length.

  10. A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis

    CERN Document Server

    Hoffmann, Max J; Matera, Sebastian

    2016-01-01

    Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past the application of sensitivity analysis, such as Degree of Rate Control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. In this study we present an efficient and robust three stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrat...

  11. kmos: A lattice kinetic Monte Carlo framework

    Science.gov (United States)

    Hoffmann, Max J.; Matera, Sebastian; Reuter, Karsten

    2014-07-01

    Kinetic Monte Carlo (kMC) simulations have emerged as a key tool for microkinetic modeling in heterogeneous catalysis and other materials applications. Systems, where site-specificity of all elementary reactions allows a mapping onto a lattice of discrete active sites, can be addressed within the particularly efficient lattice kMC approach. To this end we describe the versatile kmos software package, which offers a most user-friendly implementation, execution, and evaluation of lattice kMC models of arbitrary complexity in one- to three-dimensional lattice systems, involving multiple active sites in periodic or aperiodic arrangements, as well as site-resolved pairwise and higher-order lateral interactions. Conceptually, kmos achieves a maximum runtime performance which is essentially independent of lattice size by generating code for the efficiency-determining local update of available events that is optimized for a defined kMC model. For this model definition and the control of all runtime and evaluation aspects kmos offers a high-level application programming interface. Usage proceeds interactively, via scripts, or a graphical user interface, which visualizes the model geometry, the lattice occupations and rates of selected elementary reactions, while allowing on-the-fly changes of simulation parameters. We demonstrate the performance and scaling of kmos with the application to kMC models for surface catalytic processes, where for given operation conditions (temperature and partial pressures of all reactants) central simulation outcomes are catalytic activity and selectivities, surface composition, and mechanistic insight into the occurrence of individual elementary processes in the reaction network.

  12. Atomistic computer simulations of FePt nanoparticles. Thermodynamic and kinetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, M.

    2007-12-20

    In the present dissertation, a hierarchical multiscale approach for modeling FePt nanoparticles by atomistic computer simulations is developed. By describing the interatomic interactions on different levels of sophistication, various time and length scales can be accessed. Methods range from static quantum-mechanic total-energy calculations of small periodic systems to simulations of whole particles over an extended time by using simple lattice Hamiltonians. By employing these methods, the energetic and thermodynamic stability of non-crystalline multiply twinned FePt nanoparticles is investigated. Subsequently, the thermodynamics of the order-disorder transition in FePt nanoparticles is analyzed, including the influence of particle size, composition and modified surface energies by different chemical surroundings. In order to identify processes that reduce or enhance the rate of transformation from the disordered to the ordered state, the kinetics of the ordering transition in FePt nanoparticles is finally investigated by assessing the contributions of surface and volume diffusion. (orig.)

  13. Kinetic Monte Carlo method applied to nucleic acid hairpin folding.

    Science.gov (United States)

    Sauerwine, Ben; Widom, Michael

    2011-12-01

    Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure, is advantageous for being able to access behavior at long time scales, even minutes or hours. Transition rates between coarse-grained states depend upon intermediate barriers, which are not directly simulated. We propose an Arrhenius rate model and an intermediate energy model that incorporates the effects of the barrier between simulated states without enlarging the state space itself. Applying our Arrhenius rate model to DNA hairpin folding, we demonstrate improved agreement with experiment compared to the usual kinetic Monte Carlo model. Further improvement results from including rigidity of single-stranded stacking.

  14. Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

    Science.gov (United States)

    Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

    2017-02-01

    The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

  15. Coarse-Grained Langevin Approximations and Spatiotemporal Acceleration for Kinetic Monte Carlo Simulations of Diffusion of Interacting Particles

    Institute of Scientific and Technical Information of China (English)

    Sasanka ARE; Markos A.KATSOULAKIS; Anders SZEPESSY

    2009-01-01

    Kinetic Monte Carlo methods provide a powerful computational tool for the simulation of microscopic processes such as the diffusion of interacting particles on a surface, at a detailed atomistic level. However such algorithms are typically computationally expensive and are restricted to fairly small spatiotemporal scales. One approach towards overcoming this problem was the development of coarse-grained Monte Carlo algorithms. In recent literature, these methods were shown to be capable of efficiently describing much larger length scales while still incorporating information on microscopic interactions and fluctuations. In this paper, a coarse-grained Langevin system of stochastic differential equations as approximations of diffusion of interacting particles is derived, based on these earlier coarse-grained models. The authors demonstrate the asymptotic equivalence of transient and long time behavior of the Langevin approximation and the underlying microscopic process, using asymptotics methods such as large deviations for interacting particles systems, and furthermore, present corresponding numerical simulations, comparing statistical quantities like mean paths, auto correlations and power spectra of the microscopic and the approximating Langevin processes. Finally, it is shown that the Langevin approximations presented here are much more computationally efficient than conventional Kinetic Monte Carlo methods, since in addition to the reduction in the number of spatial degrees of freedom in coarse-grained Monte Carlo methods, the Langevin system of stochastic differential equations allows for multiple particle moves in a single timestep.

  16. Atomistic Monte Carlo simulations of the diffusion of P and C near grain boundaries in BCC iron

    Energy Technology Data Exchange (ETDEWEB)

    Binkele, P.; Kizler, P. [MPA, Univ. Stuttgart, Stuttgart (Germany); Schmauder, S. [IMWF, Univ. Stuttgart, Stuttgart (Germany)

    2004-07-01

    It is well known that thermal ageing of steels can be caused by the segregation of phosphorus (P) and carbon (C) to grain boundaries. Atomistic Monte Carlo simulations of the diffusion of P and C to grain boundaries in bcc iron will allow, if validated, predictions of the time-dependent segregation. Simulations of the Fe-P-C system are presented, where the diffusion of Fe and P is realized via a vacancy mechanism and the diffusion of C is realized via an interstitial mechanism. Time-dependent segregations have been simulated for different temperatures and start conditions and are found to follow Johnson-Mehl-Avrami laws. A comparison of the simulation results with available AES (Auger Electron Spectroscopy) data shows close agreement with respect to P segregation. In simulations starting with a pre-filled grain boundary in increase of P and a decrease of C in the grain boundary are found where the decrease of C proceeds significantly faster than the increase of P for any temperature. The temperature-dependent ratios of the different speeds of P- and C-segregation, due to their different diffusion mechanisms, are calculated as a result of the simulations. (orig.)

  17. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev

    2014-05-01

    Full Text Available Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1–100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

  18. Strain in the mesoscale kinetic Monte Carlo model for sintering

    DEFF Research Database (Denmark)

    Bjørk, Rasmus; Frandsen, Henrik Lund; Tikare, V.;

    2014-01-01

    Shrinkage strains measured from microstructural simulations using the mesoscale kinetic Monte Carlo (kMC) model for solid state sintering are discussed. This model represents the microstructure using digitized discrete sites that are either grain or pore sites. The algorithm used to simulate...... anisotropic strains for homogeneous powder compacts with aspect ratios different from unity. It is shown that the line direction biases shrinkage strains in proportion the compact dimension aspect ratios. A new algorithm that corrects this bias in strains is proposed; the direction for collapsing the column...

  19. On the Connection between Kinetic Monte Carlo and the Burton-Cabrera-Frank Theory

    Science.gov (United States)

    Patrone, Paul; Margetis, Dionisios; Einstein, T. L.

    2013-03-01

    In the many years since it was first proposed, the Burton- Cabrera-Frank (BCF) model of step-flow has been experimentally established as one of the cornerstones of surface physics. However, many questions remain regarding the underlying physical processes and theoretical assumptions that give rise to the BCF theory. In this work, we formally derive the BCF theory from an atomistic, kinetic Monte Carlo model of the surface in 1 +1 dimensions with one step. Our analysis (i) shows how the BCF theory describes a surface with a low density of adsorbed atoms, and (ii) establishes a set of near-equilibrium conditions ensuring that the theory remains valid for all times. Support for PP was provided by the NIST-ARRA Fellowship Award No. 70NANB10H026 through UMD. Support for TLE and PP was also provided by the CMTC at UMD, with ancillary support from the UMD MRSEC. Support for DM was provided by NSF DMS0847587 at UMD.

  20. Self-learning kinetic Monte Carlo simulations of Al diffusion in Mg

    Energy Technology Data Exchange (ETDEWEB)

    Nandipati, Giridhar; Govind, Niranjan; Andersen, Amity; Rohatgi, Aashish

    2016-03-16

    Atomistic on-lattice self-learning kinetic Monte Carlo (SLKMC) method was used to examine the vacancy-mediated diffusion of an Al atom in pure hcp Mg. Local atomic environment dependent activation barriers for vacancy-atom exchange processes were calculated on-the-fly using climbing image nudged-elastic band method (CI-NEB) and using a Mg-Al binary modified embedded-atom method (MEAM) interatomic potential. Diffusivities of vacancy and Al atom in pure Mg were obtained from SLKMC simulations and are compared with values available in the literature that are obtained from experiments and first-principle calculations. Al Diffusivities obtained from SLKMC simulations are lower, due to larger activation barriers and lower diffusivity prefactors, than those available in the literature but have same order of magnitude. We present all vacancy-Mg and vacancy-Al atom exchange processes and their activation barriers that were identified in SLKMC simulations. We will describe a simple mapping scheme to map a hcp lattice on to a simple cubic lattice that would enable hcp lattices to be simulated in an on-lattice KMC framework. We also present the pattern recognition scheme used in SLKMC simulations.

  1. A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis

    Science.gov (United States)

    Hoffmann, Max J.; Engelmann, Felix; Matera, Sebastian

    2017-01-01

    Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for the atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past, the application of sensitivity analysis, such as degree of rate control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. In this study, we present an efficient and robust three-stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrate using the CO oxidation on RuO2(110) as a prototypical reaction. In the first step, we utilize the Fisher information matrix for filtering out elementary processes which only yield negligible sensitivity. Then we employ an estimator based on the linear response theory for calculating the sensitivity measure for non-critical conditions which covers the majority of cases. Finally, we adapt a method for sampling coupled finite differences for evaluating the sensitivity measure for lattice based models. This allows for an efficient evaluation even in critical regions near a second order phase transition that are hitherto difficult to control. The combined approach leads to significant computational savings over straightforward numerical derivatives and should aid in accelerating the nano-scale design of heterogeneous catalysts.

  2. Kinetic Monte Carlo simulations of void lattice formation during irradiation

    Science.gov (United States)

    Heinisch, H. L.; Singh, B. N.

    2003-11-01

    Over the last decade, molecular dynamics simulations of displacement cascades have revealed that glissile clusters of self-interstitial crowdions are formed directly in cascades and that they migrate one-dimensionally along close-packed directions with extremely low activation energies. Occasionally, under various conditions, a crowdion cluster can change its Burgers vector and glide along a different close-packed direction. The recently developed production bias model (PBM) of microstructure evolution under irradiation has been structured specifically to take into account the unique properties of the vacancy and interstitial clusters produced in the cascades. Atomic-scale kinetic Monte Carlo (KMC) simulations have played a useful role in understanding the defect reaction kinetics of one-dimensionally migrating crowdion clusters as a function of the frequency of direction changes. This has made it possible to incorporate the migration properties of crowdion clusters and changes in reaction kinetics into the PBM. In the present paper we utilize similar KMC simulations to investigate the significant role that crowdion clusters can play in the formation and stability of void lattices. The creation of stable void lattices, starting from a random distribution of voids, is simulated by a KMC model in which vacancies migrate three-dimensionally and self-interstitial atom (SIA) clusters migrate one-dimensionally, interrupted by directional changes. The necessity of both one-dimensional migration and Burgers vectors changes of SIA clusters for the production of stable void lattices is demonstrated, and the effects of the frequency of Burgers vector changes are described.

  3. An object kinetic Monte Carlo model for the microstructure evolution of neutron-irradiated reactor pressure vessel steels

    Energy Technology Data Exchange (ETDEWEB)

    Messina, Luca; Olsson, Paer [KTH Royal Institute of Technology, Stockholm (Sweden); Chiapetto, Monica [SCK - CEN, Nuclear Materials Science Institute, Mol (Belgium); Unite Materiaux et Transformations (UMET), UMR 8207, Universite de Lille 1, ENSCL, Villeneuve d' Ascq (France); Becquart, Charlotte S. [Unite Materiaux et Transformations (UMET), UMR 8207, Universite de Lille 1, ENSCL, Villeneuve d' Ascq (France); Malerba, Lorenzo [SCK - CEN, Nuclear Materials Science Institute, Mol (Belgium)

    2016-11-15

    This work presents a full object kinetic Monte Carlo framework for the simulation of the microstructure evolution of reactor pressure vessel (RPV) steels. The model pursues a ''gray-alloy'' approach, where the effect of solute atoms is seen exclusively as a reduction of the mobility of defect clusters. The same set of parameters yields a satisfactory evolution for two different types of alloys, in very different irradiation conditions: an Fe-C-MnNi model alloy (high flux) and a high-Mn, high-Ni RPV steel (low flux). A satisfactory match with the experimental characterizations is obtained only if assuming a substantial immobilization of vacancy clusters due to solute atoms, which is here verified by means of independent atomistic kinetic Monte Carlo simulations. The microstructure evolution of the two alloys is strongly affected by the dose rate; a predominance of single defects and small defect clusters is observed at low dose rates, whereas larger defect clusters appear at high dose rates. In both cases, the predicted density of interstitial loops matches the experimental solute-cluster density, suggesting that the MnNi-rich nanofeatures might form as a consequence of solute enrichment on immobilized small interstitial loops, which are invisible to the electron microscope. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  4. Synchronous parallel kinetic Monte Carlo Diffusion in Heterogeneous Systems

    Energy Technology Data Exchange (ETDEWEB)

    Martinez Saez, Enrique [Los Alamos National Laboratory; Hetherly, Jeffery [Los Alamos National Laboratory; Caro, Jose A [Los Alamos National Laboratory

    2010-12-06

    A new hybrid Molecular Dynamics-kinetic Monte Carlo algorithm has been developed in order to study the basic mechanisms taking place in diffusion in concentrated alloys under the action of chemical and stress fields. Parallel implementation of the k-MC part based on a recently developed synchronous algorithm [1. Compo Phys. 227 (2008) 3804-3823] resorting on the introduction of a set of null events aiming at synchronizing the time for the different subdomains, added to the parallel efficiency of MD, provides the computer power required to evaluate jump rates 'on the flight', incorporating in this way the actual driving force emerging from chemical potential gradients, and the actual environment-dependent jump rates. The time gain has been analyzed and the parallel performance reported. The algorithm is tested on simple diffusion problems to verify its accuracy.

  5. Kinetic Monte Carlo simulation of the classical nucleation process

    Science.gov (United States)

    Filipponi, A.; Giammatteo, P.

    2016-12-01

    We implemented a kinetic Monte Carlo computer simulation of the nucleation process in the framework of the coarse grained scenario of the Classical Nucleation Theory (CNT). The computational approach is efficient for a wide range of temperatures and sample sizes and provides a reliable simulation of the stochastic process. The results for the nucleation rate are in agreement with the CNT predictions based on the stationary solution of the set of differential equations for the continuous variables representing the average population distribution of nuclei size. Time dependent nucleation behavior can also be simulated with results in agreement with previous approaches. The method, here established for the case in which the excess free-energy of a crystalline nucleus is a smooth-function of the size, can be particularly useful when more complex descriptions are required.

  6. Large-scale epitaxial growth kinetics of graphene: A kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Huijun; Hou, Zhonghuai, E-mail: hzhlj@ustc.edu.cn [Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2015-08-28

    Epitaxial growth via chemical vapor deposition is considered to be the most promising way towards synthesizing large area graphene with high quality. However, it remains a big theoretical challenge to reveal growth kinetics with atomically energetic and large-scale spatial information included. Here, we propose a minimal kinetic Monte Carlo model to address such an issue on an active catalyst surface with graphene/substrate lattice mismatch, which facilitates us to perform large scale simulations of the growth kinetics over two dimensional surface with growth fronts of complex shapes. A geometry-determined large-scale growth mechanism is revealed, where the rate-dominating event is found to be C{sub 1}-attachment for concave growth-front segments and C{sub 5}-attachment for others. This growth mechanism leads to an interesting time-resolved growth behavior which is well consistent with that observed in a recent scanning tunneling microscopy experiment.

  7. Parallel Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    HEFFELFINGER,GRANT S.

    2000-01-18

    Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.

  8. Monte Carlo simulation on kinetics of batch and semi-batch free radical polymerization

    KAUST Repository

    Shao, Jing

    2015-10-27

    Based on Monte Carlo simulation technology, we proposed a hybrid routine which combines reaction mechanism together with coarse-grained molecular simulation to study the kinetics of free radical polymerization. By comparing with previous experimental and simulation studies, we showed the capability of our Monte Carlo scheme on representing polymerization kinetics in batch and semi-batch processes. Various kinetics information, such as instant monomer conversion, molecular weight, and polydispersity etc. are readily calculated from Monte Carlo simulation. The kinetic constants such as polymerization rate k p is determined in the simulation without of “steady-state” hypothesis. We explored the mechanism for the variation of polymerization kinetics those observed in previous studies, as well as polymerization-induced phase separation. Our Monte Carlo simulation scheme is versatile on studying polymerization kinetics in batch and semi-batch processes.

  9. Hopping electron model with geometrical frustration: kinetic Monte Carlo simulations

    Science.gov (United States)

    Terao, Takamichi

    2016-09-01

    The hopping electron model on the Kagome lattice was investigated by kinetic Monte Carlo simulations, and the non-equilibrium nature of the system was studied. We have numerically confirmed that aging phenomena are present in the autocorrelation function C ({t,tW )} of the electron system on the Kagome lattice, which is a geometrically frustrated lattice without any disorder. The waiting-time distributions p(τ ) of hopping electrons of the system on Kagome lattice has been also studied. It is confirmed that the profile of p (τ ) obtained at lower temperatures obeys the power-law behavior, which is a characteristic feature of continuous time random walk of electrons. These features were also compared with the characteristics of the Coulomb glass model, used as a model of disordered thin films and doped semiconductors. This work represents an advance in the understanding of the dynamics of geometrically frustrated systems and will serve as a basis for further studies of these physical systems.

  10. Kinetic Monte Carlo simulation of thin film growth

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Peifeng(张佩峰); ZHENG; Xiaoping(郑小平); HE; Deyan(贺德衍)

    2003-01-01

    A three-dimensional kinetic Monte Carlo technique has been developed for simulating growth of thin Cu films. The model involves incident atom attachment, diffusion of the atoms on the growing surface, and detachment of the atoms from the growing surface. The related effect by surface atom diffusion was taken into account. A great improvement was made on calculation of the activation energy for atom diffusion based on a reasonable assumption of interaction potential between atoms. The surface roughness and the relative density of the films were simulated as the functions of growth substrate temperature and film thickness. The results showed that there exists an optimum growth temperature Topt at a given deposition rate. When the substrate temperature approaches to Topt, the growing surface becomes smoothing and the relative density of the films increases. The surface roughness minimizes and the relative density saturates at Topt. The surface roughness increases with an increment of substrate temperature when the temperature is higher than Topt. Topt iS a function of the deposition rate and the influence of the deposition rate on the surface roughness depends on the substrate temperatures. The simulation results also showed that the relative density decreases with the increasing of the deposition rate and the average thickness of the film.

  11. Empirical force field-based kinetic Monte Carlo simulation of precipitate evolution and growth in Al–Cu alloys

    Science.gov (United States)

    Joshi, Kaushik; Chaudhuri, Santanu

    2016-10-01

    Ability to accelerate the morphological evolution of nanoscale precipitates is a fundamental challenge for atomistic simulations. Kinetic Monte Carlo (KMC) methodology is an effective approach for accelerating the evolution of nanoscale systems that are dominated by so-called rare events. The quality and accuracy of energy landscape used in KMC calculations can be significantly improved using DFT-informed interatomic potentials. Using newly developed computational framework that uses molecular simulator LAMMPS as a library function inside KMC solver SPPARKS, we investigated formation and growth of Guiner–Preston (GP) zones in dilute Al–Cu alloys at different temperature and copper concentrations. The KMC simulations with angular dependent potential (ADP) predict formation of coherent disc-shaped monolayers of copper atoms (GPI zones) in early stage. Such monolayers are then gradually transformed into energetically favored GPII phase that has two aluminum layers sandwiched between copper layers. We analyzed the growth kinetics of KMC trajectory using Johnson–Mehl–Avrami (JMA) theory and obtained a phase transformation index close to 1.0. In the presence of grain boundaries, the KMC calculations predict the segregation of copper atoms near the grain boundaries instead of formation of GP zones. The computational framework presented in this work is based on open source potentials and MD simulator and can predict morphological changes during the evolution of the alloys in the bulk and around grain boundaries.

  12. Physical time scale in kinetic Monte Carlo simulations of continuous-time Markov chains.

    Science.gov (United States)

    Serebrinsky, Santiago A

    2011-03-01

    We rigorously establish a physical time scale for a general class of kinetic Monte Carlo algorithms for the simulation of continuous-time Markov chains. This class of algorithms encompasses rejection-free (or BKL) and rejection (or "standard") algorithms. For rejection algorithms, it was formerly considered that the availability of a physical time scale (instead of Monte Carlo steps) was empirical, at best. Use of Monte Carlo steps as a time unit now becomes completely unnecessary.

  13. Energy-Driven Kinetic Monte Carlo Method and Its Application in Fullerene Coalescence.

    Science.gov (United States)

    Ding, Feng; Yakobson, Boris I

    2014-09-04

    Mimicking the conventional barrier-based kinetic Monte Carlo simulation, an energy-driven kinetic Monte Carlo (EDKMC) method was developed to study the structural transformation of carbon nanomaterials. The new method is many orders magnitude faster than standard molecular dynamics or Monte Marlo (MC) simulations and thus allows us to explore rare events within a reasonable computational time. As an example, the temperature dependence of fullerene coalescence was studied. The simulation, for the first time, revealed that short capped single-walled carbon nanotubes (SWNTs) appear as low-energy metastable structures during the structural evolution.

  14. Modeling of helium bubble nucleation and growth in austenitic stainless steels using an Object Kinetic Monte Carlo method

    Science.gov (United States)

    De Backer, A.; Adjanor, G.; Domain, C.; Lescoat, M. L.; Jublot-Leclerc, S.; Fortuna, F.; Gentils, A.; Ortiz, C. J.; Souidi, A.; Becquart, C. S.

    2015-06-01

    Implantation of 10 keV helium in 316L steel thin foils was performed in JANNuS-Orsay facility and modeled using a multiscale approach. Density Functional Theory (DFT) atomistic calculations [1] were used to obtain the properties of He and He-vacancy clusters, and the Binary Collision Approximation based code MARLOWE was applied to determine the damage and He-ion depth profiles as in [2,3]. The processes involved in the homogeneous He bubble nucleation and growth were defined and implemented in the Object Kinetic Monte Carlo code LAKIMOCA [4]. In particular as the He to dpa ratio was high, self-trapping of He clusters and the trap mutation of He-vacancy clusters had to be taken into account. With this multiscale approach, the formation of bubbles was modeled up to nanometer-scale size, where bubbles can be observed by Transmission Electron Microscopy. Their densities and sizes were studied as functions of fluence (up to 5 × 1019 He/m2) at two temperatures (473 and 723 K) and for different sample thicknesses (25-250 nm). It appears that the damage is not only due to the collision cascades but is also strongly controlled by the He accumulation in pressurized bubbles. Comparison with experimental data is discussed and sensible agreement is achieved.

  15. Atomistic simulations of the Fe K-edge EXAFS in FeF3 using molecular dynamics and reverse Monte Carlo methods

    Science.gov (United States)

    Jonane, Inga; Timoshenko, Janis; Kuzmin, Alexei

    2016-10-01

    Atomistic simulations of the experimental Fe K-edge extended x-ray absorption fine structure (EXAFS) of rhombohedral (space group R\\bar{3}c) FeF3 at T = 300 K were performed using classical molecular dynamics and reverse Monte Carlo (RMC) methods. The use of two complementary theoretical approaches allowed us to account accurately for thermal disorder effects in EXAFS and to validate the developed force-field model, which was constructed as a sum of two-body Buckingham-type (Fe-F and F-F), three-body harmonic (Fe-F-Fe) and Coulomb potentials. We found that the shape of the Fe K-edge EXAFS spectrum of FeF3 is a more sensitive probe for the determination of potential parameters than the values of structural parameters (a, c, x(F)) available from diffraction studies. The best overall agreement between the experimental and theoretical EXAFS spectra calculated using ab initio multiple-scattering approach was obtained for the iron effective charge q(Fe) = 1.71. The RMC method coupled with the evolutionary algorithm was used for more elaborate analysis of the EXAFS data. The obtained results suggest that our force-field model slightly underestimates the amplitude of thermal vibrations of fluorine atoms in the direction perpendicular to the Fe-F bonds.

  16. Crossing the mesoscale no-mans land via parallel kinetic Monte Carlo.

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Cardona, Cristina (San Diego State University); Webb, Edmund Blackburn, III; Wagner, Gregory John; Tikare, Veena; Holm, Elizabeth Ann; Plimpton, Steven James; Thompson, Aidan Patrick; Slepoy, Alexander (U. S. Department of Energy, NNSA); Zhou, Xiao Wang; Battaile, Corbett Chandler; Chandross, Michael Evan

    2009-10-01

    The kinetic Monte Carlo method and its variants are powerful tools for modeling materials at the mesoscale, meaning at length and time scales in between the atomic and continuum. We have completed a 3 year LDRD project with the goal of developing a parallel kinetic Monte Carlo capability and applying it to materials modeling problems of interest to Sandia. In this report we give an overview of the methods and algorithms developed, and describe our new open-source code called SPPARKS, for Stochastic Parallel PARticle Kinetic Simulator. We also highlight the development of several Monte Carlo models in SPPARKS for specific materials modeling applications, including grain growth, bubble formation, diffusion in nanoporous materials, defect formation in erbium hydrides, and surface growth and evolution.

  17. Kinetic Monte Carlo Studies of Hydrogen Abstraction from Graphite

    CERN Document Server

    Cuppen, H M

    2008-01-01

    We present Monte Carlo simulations on Eley-Rideal abstraction reactions of atomic hydrogen chemisorbed on graphite. The results are obtained via a hybrid approach where energy barriers derived from density functional theory calculations are used as input to Monte Carlo simulations. By comparing with experimental data, we discriminate between contributions from different Eley-Rideal mechanisms. A combination of two different mechanisms yields good quantitative and qualitative agreement between the experimentally derived and the simulated Eley-Rideal abstraction cross sections and surface configurations. These two mechanisms include a direct Eley-Rideal reaction with fast diffusing H atoms and a dimer mediated Eley-Rideal mechanism with increased cross section at low coverage. Such a dimer mediated Eley-Rideal mechanism has not previously been proposed and serves as an alternative explanation to the steering behavior often given as the cause of the coverage dependence observed in Eley-Rideal reaction cross sect...

  18. OBJECT KINETIC MONTE CARLO SIMULATIONS OF RADIATION DAMAGE ACCUMULATION IN TUNGSTEN

    Energy Technology Data Exchange (ETDEWEB)

    Nandipati, Giridhar; Setyawan, Wahyu; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.

    2016-09-01

    The objective of this work is to understand the accumulation of radiation damage created by primary knock-on atoms (PKAs) of various energies, at 300 K and for a dose rate of 10-4 dpa/s in bulk tungsten using the object kinetic Monte Carlo (OKMC) method.

  19. Lattice gas models and kinetic Monte Carlo simulations of epitaxial growth

    NARCIS (Netherlands)

    Biehl, Michael; Voigt, A

    2005-01-01

    A brief introduction is given to Kinetic Monte Carlo (KMC) simulations of epitaxial crystal growth. Molecular Beam Epitaxy (MBE) serves as the prototype example for growth far from equilibrium. However, many of the aspects discussed here would carry over to other techniques as well. A variety of app

  20. Kinetic Monte Carlo studies of the reaction kinetics of crystal defects that diffuse one-dimensionally with occasional transverse migration

    DEFF Research Database (Denmark)

    Heinisch, H.L.; Trinkaus, H.; Singh, Bachu Narain

    2007-01-01

    and confirmed by kinetic Monte Carlo (KMC) simulations. Here we report on KMC simulations investigating a different transition from 1D to 3D diffusion of 1D gliding loops for which their 1D migration is interrupted by occasional 2D migration due to conservative climb by dislocation core diffusion within a plane...... transverse to their 1D glide direction. Their transition from 1D to 3D kinetics is significantly different from that due to direction changes. The KMC results are compared to an analytical description of this diffusion mode in the form of a master curve relating the 1D normalized sink strength...

  1. Interacting multiagent systems kinetic equations and Monte Carlo methods

    CERN Document Server

    Pareschi, Lorenzo

    2014-01-01

    The description of emerging collective phenomena and self-organization in systems composed of large numbers of individuals has gained increasing interest from various research communities in biology, ecology, robotics and control theory, as well as sociology and economics. Applied mathematics is concerned with the construction, analysis and interpretation of mathematical models that can shed light on significant problems of the natural sciences as well as our daily lives. To this set of problems belongs the description of the collective behaviours of complex systems composed by a large enough number of individuals. Examples of such systems are interacting agents in a financial market, potential voters during political elections, or groups of animals with a tendency to flock or herd. Among other possible approaches, this book provides a step-by-step introduction to the mathematical modelling based on a mesoscopic description and the construction of efficient simulation algorithms by Monte Carlo methods. The ar...

  2. Domain-growth kinetics and aspects of pinning: A Monte Carlo simulation study

    DEFF Research Database (Denmark)

    Castán, T.; Lindgård, Per-Anker

    1991-01-01

    By means of Monte Carlo computer simulations we study the domain-growth kinetics after a quench across a first-order line to very low and moderate temperatures in a multidegenerate system with nonconserved order parameter. The model is a continuous spin model relevant for martensitic transformati......By means of Monte Carlo computer simulations we study the domain-growth kinetics after a quench across a first-order line to very low and moderate temperatures in a multidegenerate system with nonconserved order parameter. The model is a continuous spin model relevant for martensitic...... transformations, surface reconstructions, and magnetic transitions. No external impurities are introduced, but the model has a number of intrinsic, annealable pinning mechanisms, which strongly influences the growth kinetics. It allows a study of pinning effects of three kinds: (a) pinning of domain walls...

  3. Calculating kinetics parameters and reactivity changes with continuous-energy Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Kiedrowski, Brian C [Los Alamos National Laboratory; Brown, Forrest B [Los Alamos National Laboratory; Wilson, Paul [UNIV. WISCONSIN

    2009-01-01

    The iterated fission probability interpretation of the adjoint flux forms the basis for a method to perform adjoint weighting of tally scores in continuous-energy Monte Carlo k-eigenvalue calculations. Applying this approach, adjoint-weighted tallies are developed for two applications: calculating point reactor kinetics parameters and estimating changes in reactivity from perturbations. Calculations are performed in the widely-used production code, MCNP, and the results of both applications are compared with discrete ordinates calculations, experimental measurements, and other Monte Carlo calculations.

  4. Atomistic Calculations of the Effect of Minor Actinides on Thermodynamic and Kinetic Properties of UO{sub 2{+-}x}

    Energy Technology Data Exchange (ETDEWEB)

    Deo, Chaitanya; Adnersson, Davis; Battaile, Corbett; uberuaga, Blas

    2012-10-30

    The team will examine how the incorporation of actinide species important for mixed oxide (MOX) and other advanced fuel designs impacts thermodynamic quantities of the host UO{sub 2} nuclear fuel and how Pu, Np, Cm and Am influence oxygen mobility. In many cases, the experimental data is either insufficient or missing. For example, in the case of pure NpO2, there is essentially no experimental data on the hyperstoichiometric form it is not even known if hyperstoichiometry NpO{sub 2{+-}x} is stable. The team will employ atomistic modeling tools to calculate these quantities

  5. Predicting dislocation climb and creep from explicit atomistic details.

    Science.gov (United States)

    Kabir, Mukul; Lau, Timothy T; Rodney, David; Yip, Sidney; Van Vliet, Krystyn J

    2010-08-27

    Here we report kinetic Monte Carlo simulations of dislocation climb in heavily deformed, body-centered cubic iron comprising a supersaturation of vacancies. This approach explicitly incorporates the effect of nonlinear vacancy-dislocation interaction on vacancy migration barriers as determined from atomistic calculations, and enables observations of diffusivity and climb over time scales and temperatures relevant to power-law creep. By capturing the underlying microscopic physics, the calculated stress exponents for steady-state creep rates agree quantitatively with the experimentally measured range, and qualitatively with the stress dependence of creep activation energies.

  6. Monte Carlo simulation for kinetic chemotaxis model: An application to the traveling population wave

    Science.gov (United States)

    Yasuda, Shugo

    2017-02-01

    A Monte Carlo simulation of chemotactic bacteria is developed on the basis of the kinetic model and is applied to a one-dimensional traveling population wave in a microchannel. In this simulation, the Monte Carlo method, which calculates the run-and-tumble motions of bacteria, is coupled with a finite volume method to calculate the macroscopic transport of the chemical cues in the environment. The simulation method can successfully reproduce the traveling population wave of bacteria that was observed experimentally and reveal the microscopic dynamics of bacterium coupled with the macroscopic transports of the chemical cues and bacteria population density. The results obtained by the Monte Carlo method are also compared with the asymptotic solution derived from the kinetic chemotaxis equation in the continuum limit, where the Knudsen number, which is defined by the ratio of the mean free path of bacterium to the characteristic length of the system, vanishes. The validity of the Monte Carlo method in the asymptotic behaviors for small Knudsen numbers is numerically verified.

  7. Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

    OpenAIRE

    Arampatzis, Giorgos; Katsoulakis, Markos A.; Plechac, Petr; Taufer, Michela; Xu, Lifan

    2011-01-01

    We present a mathematical framework for constructing and analyzing parallel algorithms for lattice Kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. The algorithms can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processin...

  8. Kinetic Monte Carlo simulation of physical vapor deposition of thin Cu film

    Institute of Scientific and Technical Information of China (English)

    WANG Jun; CHEN Chang-qi; ZHU Wu

    2004-01-01

    A two-dimensional Kinetic Monte Carlo method has been developed for simulating the physical vapor deposition of thin Cu films on Cu substrate. An improved embedded atom method was used to calculate the interatomic potential and determine the diffusion barrier energy and residence time. Parameters, including incident angle,deposition rate and substrate temperature, were investigated and discussed in order to find their influences on the thin film morphology.

  9. Efficient 3D Kinetic Monte Carlo Method for Modeling of Molecular Structure and Dynamics

    DEFF Research Database (Denmark)

    Panshenskov, Mikhail; Solov'yov, Ilia; Solov'yov, Andrey V.

    2014-01-01

    Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with...... the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system....

  10. Monte Carlo simulation on teaching of luminescence and excited states decay kinetics; Simulacao Monte Carlo no ensino de luminescencia e cinetica de decaimento de estado excitado

    Energy Technology Data Exchange (ETDEWEB)

    Winnischofer, Herbert; Araujo, Marcio Peres de; Dias Junior, Lauro Camargo; Novo, Joao Batista Marques [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil)

    2010-07-01

    A software based in the Monte Carlo method have been developed aiming the teaching of important cases of mechanisms found in luminescence and in excited states decay kinetics, including: multiple decays, consecutive decays and coupled systems decays. The Monte Carlo Method allows the student to easily simulate and visualize the luminescence mechanisms, focusing on the probabilities of the related steps. The software CINESTEX was written for FreeBASIC compiler; it assumes first-order kinetics and any number of excited states, where the pathways are allowed with probabilities assigned by the user. (author)

  11. Kinetic Monte Carlo simulations of boron activation in implanted Si under laser thermal annealing

    Science.gov (United States)

    Fisicaro, Giuseppe; Pelaz, Lourdes; Aboy, Maria; Lopez, Pedro; Italia, Markus; Huet, Karim; Cristiano, Filadelfo; Essa, Zahi; Yang, Qui; Bedel-Pereira, Elena; Quillec, Maurice; La Magna, Antonino

    2014-02-01

    We investigate the correlation between dopant activation and damage evolution in boron-implanted silicon under excimer laser irradiation. The dopant activation efficiency in the solid phase was measured under a wide range of irradiation conditions and simulated using coupled phase-field and kinetic Monte Carlo models. With the inclusion of dopant atoms, the presented code extends the capabilities of a previous version, allowing its definitive validation by means of detailed comparisons with experimental data. The stochastic method predicts the post-implant kinetics of the defect-dopant system in the far-from-equilibrium conditions caused by laser irradiation. The simulations explain the dopant activation dynamics and demonstrate that the competitive dopant-defect kinetics during the first laser annealing treatment dominates the activation phenomenon, stabilizing the system against additional laser irradiation steps.

  12. A Monte Carlo simulation for kinetic chemotaxis models: an application to the traveling population wave

    CERN Document Server

    Yasuda, Shugo

    2015-01-01

    A Monte Carlo simulation for the chemotactic bacteria is developed on the basis of the kinetic modeling, i.e., the Boltzmann transport equation, and applied to the one-dimensional traveling population wave in a micro channel.In this method, the Monte Carlo method, which calculates the run-and-tumble motions of bacteria, is coupled with a finite volume method to solve the macroscopic transport of the chemical cues in the field. The simulation method can successfully reproduce the traveling population wave of bacteria which was observed experimentally. The microscopic dynamics of bacteria, e.g., the velocity autocorrelation function and velocity distribution function of bacteria, are also investigated. It is found that the bacteria which form the traveling population wave create quasi-periodic motions as well as a migratory movement along with the traveling population wave. Simulations are also performed with changing the sensitivity and modulation parameters in the response function of bacteria. It is found th...

  13. On grain growth kinetics in two-phase polycrystalline materials through Monte Carlo simulation

    Indian Academy of Sciences (India)

    K R Phaneesh; Anirudh Bhat; Gautam Mukherjee; K T Kashyap

    2013-08-01

    Monte Carlo Potts model simulation was carried out on a 2D square lattice for various surface fractions of second phase particles for over 50,000 iterations. The observations are in good agreement with known theoretical and experimental results with respect to both growth kinetics as well as grain size distribution. Further, the average grain size and the largest grain size were computed for various surface fractions which have indicated normal grain growth and microstructure homogeneity. The surface fraction of the second phase particles interacting with the grain boundaries (), hitherto not computed through the simulation route, is shown to vary inversely as the average grain size due to Zener pinning.

  14. Non-Arrhenius temperature dependence of the island density of one-dimensional Al chains on Si(100): A kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Albia, Jason R.; Albao, Marvin A., E-mail: maalbao@uplb.edu.ph [Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, Los Baños 4031 (Philippines)

    2015-03-15

    Classical nucleation theory predicts that the evolution of mean island density with temperature during growth in one-dimensional systems obeys the Arrhenius relation. In this study, kinetic Monte Carlo simulations of a suitable atomistic lattice-gas model were performed to investigate the experimentally observed non-Arrhenius scaling behavior of island density in the case of one-dimensional Al islands grown on Si(100). Previously, it was proposed that adatom desorption resulted in a transition temperature signaling the departure from classical predictions. Here, the authors demonstrate that desorption above the transition temperature is not possible. Instead, the authors posit that the existence of a transition temperature is due to a combination of factors such as reversibility of island growth, presence of C-defects, adatom diffusion rates, as well as detachment rates at island ends. In addition, the authors show that the anomalous non-Arrhenius behavior vanishes when adatom binds irreversibly with C-defects as observed in In on Si(100) studies.

  15. Ligand-receptor binding kinetics in surface plasmon resonance cells: A Monte Carlo analysis

    CERN Document Server

    Carroll, Jacob; Forsten-Williams, Kimberly; Täuber, Uwe C

    2016-01-01

    Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation description is appropriate. This approximation however ignores the spatial fluctuations as well as temporal correlations induced by multiple local rebinding events, which become prominent for slow diffusion rates and high binding affinities. We report detailed Monte Carlo simulations of ligand binding kinetics in an SPR cell subject to laminar flow. We extract the binding and dissociation rates by means of the techniques frequently employed in experimental analysis that are motivated by the mean-field approximation. We find major discrepancies in a wide parameter regime between the thus extracted rates and the known input simulation values. These results underscore the crucial quantitative importance of s...

  16. Kinetic Monte Carlo simulation of dopant-defect systems under submicrosecond laser thermal processes

    Energy Technology Data Exchange (ETDEWEB)

    Fisicaro, G.; Pelaz, Lourdes; Lopez, P.; Italia, M.; Huet, K.; Venturini, J.; La Magna, A. [CNR IMM, Z.I. VIII Strada 5, I -95121 Catania (Italy); Department of Electronics, University of Valladolid, 47011 Valladolid (Spain); CNR IMM, Z.I. VIII Strada 5, I -95121 Catania (Italy); Excico 13-21 Quai des Gresillons, 92230 Gennevilliers (France); CNR IMM, Z.I. VIII Strada 5, I -95121 Catania (Italy)

    2012-11-06

    An innovative Kinetic Monte Carlo (KMC) code has been developed, which rules the post-implant kinetics of the defects system in the extremely far-from-the equilibrium conditions caused by the laser irradiation close to the liquid-solid interface. It considers defect diffusion, annihilation and clustering. The code properly implements, consistently to the stochastic formalism, the fast varying local event rates related to the thermal field T(r,t) evolution. This feature of our numerical method represents an important advancement with respect to current state of the art KMC codes. The reduction of the implantation damage and its reorganization in defect aggregates are studied as a function of the process conditions. Phosphorus activation efficiency, experimentally determined in similar conditions, has been related to the emerging damage scenario.

  17. Solving the master equation without kinetic Monte Carlo: Tensor train approximations for a CO oxidation model

    Energy Technology Data Exchange (ETDEWEB)

    Gelß, Patrick, E-mail: p.gelss@fu-berlin.de; Matera, Sebastian, E-mail: matera@math.fu-berlin.de; Schütte, Christof, E-mail: schuette@mi.fu-berlin.de

    2016-06-01

    In multiscale modeling of heterogeneous catalytic processes, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. Usually, this is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO{sub 2}(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased stiffness.

  18. Kinetic Monte Carlo Simulation of Cation Diffusion in Low-K Ceramics

    Science.gov (United States)

    Good, Brian

    2013-01-01

    Low thermal conductivity (low-K) ceramic materials are of interest to the aerospace community for use as the thermal barrier component of coating systems for turbine engine components. In particular, zirconia-based materials exhibit both low thermal conductivity and structural stability at high temperature, making them suitable for such applications. Because creep is one of the potential failure modes, and because diffusion is a mechanism by which creep takes place, we have performed computer simulations of cation diffusion in a variety of zirconia-based low-K materials. The kinetic Monte Carlo simulation method is an alternative to the more widely known molecular dynamics (MD) method. It is designed to study "infrequent-event" processes, such as diffusion, for which MD simulation can be highly inefficient. We describe the results of kinetic Monte Carlo computer simulations of cation diffusion in several zirconia-based materials, specifically, zirconia doped with Y, Gd, Nb and Yb. Diffusion paths are identified, and migration energy barriers are obtained from density functional calculations and from the literature. We present results on the temperature dependence of the diffusivity, and on the effects of the presence of oxygen vacancies in cation diffusion barrier complexes as well.

  19. Kinetic Monte Carlo simulation of surface segregation in Pd–Cu alloys

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Feng [Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University (China); He, Xiang [Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008 (China); Chen, Zhao-Xu, E-mail: zxchen@nju.edu.cn [Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University (China); Huang, Yu-Gai [Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University (China); JiangSu Second Normal University, Nanjing (China)

    2015-11-05

    The knowledge of surface composition and atomic arrangement is prerequisite for understanding of catalytic properties of an alloy catalyst. Gaining such knowledge is rather difficult, especially for those possessing surface segregation. Pd–Cu alloy is used in many fields and possesses surface segregation. In this paper kinetic Monte Carlo method is used to explore the surface composition and structure and to examine the effects of bulk composition and temperature on the surface segregation of Pd–Cu alloys. It is shown that the segregation basically completes within 900 s at 500 K. Below 900 K and within 20 min the enriched surface Cu atoms mainly come from the top five layers. For the first time we demonstrate that there exists a “bulk-inside flocking” or clustering phenomenon (the same component element congregates in bulk) in Pd–Cu alloys. Our results indicate that for alloys with higher Cu content there are small Pd ensembles like monomers, dimers and trimers with contiguous subsurface Pd atoms. - Highlights: • Kinetic Monte Carlo was first used to study surface segregation of Pd–Cu alloys. • Bulk-inside flocking (the same component element congregates in bulk) was observed. • Small Pd ensembles with contiguous subsurface Pd exist on surfaces of Cu-rich alloys.

  20. Accelerated kinetics of amorphous silicon using an on-the-fly off-lattice kinetic Monte-Carlo method

    Science.gov (United States)

    Joly, Jean-Francois; El-Mellouhi, Fedwa; Beland, Laurent Karim; Mousseau, Normand

    2011-03-01

    The time evolution of a series of well relaxed amorphous silicon models was simulated using the kinetic Activation-RelaxationTechnique (kART), an on-the-fly off-lattice kinetic Monte Carlo method. This novel algorithm uses the ART nouveau algorithm to generate activated events and links them with local topologies. It was shown to work well for crystals with few defects but this is the first time it is used to study an amorphous material. A parallel implementation allows us to increase the speed of the event generation phase. After each KMC step, new searches are initiated for each new topology encountered. Well relaxed amorphous silicon models of 1000 atoms described by a modified version of the empirical Stillinger-Weber potential were used as a starting point for the simulations. Initial results show that the method is faster by orders of magnitude compared to conventional MD simulations up to temperatures of 500 K. Vacancy-type defects were also introduced in this system and their stability and lifetimes are calculated.

  1. A global reaction route mapping-based kinetic Monte Carlo algorithm

    Science.gov (United States)

    Mitchell, Izaac; Irle, Stephan; Page, Alister J.

    2016-07-01

    We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

  2. Kinetic Monte Carlo simulation of film morphologies at the initial stages

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The morphologies at the initial stages of thin film growth were studied by using Kinetic Monte Carlo techniques.A more efficient model was used to calculate the activity energy.The model involves incident atom attachment,diffusion,detachment from the surface,detached atom returning,and dimer diffusion.We edited a set of software of the model and simulated the surface morphologies by the principle of computer graphics.It is shown that the nucleuses formed at the initial stages and the surface morphologies at high temperatures are very different from those at low temperatures.The later surface growth depends on the nucleuses at the initial stages.The mechanism results from the atom thermal movement,the temperature determines the diffusion ability,and the deposition rate determines the diffusion time.

  3. Kinetic Monte Carlo simulation of microalloying effect in Al-Ag alloys

    Institute of Scientific and Technical Information of China (English)

    ZHOU Ming; LI Shi-chen; ZHENG Zi-qiao; YANG Pei-yong

    2007-01-01

    The kinetic Monte Carlo method, which based on the Multi-States Ising Model, was applied to simulate the effect of microelements on the microstructural evolution of Al-Ag alloys during initial aging stage. The simulation results suggest that the microelements In, Sn and Be have a dramatic depression effect on the Ag clustering because of their strong tendency to co-existed with vacancies. There are no significant effects on the process of Ag clustering in Al-Ag alloys containing Li or Cd, because of little interaction between Li/Cd and Ag/vacancies. Microelements can influence the aging by interacting with vacancies and the atoms of precipitated composition, in which the former seems more important. In this model, "vacancy-locking" and "vacancy clusters" are two important mechanisms in the aging process.

  4. Synchronous parallel Kinetic Monte Carlo: Implementation and results for object and lattice approaches

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Bragado, Ignacio, E-mail: ignacio.martin@imdea.org [IMDEA Materials Institute, C/ Eric Kandel 2, 28906 Getafe, Madrid (Spain); Abujas, J.; Galindo, P.L.; Pizarro, J. [Departamento de Ingeniería Informática, Universidad de Cádiz, Puerto Real, Cádiz (Spain)

    2015-06-01

    An adaptation of the synchronous parallel Kinetic Monte Carlo (spKMC) algorithm developed by Martinez et al. (2008) to the existing KMC code MMonCa (Martin-Bragado et al. 2013) is presented in this work. Two cases, general enough to provide an idea of the current state-of-the-art in parallel KMC, are presented: Object KMC simulations of the evolution of damage in irradiated iron, and Lattice KMC simulations of epitaxial regrowth of amorphized silicon. The results allow us to state that (a) the parallel overhead is critical, and severely degrades the performance of the simulator when it is comparable to the CPU time consumed per event, (b) the balance between domains is important, but not critical, (c) the algorithm and its implementation are correct and (d) further improvements are needed for spKMC to become a general, all-working solution for KMC simulations.

  5. Kinetic Monte Carlo simulations of temperature programed desorption of O/Rh(111).

    Science.gov (United States)

    Franz, T; Mittendorfer, F

    2010-05-21

    We present a kinetic Monte Carlo simulation based on ab initio calculations for the thermal desorption of oxygen from a Rh(111) surface. Several models have been used for the parametrization of the interaction between the adsorbed atoms. We find that models based on a parametrization with only pairwise interactions have a relatively large error in the predicted adsorption energies. This error can be significantly reduced by including three- and four-body interactions. In addition, we find that a significant amount of atoms adsorb in a second adsorption site - the hcp-hollow site - at an elevated temperature. Consequently, only a many-body multisite model of the oxygen interactions yields appropriate desorption spectra for the full coverage range, while more simple models only capture the correct shape in the low-coverage case. Our parametrization allows us to predict the adsorption energies of an arbitrary configuration of adsorbates with a mean average error of less than 6 meV/atom.

  6. Kinetic Monte Carlo simulation of film morphologies at the initial stages

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The morphologies at the initial stages of thin film growth were studied by using Kinetic Monte Carlo techniques. A more efficient model was used to calculate the activity energy. The model involves incident atom attachment, diffusion, detachment from the surface, detached atom returning, and dimer diffusion. We edited a set of software of the model and simulated the surface morphologies by the principle of computer graphics. It is shown that the nucleuses formed at the initial stages and the surface morphologies at high temperatures are very different from those at low temperatures. The later surface growth depends on the nucleuses at the initial stages. The mechanism results from the atom thermal movement, the temperature determines the diffusion ability, and the deposition rate determines the diffusion time.

  7. Spin kinetic Monte Carlo method for nanoferromagnetism and magnetization dynamics of nanomagnets with large magnetic anisotropy

    Institute of Scientific and Technical Information of China (English)

    LIU Bang-gui; ZHANG Kai-cheng; LI Ying

    2007-01-01

    The Kinetic Monte Carlo (KMC) method based on the transition-state theory, powerful and famous for sim-ulating atomic epitaxial growth of thin films and nanostruc-tures, was used recently to simulate the nanoferromagnetism and magnetization dynamics of nanomagnets with giant mag-netic anisotropy. We present a brief introduction to the KMC method and show how to reformulate it for nanoscale spin systems. Large enough magnetic anisotropy, observed exper-imentally and shown theoretically in terms of first-principle calculation, is not only essential to stabilize spin orientation but also necessary in making the transition-state barriers dur-ing spin reversals for spin KMC simulation. We show two applications of the spin KMC method to monatomic spin chains and spin-polarized-current controlled composite nano-magnets with giant magnetic anisotropy. This spin KMC method can be applied to other anisotropic nanomagnets and composite nanomagnets as long as their magnetic anisotropy energies are large enough.

  8. Miming the cancer-immune system competition by kinetic Monte Carlo simulations

    Science.gov (United States)

    Bianca, Carlo; Lemarchand, Annie

    2016-10-01

    In order to mimic the interactions between cancer and the immune system at cell scale, we propose a minimal model of cell interactions that is similar to a chemical mechanism including autocatalytic steps. The cells are supposed to bear a quantity called activity that may increase during the interactions. The fluctuations of cell activity are controlled by a so-called thermostat. We develop a kinetic Monte Carlo algorithm to simulate the cell interactions and thermalization of cell activity. The model is able to reproduce the well-known behavior of tumors treated by immunotherapy: the first apparent elimination of the tumor by the immune system is followed by a long equilibrium period and the final escape of cancer from immunosurveillance.

  9. Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations.

    Science.gov (United States)

    Arampatzis, Georgios; Katsoulakis, Markos A

    2014-03-28

    In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-"coupled"- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz-Kalos-Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB

  10. Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations

    Science.gov (United States)

    Arampatzis, Georgios; Katsoulakis, Markos A.

    2014-03-01

    In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-"coupled"- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz-Kalos-Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB

  11. Anisotropic hydrogen diffusion in α-Zr and Zircaloy predicted by accelerated kinetic Monte Carlo simulations

    Science.gov (United States)

    Zhang, Yongfeng; Jiang, Chao; Bai, Xianming

    2017-01-01

    This report presents an accelerated kinetic Monte Carlo (KMC) method to compute the diffusivity of hydrogen in hcp metals and alloys, considering both thermally activated hopping and quantum tunneling. The acceleration is achieved by replacing regular KMC jumps in trapping energy basins formed by neighboring tetrahedral interstitial sites, with analytical solutions for basin exiting time and probability. Parameterized by density functional theory (DFT) calculations, the accelerated KMC method is shown to be capable of efficiently calculating hydrogen diffusivity in α-Zr and Zircaloy, without altering the kinetics of long-range diffusion. Above room temperature, hydrogen diffusion in α-Zr and Zircaloy is dominated by thermal hopping, with negligible contribution from quantum tunneling. The diffusivity predicted by this DFT + KMC approach agrees well with that from previous independent experiments and theories, without using any data fitting. The diffusivity along is found to be slightly higher than that along , with the anisotropy saturated at about 1.20 at high temperatures, resolving contradictory results in previous experiments. Demonstrated using hydrogen diffusion in α-Zr, the same method can be extended for on-lattice diffusion in hcp metals, or systems with similar trapping basins. PMID:28106154

  12. Microscopic distribution functions, structure, and kinetic energy of liquid and solid neon: quantum Monte Carlo simulations.

    Science.gov (United States)

    Neumann, Martin; Zoppi, Marco

    2002-03-01

    We have performed extensive path integral Monte Carlo simulations of liquid and solid neon, in order to derive the kinetic energy as well as the single-particle and pair distribution functions of neon atoms in the condensed phases. From the single-particle distribution function n(r) one can derive the momentum distribution and thus obtain an independent estimate of the kinetic energy. The simulations have been carried out using mostly the semiempirical HFD-C2 pair potential by Aziz et al. [R. A. Aziz, W. J. Meath, and A. R. Allnatt, Chem. Phys. 79, 295 (1983)], but, in a few cases, we have also used the Lennard-Jones potential. The differences between the potentials, as measured by the properties investigated, are not very large, especially when compared with the actual precision of the experimental data. The simulation results have been compared with all the experimental information that is available from neutron scattering. The overall agreement with the experiments is very good.

  13. Clustering and heterogeneous dynamics in a kinetic Monte Carlo model of self-propelled hard disks.

    Science.gov (United States)

    Levis, Demian; Berthier, Ludovic

    2014-06-01

    We introduce a kinetic Monte Carlo model for self-propelled hard disks to capture with minimal ingredients the interplay between thermal fluctuations, excluded volume, and self-propulsion in large assemblies of active particles. We analyze in detail the resulting (density, self-propulsion) nonequilibrium phase diagram over a broad range of parameters. We find that purely repulsive hard disks spontaneously aggregate into fractal clusters as self-propulsion is increased and rationalize the evolution of the average cluster size by developing a kinetic model of reversible aggregation. As density is increased, the nonequilibrium clusters percolate to form a ramified structure reminiscent of a physical gel. We show that the addition of a finite amount of noise is needed to trigger a nonequilibrium phase separation, showing that demixing in active Brownian particles results from a delicate balance between noise, interparticle interactions, and self-propulsion. We show that self-propulsion has a profound influence on the dynamics of the active fluid. We find that the diffusion constant has a nonmonotonic behavior as self-propulsion is increased at finite density and that activity produces strong deviations from Fickian diffusion that persist over large time scales and length scales, suggesting that systems of active particles generically behave as dynamically heterogeneous systems.

  14. Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics.

    Science.gov (United States)

    Tewari, Shivendra G; Zhou, Yifan; Otto, Bradley J; Dash, Ranjan K; Kwok, Wai-Meng; Beard, Daniel A

    2014-01-01

    The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance.

  15. Mobility of large clusters on a semiconductor surface: Kinetic Monte Carlo simulation results

    Science.gov (United States)

    M, Esen; A, T. Tüzemen; M, Ozdemir

    2016-01-01

    The mobility of clusters on a semiconductor surface for various values of cluster size is studied as a function of temperature by kinetic Monte Carlo method. The cluster resides on the surface of a square grid. Kinetic processes such as the diffusion of single particles on the surface, their attachment and detachment to/from clusters, diffusion of particles along cluster edges are considered. The clusters considered in this study consist of 150-6000 atoms per cluster on average. A statistical probability of motion to each direction is assigned to each particle where a particle with four nearest neighbors is assumed to be immobile. The mobility of a cluster is found from the root mean square displacement of the center of mass of the cluster as a function of time. It is found that the diffusion coefficient of clusters goes as D = A(T)Nα where N is the average number of particles in the cluster, A(T) is a temperature-dependent constant and α is a parameter with a value of about -0.64 a value of -0.5. The diffusion coefficient is found to change by one order of magnitude as a function of cluster size.

  16. Anisotropic hydrogen diffusion in α-Zr and Zircaloy predicted by accelerated kinetic Monte Carlo simulations

    Science.gov (United States)

    Zhang, Yongfeng; Jiang, Chao; Bai, Xianming

    2017-01-01

    This report presents an accelerated kinetic Monte Carlo (KMC) method to compute the diffusivity of hydrogen in hcp metals and alloys, considering both thermally activated hopping and quantum tunneling. The acceleration is achieved by replacing regular KMC jumps in trapping energy basins formed by neighboring tetrahedral interstitial sites, with analytical solutions for basin exiting time and probability. Parameterized by density functional theory (DFT) calculations, the accelerated KMC method is shown to be capable of efficiently calculating hydrogen diffusivity in α-Zr and Zircaloy, without altering the kinetics of long-range diffusion. Above room temperature, hydrogen diffusion in α-Zr and Zircaloy is dominated by thermal hopping, with negligible contribution from quantum tunneling. The diffusivity predicted by this DFT + KMC approach agrees well with that from previous independent experiments and theories, without using any data fitting. The diffusivity along is found to be slightly higher than that along , with the anisotropy saturated at about 1.20 at high temperatures, resolving contradictory results in previous experiments. Demonstrated using hydrogen diffusion in α-Zr, the same method can be extended for on-lattice diffusion in hcp metals, or systems with similar trapping basins.

  17. Monte Carlo simulation of the kinetic effects on GaAs/GaAs(001) MBE growth

    Science.gov (United States)

    Ageev, Oleg A.; Solodovnik, Maxim S.; Balakirev, Sergey V.; Mikhaylin, Ilya A.; Eremenko, Mikhail M.

    2017-01-01

    The molecular beam epitaxial growth of GaAs on the GaAs(001)-(2×4) surface is investigated using a kinetic Monte Carlo-based method. The developed algorithm permits to focus on the kinetic effects in a wide range of growth conditions and enables considerable computational speedup. The simulation results show that the growth rate has a dramatic influence upon both the island morphology and Ga surface diffusion length. The average island size reduces with increasing growth rate while the island density increases with increasing growth rate as well as As4/Ga beam equivalent pressure ratio. As the growth rate increases, the island density becomes weaker dependent upon the As4/Ga pressure ratio and approaches to a saturation value. We also discuss three characteristics of Ga surface diffusion, namely a diffusion length of a Ga adatom deposited first, an average diffusion length, and an island spacing as an average distance between islands. The calculations show that the As4/Ga pressure ratio dependences of these characteristics obey the same law, but with different coefficients. An increase of the As4/Ga pressure ratio leads to a decrease in both the diffusion length and island spacing. However, its influence becomes stronger with increasing growth rate for the first Ga adatom diffusion length and weaker for the average diffusion length and for the island spacing.

  18. Monte-Carlo simulation for fragment mass and kinetic energy distributions from neutron induced fission of 235U

    CERN Document Server

    Montoya, M; Rojas, J

    2007-01-01

    The mass and kinetic energy distribution of nuclear fragments from thermal neutron induced fission of 235U have been studied using a Monte-Carlo simulation. Besides reproducing the pronounced broadening on the standard deviation of the final fragment kinetic energy distribution $\\sigma_{e}(m)$ around the mass number m = 109, our simulation also produces a second broadening around m = 125, that is in agreement with the experimental data obtained by Belhafaf et al. These results are consequence of the characteristics of the neutron emission, the variation in the primary fragment mean kinetic energy and the yield as a function of the mass.

  19. Monte Carlo simulations of protein amyloid formation reveal origin of sigmoidal aggregation kinetics.

    Science.gov (United States)

    Linse, Björn; Linse, Sara

    2011-07-01

    Severe conditions and lack of cure for many amyloid diseases make it highly desired to understand the underlying principles of formation of fibrillar aggregates (amyloid). Here, amyloid formation from peptides was studied using Monte Carlo simulations. Systems of 20, 50, 100, 200 or 500 hexapeptides were simulated. Association kinetics were modeled equal for fibrillar and other (inter- and intra-peptide) contacts and assumed to be faster the lower the effective contact order, which represents the distance in space. Attempts to form contacts were thus accepted with higher probability the lower the effective contact order, whereby formation of new contacts next to preexisting ones is favored by shorter physical separation. Kinetic discrimination was invoked by using two different life-times for formed contacts. Contacts within amyloid fibrils were assumed to have on average longer life-time than other contacts. We find that the model produces fibrillation kinetics with a distinct lag phase, and that the fibrillar contacts need to dissociate on average 5-20 times slower than all other contacts for the fibrillar structure to dominate at equilibrium. Analysis of the species distribution along the aggregation process shows that no other intermediate is ever more populated than the dimer. Instead of a single nucleation event there is a concomitant increase in average aggregate size over the whole system, and the occurrence of multiple parallel processes makes the process more reproducible the larger the simulated system. The sigmoidal shape of the aggregation curves arises from cooperativity among multiple interactions within each pair of peptides in a fibril. A governing factor is the increasing probability as the aggregation process proceeds of neighboring reinforcing contacts. The results explain the very strong bias towards cross β-sheet fibrils in which the possibilities for cooperativity among interactions involving neighboring residues and the repetitive use of

  20. The kinetic activation-relaxation technique: an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search

    Science.gov (United States)

    Mousseau, Nomand

    2012-02-01

    While kinetic Monte Carlo algorithm has been proposed almost 40 years ago, its application in materials science has been mostly limited to lattice-based motion due to the difficulties associated with identifying new events and building usable catalogs when atoms moved into off-lattice position. Here, I present the kinetic activation-relaxation technique (kinetic ART) is an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search [1]. It combines ART nouveau [2], a very efficient unbiased open-ended activated method for finding transition states, with a topological classification [3] that allows a discrete cataloguing of local environments in complex systems, including disordered materials. In kinetic ART, local topologies are first identified for all atoms in a system. ART nouveau event searches are then launched for new topologies, building an extensive catalog of barriers and events. Next, all low energy events are fully reconstructed and relaxed, allowing to take complete account of elastic effects in the system's kinetics. Using standard kinetic Monte Carlo, the clock is brought forward and an event is then selected and applied before a new search for topologies is launched. In addition to presenting the various elements of the algorithm, I will discuss three recent applications to ion-bombarded silicon, defect diffusion in Fe and structural relaxation in amorphous silicon.[4pt] This work was done in collaboration with Laurent Karim B'eland, Peter Brommer, Fedwa El-Mellouhi, Jean-Francois Joly and Laurent Lewis.[4pt] [1] F. El-Mellouhi, N. Mousseau and L.J. Lewis, Phys. Rev. B. 78, 153202 (2008); L.K. B'eland et al., Phys. Rev. E 84, 046704 (2011).[2] G.T. Barkema and N. Mousseau, Phys. Rev. Lett. 77, 4358 (1996); E. Machado-Charry et al., J. Chem Phys. 135, 034102, (2011).[3] B.D. McKay, Congressus Numerantium 30, 45 (1981).

  1. Kinetic Monte Carlo investigation of pit formation at the CaCO 3(101¯4) surface-water interface

    Science.gov (United States)

    McCoy, J. M.; LaFemina, John P.

    1997-03-01

    On the basis of quantitative information derived from atomic-force microscopy (AFM) studies of shallow pit formation at the CaCO 3(101¯4) surface-water interface in the surface-reaction regime, we have developed a kinetic Monte Carlo (KMC) model which reproduces quantitatively the experimental behaviour of the time-evolution of the pits. This allows the rates of all the important elementary atomistic processes involved in the dissolution to be obtained, rates not readily obtainable directly from AFM data. The KMC model also provides important insight into the evolution of very small pits, which in principle can be resolved using AFM, but which in practice are very difficult to observe because of the low probability of their occurrence in the microscope scan area. The KMC simulations show that the growing pits exhibit two different growth regimes, in agreement with the predictions of a simple terrace-ledge-kink (TLK) model. For very small pits the linear pit size increases exponentially with time and the pit edges accelerate (double-kink self-annihilation regime). Having attained a certain pit size (˜25 nm for a temperature of 300 K), thereafter the pit sizes increase linearly with time, the pit edges maintaining a constant velocity (kink-kink annihilation regime). A comparison of the quantitative predictions of the TLK model with KMC simulations shows that, in spite of its simplicity, the TLK model provides a satisfactory semi-quantitative description of the pit evolution. The KMC model presented provides the starting point for the development of a more comprehensive model of the calcite-water interface which will include the effects of adsorbates and other variations in interface conditions. Published by Elsevier Science B.V.

  2. Monte-Carlo modelling of nano-material photocatalysis: bridging photocatalytic activity and microscopic charge kinetics.

    Science.gov (United States)

    Liu, Baoshun

    2016-04-28

    In photocatalysis, it is known that light intensity, organic concentration, and temperature affect the photocatalytic activity by changing the microscopic kinetics of holes and electrons. However, how the microscopic kinetics of holes and electrons relates to the photocatalytic activity was not well known. In the present research, we developed a Monte-Carlo random walking model that involved all of the charge kinetics, including the photo-generation, the recombination, the transport, and the interfacial transfer of holes and electrons, to simulate the overall photocatalytic reaction, which we called a "computer experiment" of photocatalysis. By using this model, we simulated the effect of light intensity, temperature, and organic surface coverage on the photocatalytic activity and the density of the free electrons that accumulate in the simulated system. It was seen that the increase of light intensity increases the electron density and its mobility, which increases the probability for a hole/electron to find an electron/hole for recombination, and consequently led to an apparent kinetics that the quantum yield (QY) decreases with the increase of light intensity. It was also seen that the increase of organic surface coverage could increase the rate of hole interfacial transfer and result in the decrease of the probability for an electron to recombine with a hole. Moreover, the increase of organic coverage on the nano-material surface can also increase the accumulation of electrons, which enhances the mobility for electrons to undergo interfacial transfer, and finally leads to the increase of photocatalytic activity. The simulation showed that the temperature had a more complicated effect, as it can simultaneously change the activation of electrons, the interfacial transfer of holes, and the interfacial transfer of electrons. It was shown that the interfacial transfer of holes might play a main role at low temperature, with the temperature-dependence of QY

  3. Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions

    Science.gov (United States)

    Nielsen, Jens; d'Avezac, Mayeul; Hetherington, James; Stamatakis, Michail

    2013-12-01

    Ab initio kinetic Monte Carlo (KMC) simulations have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These simulations necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for simulating catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce parallelization with OpenMP. We further benchmark our framework by simulating a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.

  4. Nanostructure evolution of neutron-irradiated reactor pressure vessel steels: Revised Object kinetic Monte Carlo model

    Science.gov (United States)

    Chiapetto, M.; Messina, L.; Becquart, C. S.; Olsson, P.; Malerba, L.

    2017-02-01

    This work presents a revised set of parameters to be used in an Object kinetic Monte Carlo model to simulate the microstructure evolution under neutron irradiation of reactor pressure vessel steels at the operational temperature of light water reactors (∼300 °C). Within a "grey-alloy" approach, a more physical description than in a previous work is used to translate the effect of Mn and Ni solute atoms on the defect cluster diffusivity reduction. The slowing down of self-interstitial clusters, due to the interaction between solutes and crowdions in Fe is now parameterized using binding energies from the latest DFT calculations and the solute concentration in the matrix from atom-probe experiments. The mobility of vacancy clusters in the presence of Mn and Ni solute atoms was also modified on the basis of recent DFT results, thereby removing some previous approximations. The same set of parameters was seen to predict the correct microstructure evolution for two different types of alloys, under very different irradiation conditions: an Fe-C-MnNi model alloy, neutron irradiated at a relatively high flux, and a high-Mn, high-Ni RPV steel from the Swedish Ringhals reactor surveillance program. In both cases, the predicted self-interstitial loop density matches the experimental solute cluster density, further corroborating the surmise that the MnNi-rich nanofeatures form by solute enrichment of immobilized small interstitial loops, which are invisible to the electron microscope.

  5. Kinetic Monte Carlo Simulation of EB-PVD Film: Effects of Substrate Temperature

    Institute of Scientific and Technical Information of China (English)

    SHAN Ying-chun; HE Xiao-dong; LI Ming-wei; LI Yao; XU Jiu-jun

    2006-01-01

    The 2D kinetic Monte Carlo (KMC) simulation was used to study the effects of different substrate temperatures on the microstructure of Ni-Cr films in the process of deposition by the electron beam physical vapor deposition (EB-PVD). In the KMC model, substrate was assumed to be a "surface" of tight-packed rows, and the simulation includes two phenomena: adatom-surface collision and adatom diffusion. While the interaction between atoms was described by the embedded atom method, the jumping energy was calculated by the molecular static (MS) calculation. The initial location of the adatom was defined by the Momentum Scheme. The results reveal that there exists a critical substrate temperature which means that the lowest packing density and the highest surface roughness structure will be achieved when the temperature is lower than the smaller critical value, while the roughness of both surfaces and the void contents keep decreasing with the substrate temperature increasing until it reaches the higher critical value. The results also indicate that the critical substrate temperature rises as the deposition rate increases.

  6. Lattice based Kinetic Monte Carlo Simulations of a complex chemical reaction network

    Science.gov (United States)

    Danielson, Thomas; Savara, Aditya; Hin, Celine

    Lattice Kinetic Monte Carlo (KMC) simulations offer a powerful alternative to using ordinary differential equations for the simulation of complex chemical reaction networks. Lattice KMC provides the ability to account for local spatial configurations of species in the reaction network, resulting in a more detailed description of the reaction pathway. In KMC simulations with a large number of reactions, the range of transition probabilities can span many orders of magnitude, creating subsets of processes that occur more frequently or more rarely. Consequently, processes that have a high probability of occurring may be selected repeatedly without actually progressing the system (i.e. the forward and reverse process for the same reaction). In order to avoid the repeated occurrence of fast frivolous processes, it is necessary to throttle the transition probabilities in such a way that avoids altering the overall selectivity. Likewise, as the reaction progresses, new frequently occurring species and reactions may be introduced, making a dynamic throttling algorithm a necessity. We present a dynamic steady-state detection scheme with the goal of accurately throttling rate constants in order to optimize the KMC run time without compromising the selectivity of the reaction network. The algorithm has been applied to a large catalytic chemical reaction network, specifically that of methanol oxidative dehydrogenation, as well as additional pathways on CeO2(111) resulting in formaldehyde, CO, methanol, CO2, H2 and H2O as gas products.

  7. Kinetic Monte Carlo Simulations and Molecular Conductance Measurements of the Bacterial Decaheme Cytochrome MtrF

    Energy Technology Data Exchange (ETDEWEB)

    Byun, H. S.; Pirbadian, S.; Nakano, Aiichiro; Shi, Liang; El-Naggar, Mohamed Y.

    2014-09-05

    Microorganisms overcome the considerable hurdle of respiring extracellular solid substrates by deploying large multiheme cytochrome complexes that form 20 nanometer conduits to traffic electrons through the periplasm and across the cellular outer membrane. Here we report the first kinetic Monte Carlo simulations and single-molecule scanning tunneling microscopy (STM) measurements of the Shewanella oneidensis MR-1 outer membrane decaheme cytochrome MtrF, which can perform the final electron transfer step from cells to minerals and microbial fuel cell anodes. We find that the calculated electron transport rate through MtrF is consistent with previously reported in vitro measurements of the Shewanella Mtr complex, as well as in vivo respiration rates on electrode surfaces assuming a reasonable (experimentally verified) coverage of cytochromes on the cell surface. The simulations also reveal a rich phase diagram in the overall electron occupation density of the hemes as a function of electron injection and ejection rates. Single molecule tunneling spectroscopy confirms MtrF's ability to mediate electron transport between an STM tip and an underlying Au(111) surface, but at rates higher than expected from previously calculated heme-heme electron transfer rates for solvated molecules.

  8. Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems

    Science.gov (United States)

    Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan

    2012-03-01

    Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.

  9. Generating relevant kinetic Monte Carlo catalogs using temperature accelerated dynamics with control over the accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Chatterjee, Abhijit [Los Alamos National Laboratory; Voter, Arthur [Los Alamos National Laboratory

    2009-01-01

    We develop a variation of the temperature accelerated dynamics (TAD) method, called the p-TAD method, that efficiently generates an on-the-fly kinetic Monte Carlo (KMC) process catalog with control over the accuracy of the catalog. It is assumed that transition state theory is valid. The p-TAD method guarantees that processes relevant at the timescales of interest to the simulation are present in the catalog with a chosen confidence. A confidence measure associated with the process catalog is derived. The dynamics is then studied using the process catalog with the KMC method. Effective accuracy of a p-TAD calculation is derived when a KMC catalog is reused for conditions different from those the catalog was originally generated for. Different KMC catalog generation strategies that exploit the features of the p-TAD method and ensure higher accuracy and/or computational efficiency are presented. The accuracy and the computational requirements of the p-TAD method are assessed. Comparisons to the original TAD method are made. As an example, we study dynamics in sub-monolayer Ag/Cu(110) at the time scale of seconds using the p-TAD method. It is demonstrated that the p-TAD method overcomes several challenges plaguing the conventional KMC method.

  10. Effect of nonlinearity in hybrid kinetic Monte Carlo-continuum models.

    Science.gov (United States)

    Balter, Ariel; Lin, Guang; Tartakovsky, Alexandre M

    2012-01-01

    Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a kinetic Monte Carlo (KMC) model for a surface to a finite-difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition-dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition-dissolution model including competitive adsorption, which leads to a nonlinear rate, and show that in this case the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.

  11. Comprehensive modeling of solid phase epitaxial growth using Lattice Kinetic Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Bragado, Ignacio, E-mail: ignacio.martin@imdea.org [IMDEA Materials Institute, C/ Eric Kandel 2, Parque Científico y Tecnológico de Getafe 28906 Madrid, Getafe (Spain)

    2013-05-15

    Damage evolution of irradiated silicon is, and has been, a topic of interest for the last decades for its applications to the semiconductor industry. In particular, sometimes, the damage is heavy enough to collapse the lattice and to locally amorphize the silicon, while in other cases amorphization is introduced explicitly to improve other implanted profiles. Subsequent annealing of the implanted samples heals the amorphized regions through Solid Phase Epitaxial Regrowth (SPER). SPER is a complicated process. It is anisotropic, it generates defects in the recrystallized silicon, it has a different amorphous/crystalline (A/C) roughness for each orientation, leaving pits in Si(1 1 0), and in Si(1 1 1) it produces two modes of recrystallization with different rates. The recently developed code MMonCa has been used to introduce a physically-based comprehensive model using Lattice Kinetic Monte Carlo that explains all the above singularities of silicon SPER. The model operates by having, as building blocks, the silicon lattice microconfigurations and their four twins. It detects the local configurations, assigns microscopical growth rates, and reconstructs the positions of the lattice locally with one of those building blocks. The overall results reproduce the (a) anisotropy as a result of the different growth rates, (b) localization of SPER induced defects, (c) roughness trends of the A/C interface, (d) pits on Si(1 1 0) regrown surfaces, and (e) bimodal Si(1 1 1) growth. It also provides physical insights of the nature and shape of deposited defects and how they assist in the occurrence of all the above effects.

  12. Evaluation of the interindividual human variation in bioactivation of methyleugenol using physiologically based kinetic modeling and Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Al-Subeihi, Ala' A.A., E-mail: subeihi@yahoo.com [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands); BEN-HAYYAN-Aqaba International Laboratories, Aqaba Special Economic Zone Authority (ASEZA), P. O. Box 2565, Aqaba 77110 (Jordan); Alhusainy, Wasma; Kiwamoto, Reiko; Spenkelink, Bert [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands); Bladeren, Peter J. van [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands); Nestec S.A., Avenue Nestlé 55, 1800 Vevey (Switzerland); Rietjens, Ivonne M.C.M.; Punt, Ans [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands)

    2015-03-01

    The present study aims at predicting the level of formation of the ultimate carcinogenic metabolite of methyleugenol, 1′-sulfooxymethyleugenol, in the human population by taking variability in key bioactivation and detoxification reactions into account using Monte Carlo simulations. Depending on the metabolic route, variation was simulated based on kinetic constants obtained from incubations with a range of individual human liver fractions or by combining kinetic constants obtained for specific isoenzymes with literature reported human variation in the activity of these enzymes. The results of the study indicate that formation of 1′-sulfooxymethyleugenol is predominantly affected by variation in i) P450 1A2-catalyzed bioactivation of methyleugenol to 1′-hydroxymethyleugenol, ii) P450 2B6-catalyzed epoxidation of methyleugenol, iii) the apparent kinetic constants for oxidation of 1′-hydroxymethyleugenol, and iv) the apparent kinetic constants for sulfation of 1′-hydroxymethyleugenol. Based on the Monte Carlo simulations a so-called chemical-specific adjustment factor (CSAF) for intraspecies variation could be derived by dividing different percentiles by the 50th percentile of the predicted population distribution for 1′-sulfooxymethyleugenol formation. The obtained CSAF value at the 90th percentile was 3.2, indicating that the default uncertainty factor of 3.16 for human variability in kinetics may adequately cover the variation within 90% of the population. Covering 99% of the population requires a larger uncertainty factor of 6.4. In conclusion, the results showed that adequate predictions on interindividual human variation can be made with Monte Carlo-based PBK modeling. For methyleugenol this variation was observed to be in line with the default variation generally assumed in risk assessment. - Highlights: • Interindividual human differences in methyleugenol bioactivation were simulated. • This was done using in vitro incubations, PBK modeling

  13. Thermal aging stability of infiltrated solid oxide fuel cell electrode microstructures: A three-dimensional kinetic Monte Carlo simulation

    Science.gov (United States)

    Zhang, Yanxiang; Ni, Meng; Yan, Mufu; Chen, Fanglin

    2015-12-01

    Nanostructured electrodes are widely used for low temperature solid oxide fuel cells, due to their remarkably high activity. However, the industrial applications of the infiltrated electrodes are hindered by the durability issues, such as the microstructure stability against thermal aging. Few strategies are available to overcome this challenge due to the limited knowledge about the coarsening kinetics of the infiltrated electrodes and how the potentially important factors affect the stability. In this work, the generic thermal aging kinetics of the three-dimensional microstructures of the infiltrate electrodes is investigated by a kinetic Monte Carlo simulation model considering surface diffusion mechanism. Effects of temperature, infiltration loading, wettability, and electrode configuration are studied and the key geometric parameters are calculated such as the infiltrate particle size, the total and percolated quantities of three-phase boundary length and infiltrate surface area, and the tortuosity factor of infiltrate network. Through parametric study, several strategies to improve the thermal aging stability are proposed.

  14. Preliminary Comparison of Reaction Rate theory and Object Kinetic Monte Carlo Simulations of Defect Cluster Dynamics under Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Stoller, Roger E [ORNL; Golubov, Stanislav I [ORNL; Becquart, C. S. [Universite de Lille; Domain, C. [EDF R& D, Clamart, France

    2006-09-01

    The multiscale modeling scheme encompasses models from the atomistic to the continuum scale. Phenomena at the mesoscale are typically simulated using reaction rate theory (RT), Monte Carlo (MC), or phase field models. These mesoscale models are appropriate for application to problems that involve intermediate length scales ( m to >mm), and timescales from diffusion (~ s) to long-term microstructural evolution (~years). Phenomena at this scale have the most direct impact on mechanical properties in structural materials of interest to nuclear energy systems, and are also the most accessible to direct comparison between the results of simulations and experiments. Recent advances in computational power have substantially expanded the range of application for MC models. Although the RT and MC models can be used simulate the same phenomena, many of the details are handled quite differently in the two approaches. A direct comparison of the RT and MC descriptions has been made in the domain of point defect cluster dynamics modeling, which is relevant to both the nucleation and evolution of radiation-induced defect structures. The relative merits and limitations of the two approaches are discussed, and the predictions of the two approaches are compared for specific irradiation conditions.

  15. Large scale application of kinetic ART, a near order-1 topologically- based off-lattice kinetic Monte-Carlo algorithm with on-the-fly calculation of events

    Science.gov (United States)

    Beland, Laurent Karim; El-Mellouhi, Fedwa; Mousseau, Normand

    2010-03-01

    Using a topological classification of eventsfootnotetextB. D. McKay, Congressus Numerantium 30, 45 (1981). combined with the Activation-Relaxation Technique (ART nouveau) for the generation of diffusion pathways, the kinetic ART (k-ART)footnotetextF. El-Mellouhi, N. Mousseau and L. J. Lewis, Phys Rev B, 78,15 (2008). lifts many restrictions generally associated with standard kinetic Monte Carlo algorithms. In particular, it can treat on and off-lattice atomic positions and handles exactly long-range elastic deformation. Here we introduce a set of modifications to k-ART that reduce the computational cost of the algorithm to near order 1 and show applications of the algorithm to the diffusion of vacancy and interstitial complexes in large models of crystalline Si (100 000 atoms).

  16. KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations

    Science.gov (United States)

    Leetmaa, Mikael; Skorodumova, Natalia V.

    2014-09-01

    KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily extended and customized by the user to allow for the development of complex custom KMC models for specific systems without having to modify the core functionality of the program. Analysis modules and on-the-fly elementary step diffusion rate calculations can be implemented as plugins following a well-defined API. The plugin modules are loosely coupled to the core KMCLib program via the Python scripting language. KMCLib is written as a Python module with a backend C++ library. After initial compilation of the backend library KMCLib is used as a Python module; input to the program is given as a Python script executed using a standard Python interpreter. We give a detailed description of the features and implementation of the code and demonstrate its scaling behavior and parallel performance with a simple one-dimensional A-B-C lattice KMC model and a more complex three-dimensional lattice KMC model of oxygen-vacancy diffusion in a fluorite structured metal oxide. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Catalogue identifier: AESZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 49 064 No. of bytes in distributed program, including test data, etc.: 1 575 172 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer that can run a C++ compiler and a Python interpreter. Operating system: Tested on Ubuntu 12

  17. Displacement cascades and defect annealing in tungsten, Part II: Object kinetic Monte Carlo simulation of tungsten cascade aging

    Energy Technology Data Exchange (ETDEWEB)

    Nandipati, Giridhar, E-mail: giridhar.nandipati@pnnl.gov [Pacific Northwest National Laboratory, Richland, WA (United States); Setyawan, Wahyu; Heinisch, Howard L. [Pacific Northwest National Laboratory, Richland, WA (United States); Roche, Kenneth J. [Pacific Northwest National Laboratory, Richland, WA (United States); Department of Physics, University of Washington, Seattle, WA 98195 (United States); Kurtz, Richard J. [Pacific Northwest National Laboratory, Richland, WA (United States); Wirth, Brian D. [University of Tennessee, Knoxville, TN (United States)

    2015-07-15

    The results of object kinetic Monte Carlo (OKMC) simulations of the annealing of primary cascade damage in bulk tungsten using a comprehensive database of cascades obtained from molecular dynamics (Setyawan et al.) are described as a function of primary knock-on atom (PKA) energy at temperatures of 300, 1025 and 2050 K. An increase in SIA clustering coupled with a decrease in vacancy clustering with increasing temperature, in addition to the disparate mobilities of SIAs versus vacancies, causes an interesting effect of temperature on cascade annealing. The annealing efficiency (the ratio of the number of defects after and before annealing) exhibits an inverse U-shape curve as a function of temperature. The capabilities of the newly developed OKMC code KSOME (kinetic simulations of microstructure evolution) used to carry out these simulations are described.

  18. Displacement cascades and defect annealing in tungsten, Part II: Object kinetic Monte Carlo Simulation of Tungsten Cascade Aging

    Energy Technology Data Exchange (ETDEWEB)

    Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.

    2015-07-01

    The results of object kinetic Monte Carlo (OKMC) simulations of the annealing of primary cascade damage in bulk tungsten using a comprehensive database of cascades obtained from molecular dynamics (Setyawan et al.) are described as a function of primary knock-on atom (PKA) energy at temperatures of 300, 1025 and 2050 K. An increase in SIA clustering coupled with a decrease in vacancy clustering with increasing temperature, in addition to the disparate mobilities of SIAs versus vacancies, causes an interesting effect of temperature on cascade annealing. The annealing efficiency (the ratio of the number of defects after and before annealing) exhibits an inverse U-shape curve as a function of temperature. The capabilities of the newly developed OKMC code KSOME (kinetic simulations of microstructure evolution) used to carry out these simulations are described.

  19. Kinetic Monte Carlo simulations of travelling pulses and spiral waves in the lattice Lotka-Volterra model.

    Science.gov (United States)

    Makeev, Alexei G; Kurkina, Elena S; Kevrekidis, Ioannis G

    2012-06-01

    Kinetic Monte Carlo simulations are used to study the stochastic two-species Lotka-Volterra model on a square lattice. For certain values of the model parameters, the system constitutes an excitable medium: travelling pulses and rotating spiral waves can be excited. Stable solitary pulses travel with constant (modulo stochastic fluctuations) shape and speed along a periodic lattice. The spiral waves observed persist sometimes for hundreds of rotations, but they are ultimately unstable and break-up (because of fluctuations and interactions between neighboring fronts) giving rise to complex dynamic behavior in which numerous small spiral waves rotate and interact with each other. It is interesting that travelling pulses and spiral waves can be exhibited by the model even for completely immobile species, due to the non-local reaction kinetics.

  20. A generalized Ising model for studying alloy evolution under irradiation and its use in kinetic Monte Carlo simulations

    Science.gov (United States)

    Huang, Chen-Hsi; Marian, Jaime

    2016-10-01

    We derive an Ising Hamiltonian for kinetic simulations involving interstitial and vacancy defects in binary alloys. Our model, which we term ‘ABVI’, incorporates solute transport by both interstitial defects and vacancies into a mathematically-consistent framework, and thus represents a generalization to the widely-used ABV model for alloy evolution simulations. The Hamiltonian captures the three possible interstitial configurations in a binary alloy: A-A, A-B, and B-B, which makes it particularly useful for irradiation damage simulations. All the constants of the Hamiltonian are expressed in terms of bond energies that can be computed using first-principles calculations. We implement our ABVI model in kinetic Monte Carlo simulations and perform a verification exercise by comparing our results to published irradiation damage simulations in simple binary systems with Frenkel pair defect production and several microstructural scenarios, with matching agreement found.

  1. Kinetic Monte Carlo simulation of growth of BaTiO3 thin film via pulsed laser deposition

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Considering the characteristics of perovskite structure, a kinetic Monte Carlo(KMC) model, in which Bom-Mayer-Huggins(BMH) potential was introduced to calculate the interatomic interactions and the bonding ratio was defined to reflect the crystallinity, was developed to simulate the growth of BaTiO3 thin film via pulsed laser deposition(PLD). Not only the atoms deposition and adatoms diffusion, but also the bonding of adatoms were considered distinguishing with the traditional algorithm. The effects of substrate temperature, laser pulse repetition rate and incident kinetic energy on BaTiO3 thin film growth were investigated at submonolayer regime. The results show that the island density decreases and the bonding ratio increases with the increase of substrate temperature from 700 to 850 K. With the laser pulse repetition rate increasing, the island density decreases while the bonding ratio increases. With the incident kinetic energy increasing, the island density decreases except 6.2 eV<Ek<9.6 eV, and the bonding ratio increases at Ek<9.6 eV. The simulation results were discussed compared with the previous experimental results.

  2. Meaningful timescales from Monte Carlo simulations of molecular systems

    CERN Document Server

    Costa, Liborio I

    2016-01-01

    A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems with atomistic detail is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is associated with minima in the energy landscape, in the proposed method, the state of the system is associated with the set of paths traveled by the atoms and the transition probabilities for an atom to be displaced are proportional to the corresponding velocities. In this way, the number of possible state-to-state transitions is reduced to a discrete set, and a direct link between the Monte Carlo time step and true physical time is naturally established. The resulting rejection-free algorithm is validated against event-driven molecular dynamics: the equilibrium and non-equilibrium dynamics of hard disks converge to the exact results with decreasing displacement size.

  3. Monte-Carlo approach to particle-field interactions and the kinetics of the chiral phase transition

    CERN Document Server

    Greiner, Carsten; van Hees, Hendrik; Meistrenko, Alex

    2015-01-01

    The kinetics of the chiral phase transition is studied within a linear quark-meson-$\\sigma$ model, using a Monte-Carlo approach to semiclassical particle-field dynamics. The meson fields are described on the mean-field level and quarks and antiquarks as ensembles of test particles. Collisions between quarks and antiquarks as well as the $q\\overline{q}$ annihilation to $\\sigma$ mesons and the decay of $\\sigma$ mesons is treated, using the corresponding transition-matrix elements from the underlying quantum field theory, obeying strictly the rule of detailed balance and energy-momentum conservation. The approach allows to study fluctuations without making ad hoc assumptions concerning the statistical nature of the random process as necessary in Langevin-Fokker-Planck frameworks.

  4. Monte Carlo simulation on kinetic behavior of one-pot hyperbranched polymerization based on AA*+CB2

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Monte Carlo simulation was applied to investigate the kinetic behavior of AA*+CB2 system.The algorithm consisted of two procedures to simulate the in-situ synthesis of AB2-like intermediate and the subsequent polymerization,respectively.In order to improve the accuracy of the prediction,the mobility distinction between different scale molecules in polymerization was taken into account by relating the reaction rate constants to the collision possibility of each pair of species.The feed ratio of initial monomers and the activity difference between the two functional groups within AA* were studied systematically to catch the essential features of the reaction.Simulation results have revealed that the achievable maximum conversion primarily depends on the extent of the reactivity difference between A and A*-groups,and it is suggested that A*-group should be at least 10 times more active than A-group to achieve high number-average degree of polymerization.

  5. Generalized Temporal Acceleration Scheme for Kinetic Monte Carlo Simulations of Surface Catalytic Processes by Scaling the Rates of Fast Reactions.

    Science.gov (United States)

    Dybeck, Eric Christopher; Plaisance, Craig Patrick; Neurock, Matthew

    2017-02-14

    A novel algorithm has been developed to achieve temporal acceleration during kinetic Monte Carlo (KMC) simulations of surface catalytic processes. This algorithm allows for the direct simulation of reaction networks containing kinetic processes occurring on vastly disparate timescales which computationally overburden standard KMC methods. Previously developed methods for temporal acceleration in KMC have been designed for specific systems and often require a priori information from the user such as identifying the fast and slow processes. In the approach presented herein, quasi-equilibrated processes are identified automatically based on previous executions of the forward and reverse reactions. Temporal acceleration is achieved by automatically scaling the intrinsic rate constants of the quasi-equilibrated processes, bringing their rates closer to the timescales of the slow kinetically relevant non-equilibrated processes. All reactions are still simulated directly, although with modified rate constants. Abrupt changes in the underlying dynamics of the reaction network are identified during the simulation and the reaction rate constants are rescaled accordingly. The algorithm has been utilized here to model the Fischer-Tropsch synthesis reaction over ruthenium nanoparticles. This reaction network has multiple timescale-disparate processes which would be intractable to simulate without the aid of temporal acceleration. The accelerated simulations are found to give reaction rates and selectivities indistinguishable from those calculated by an equivalent mean-field kinetic model. The computational savings of the algorithm can span many orders of magnitude in realistic systems and the computational cost is not limited by the magnitude of the timescale disparity in the system processes. Furthermore, the algorithm has been designed in a generic fashion and can easily be applied to other surface catalytic processes of interest.

  6. Thermodynamics and simulation of hard-sphere fluid and solid: Kinetic Monte Carlo method versus standard Metropolis scheme

    Science.gov (United States)

    Ustinov, E. A.

    2017-01-01

    The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure-chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs-Duhem equation as a constraint. A detailed thermodynamic analysis of the hard-sphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems.

  7. A kinetic Monte Carlo study of desorption of H2 from graphite (0001)

    CERN Document Server

    Gavardi, E; Hornekaer, L; 10.1016/j.cplett.2009.07.003

    2009-01-01

    The formation of H2 in the interstellar medium proceeds on the surfaces of silicate or carbonaceous particles. To get a deeper insight of its formation on the latter substrate, this letter focuses on H2 desorption from graphite (0001) in Temperature-Programmed-Desorption Monte-Carlo simulations. The results are compared to experimental results which show two main peaks and an intermediate shoulder for high initial coverage. The simulation program includes barriers obtained by ab-initio methods and is further optimised to match two independent experimental observations. The simulations reproduce the two experimental observed desorption peaks. Additionally, a possible origin of the intermediate peak is given.

  8. Atomistic simulations of nanoindentation

    Directory of Open Access Journals (Sweden)

    Izabela Szlufarska

    2006-05-01

    Full Text Available Our understanding of mechanics is pushed to its limit when the functionality of devices is controlled at the nanometer scale. A fundamental understanding of nanomechanics is needed to design materials with optimum properties. Atomistic simulations can bring an important insight into nanostructure-property relations and, when combined with experiments, they become a powerful tool to move nanomechanics from basic science to the application area. Nanoindentation is a well-established technique for studying mechanical response. We review recent advances in modeling (atomistic and beyond of nanoindentation and discuss how they have contributed to our current state of knowledge.

  9. Ag diffusion in SiC high-energy grain boundaries: kinetic Monte Carlo study with first-principle calculations

    CERN Document Server

    Ko, Hyunseok; Szlufarska, Izabela; Morgan, Dane

    2016-01-01

    The diffusion of silver (Ag) impurities in high energy grain boundaries (HEGBs) of cubic (3C) silicon carbide (SiC) is studied using an ab initio based kinetic Monte Carlo (kMC) model. This study assesses the hypothesis that the HEGB diffusion is responsible for Ag release in Tristructural-Isotropic fuel particles, and provides a specific example to increase understanding of impurity diffusion in highly disordered grain boundaries. The HEGB environment was modeled by an amorphous SiC. The structure and stability of Ag defects were calculated using density functional theory code. The defect energetics suggested that the fastest diffusion takes place via an interstitial mechanism in a-SiC. The formation energy of Ag interstitials and the kinetic resolved activation energies between them were well approximated with Gaussian distributions that were then sampled in the kMC. The diffusion of Ag was simulated with the effective medium model using kMC. At 1200-1600C, Ag in a HEGB is predicted to exhibit an Arrhenius ...

  10. Nuclear reactor transient analysis via a quasi-static kinetics Monte Carlo method

    Energy Technology Data Exchange (ETDEWEB)

    Jo, YuGwon; Cho, Bumhee; Cho, Nam Zin, E-mail: nzcho@kaist.ac.kr [Korea Advanced Institute of Science and Technology 291 Daehak-ro, Yuseong-gu, Daejeon, Korea 305-701 (Korea, Republic of)

    2015-12-31

    The predictor-corrector quasi-static (PCQS) method is applied to the Monte Carlo (MC) calculation for reactor transient analysis. To solve the transient fixed-source problem of the PCQS method, fission source iteration is used and a linear approximation of fission source distributions during a macro-time step is introduced to provide delayed neutron source. The conventional particle-tracking procedure is modified to solve the transient fixed-source problem via MC calculation. The PCQS method with MC calculation is compared with the direct time-dependent method of characteristics (MOC) on a TWIGL two-group problem for verification of the computer code. Then, the results on a continuous-energy problem are presented.

  11. Nuclear reactor transient analysis via a quasi-static kinetics Monte Carlo method

    Science.gov (United States)

    Jo, YuGwon; Cho, Bumhee; Cho, Nam Zin

    2015-12-01

    The predictor-corrector quasi-static (PCQS) method is applied to the Monte Carlo (MC) calculation for reactor transient analysis. To solve the transient fixed-source problem of the PCQS method, fission source iteration is used and a linear approximation of fission source distributions during a macro-time step is introduced to provide delayed neutron source. The conventional particle-tracking procedure is modified to solve the transient fixed-source problem via MC calculation. The PCQS method with MC calculation is compared with the direct time-dependent method of characteristics (MOC) on a TWIGL two-group problem for verification of the computer code. Then, the results on a continuous-energy problem are presented.

  12. Kinetic Monte Carlo Simulation of the oscillatory catalytic CO oxidation using a modified Ziff-Gulari-Barshad model

    Science.gov (United States)

    Sinha, Indrajit; Mukherjee, Ashim K.

    2014-03-01

    The oxidation of CO on Pt-group metal surfaces has attracted widespread attention since a long time due to its interesting oscillatory kinetics and spatiotemporal behavior. The use of STM in conjunction with other experimental data has confirmed the validity of the surface reconstruction (SR) model under low pressure and the more recent surface oxide (SO) model which is possible under sub-atmospheric pressure conditions [1]. In the SR model the surface is periodically reconstructed below a certain low critical CO-coverage and this reconstruction is lifted above a second, higher critical CO-coverage. Alternatively the SO model proposes periodic switching between a low-reactivity metallic surface and a high-reactivity oxide surface. Here we present an overview of our recent kinetic Monte Carlo (KMC) simulation studies on the oscillatory kinetics of surface catalyzed CO oxidation. Different modifications of the lattice gas Ziff-Gulari-Barshad (ZGB) model have been utilized or proposed for this purpose. First we present the effect of desorption on the ZGB reactive to poisoned irreversible phase transition in the SR model. Next we discuss our recent research on KMC simulation of the SO model. The ZGB framework is utilized to propose a new model incorporating not only the standard Langmuir-Hinshelwood (LH) mechanism, but also introducing the Mars-van Krevelen (MvK) mechanism for the surface oxide phase [5]. Phase diagrams, which are plots between long time averages of various oscillating quantities against the normalized CO pressure, show two or three transitions depending on the CO coverage critical threshold (CT) value beyond which all adsorbed oxygen atoms are converted to surface oxide.

  13. Ion beam processing of surfaces and interfaces. Modeling and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liedke, Bartosz

    2011-03-24

    Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In

  14. Monte Carlo simulation of spinodal decomposition in a ternary alloy within a three-phases field: comparison to phase transformation of ferrite in duplex stainless steels

    Science.gov (United States)

    Emo, Jonathan; Pareige, Cristelle; Saillet, Sébastien; Domain, Christophe; Pareige, Philippe

    2014-06-01

    This work proposes to model phase transformations occurring in duplex stainless steels using atomistic kinetic Monte Carlo in a ternary model alloy. Kinetics are simulated in the three-phase field of a ternary system. Influence of the precipitation of the third phase on the kinetic of spinodal decomposition between the two other phases is studied in order to understand the synergy between spinodal decomposition and G-phase precipitation which exists in duplex stainless steels. Simulation results are compared to experimental data obtained with atom probe tomography.

  15. Monte Carlo方法在气体动理论中的应用%The Application of Monte Carlo Method in Kinetic Theory of Gases

    Institute of Scientific and Technical Information of China (English)

    张玲芬

    2003-01-01

    Monte Carco方法的随机抽样理论,对物理现象的研究,提供了其它方法不可替代的计算手段,利用它可以方便地进行数值积分计算和计算机模拟.文章介绍了Monte Carlo方法的基本原理和计算步骤,并通过两个具体实例阐明Monte Carlo方法在分子动理论中的应用.

  16. Calculation of Reactor Kinetics Parameters βeff and Λ with Monte Carlo Differential Operator Sampling

    Science.gov (United States)

    Nagaya, Yasunobu

    2014-06-01

    The methods to calculate the kinetics parameters of βeff and Λ with the differential operator sampling have been reviewed. The comparison of the results obtained with the differential operator sampling and iterated fission probability approaches has been performed. It is shown that the differential operator sampling approach gives the same results as the iterated fission probability approach within the statistical uncertainty. In addition, the prediction accuracy of the evaluated nuclear data library JENDL-4.0 for the measured βeff/Λ and βeff values is also examined. It is shown that JENDL-4.0 gives a good prediction except for the uranium-233 systems. The present results imply the need for revisiting the uranium-233 nuclear data evaluation and performing the detailed sensitivity analysis.

  17. Atomistic modeling at experimental strain rates and timescales

    Science.gov (United States)

    Yan, Xin; Cao, Penghui; Tao, Weiwei; Sharma, Pradeep; Park, Harold S.

    2016-12-01

    Modeling physical phenomena with atomistic fidelity and at laboratory timescales is one of the holy grails of computational materials science. Conventional molecular dynamics (MD) simulations enable the elucidation of an astonishing array of phenomena inherent in the mechanical and chemical behavior of materials. However, conventional MD, with our current computational modalities, is incapable of resolving timescales longer than microseconds (at best). In this short review article, we briefly review a recently proposed approach—the so-called autonomous basin climbing (ABC) method—that in certain instances can provide valuable information on slow timescale processes. We provide a general summary of the principles underlying the ABC approach, with emphasis on recent methodological developments enabling the study of mechanically-driven processes at slow (experimental) strain rates and timescales. Specifically, we show that by combining a strong physical understanding of the underlying phenomena, kinetic Monte Carlo, transition state theory and minimum energy pathway methods, the ABC method has been found to be useful in a variety of mechanically-driven problems ranging from the prediction of creep-behavior in metals, constitutive laws for grain boundary sliding, void nucleation rates, diffusion in amorphous materials to protein unfolding. Aside from reviewing the basic ideas underlying this approach, we emphasize some of the key challenges encountered in our own personal research work and suggest future research avenues for exploration.

  18. Atomistic simulations of fracture

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1997-12-31

    Embedded atom interaction potentials are used to simulate the atomistic aspects of the fracture process. Simulations are presented for the behavior of cracks in pure metals and intermetallics, near the Griffith condition. The materials considered include Fe, Cu, Ni as well as Fe, Ni, Co, and Ti aluminides. The work focuses on the comparative study of fracture behavior in the different materials. The role of the atomic relaxation at the crack tip and of lattice trapping phenomena is analyzed.

  19. Atomistic simulations of bicelle mixtures.

    Science.gov (United States)

    Jiang, Yong; Wang, Hao; Kindt, James T

    2010-06-16

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets.

  20. One-dimensional model of interacting-step fluctuations on vicinal surfaces: Analytical formulas and kinetic Monte-Carlo simulations

    Science.gov (United States)

    Patrone, Paul; Einstein, T. L.; Margetis, Dionisios

    2011-03-01

    We study a 1+1D, stochastic, Burton-Cabrera-Frank (BCF) model of interacting steps fluctuating on a vicinal crystal. The step energy accounts for entropic and nearest-neighbor elastic-dipole interactions. Our goal is to formulate and validate a self-consistent mean-field (MF) formalism to approximately solve the system of coupled, nonlinear stochastic differential equations (SDEs) governing fluctuations in surface motion. We derive formulas for the time-dependent terrace width distribution (TWD) and its steady-state limit. By comparison with kinetic Monte-Carlo simulations, we show that our MF formalism improves upon models in which step interactions are linearized. We also indicate how fitting parameters of our steady state MF TWD may be used to determine the mass transport regime and step interaction energy of certain experimental systems. PP and TLE supported by NSF MRSEC under Grant DMR 05-20471 at U. of Maryland; DM supported by NSF under Grant DMS 08-47587.

  1. One-dimensional model of interacting-step fluctuations on vicinal surfaces: Analytical formulas and kinetic Monte Carlo simulations

    Science.gov (United States)

    Patrone, Paul N.; Einstein, T. L.; Margetis, Dionisios

    2010-12-01

    We study analytically and numerically a one-dimensional model of interacting line defects (steps) fluctuating on a vicinal crystal. Our goal is to formulate and validate analytical techniques for approximately solving systems of coupled nonlinear stochastic differential equations (SDEs) governing fluctuations in surface motion. In our analytical approach, the starting point is the Burton-Cabrera-Frank (BCF) model by which step motion is driven by diffusion of adsorbed atoms on terraces and atom attachment-detachment at steps. The step energy accounts for entropic and nearest-neighbor elastic-dipole interactions. By including Gaussian white noise to the equations of motion for terrace widths, we formulate large systems of SDEs under different choices of diffusion coefficients for the noise. We simplify this description via (i) perturbation theory and linearization of the step interactions and, alternatively, (ii) a mean-field (MF) approximation whereby widths of adjacent terraces are replaced by a self-consistent field but nonlinearities in step interactions are retained. We derive simplified formulas for the time-dependent terrace-width distribution (TWD) and its steady-state limit. Our MF analytical predictions for the TWD compare favorably with kinetic Monte Carlo simulations under the addition of a suitably conservative white noise in the BCF equations.

  2. A combined molecular dynamics and kinetic Monte Carlo calculation to study sputter erosion and beam assisted deposition

    CERN Document Server

    Betz, G

    2002-01-01

    To extend the time scale in molecular dynamics (MD) calculations of sputtering and ion assisted deposition we have coupled our MD calculations to a kinetic Monte Carlo (KMC) calculation. In this way we have studied surface erosion of Cu(1 0 0) under 200-600 eV Cu ion bombardment and growth of Cu on Cu(1 0 0) for deposition at thermal energies up to energies of 100 eV per atom. Target temperatures were varied from 100 to 400 K. The coupling of the MD calculation to a KMC calculation allows us to extend our calculations from a few ps, a time scale typical for MD, to times of up to seconds until the next Cu particle will impinge/be deposited on the crystal surface of about 100 nm sup 2 in size. The latter value of 1 s is quite realistic for a typical experimental sputter erosion or deposition experiment. In such a calculation thermal diffusion processes at the surface and annealing of the surface after energetic ion bombardment can be taken into account. To achieve homo-epitaxial growth of a film the results cle...

  3. Kinetic Monte Carlo simulation of nanostructural evolution under post-irradiation annealing in dilute FeMnNi

    Energy Technology Data Exchange (ETDEWEB)

    Chiapetto, M. [SCK-CEN, Nuclear Materials Science Institute, Mol (Belgium); Unite Materiaux et Transformations (UMET), UMR 8207, Universite de Lille 1, ENSCL, Villeneuve d' Ascq (France); Becquart, C.S. [Unite Materiaux et Transformations (UMET), UMR 8207, Universite de Lille 1, ENSCL, Villeneuve d' Ascq (France); Laboratoire commun EDF-CNRS, Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Domain, C. [EDF R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Moret sur Loing (France); Laboratoire commun EDF-CNRS, Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Malerba, L. [SCK-CEN, Nuclear Materials Science Institute, Mol (Belgium)

    2015-01-01

    Post-irradiation annealing experiments are often used to obtain clearer information on the nature of defects produced by irradiation. However, their interpretation is not always straightforward without the support of physical models. We apply here a physically-based set of parameters for object kinetic Monte Carlo (OKMC) simulations of the nanostructural evolution of FeMnNi alloys under irradiation to the simulation of their post-irradiation isochronal annealing, from 290 to 600 C. The model adopts a ''grey alloy'' scheme, i.e. the solute atoms are not introduced explicitly, only their effect on the properties of point-defect clusters is. Namely, it is assumed that both vacancy and SIA clusters are significantly slowed down by the solutes. The slowing down increases with size until the clusters become immobile. Specifically, the slowing down of SIA clusters by Mn and Ni can be justified in terms of the interaction between these atoms and crowdions in Fe. The results of the model compare quantitatively well with post-irradiation isochronal annealing experimental data, providing clear insight into the mechanisms that determine the disappearance or re-arrangement of defects as functions of annealing time and temperature. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  4. Comparison of atomistic and elasticity approaches for carbon diffusion near line defects in {alpha}-iron

    Energy Technology Data Exchange (ETDEWEB)

    Veiga, R.G.A., E-mail: rgaveiga@gmail.com [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Perez, M. [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Becquart, C.S. [Unite Materiaux et Transformations (UMET), Ecole Nationale Superieure de Chimie de Lille, UMR CNRS 8207, Bat. C6, F59655 Villeneuve d' Ascq Cedex (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Clouet, E. [Service de Recherches de Metallurgie Physique, CEA/Saclay, 91191 Gif-sur-Yvette (France); Domain, C. [EDF, Recherche et Developpement, Materiaux et Mecanique des Composants, Les Renardieres, F77250 Moret sur Loing (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France)

    2011-10-15

    Energy barriers for carbon migration in the neighborhood of line defects in body-centered cubic iron have been obtained by atomistic simulations. For this purpose, molecular statics with an Fe-C interatomic potential, based on the embedded atom method, has been employed. Results of these simulations have been compared to the predictions of anisotropic elasticity theory. The agreement is better for a carbon atom sitting on an octahedral site (energy minimum) than one on a tetrahedral site (saddle point). Absolute differences in the energy barriers obtained by the two methods are usually below 5 meV at distances larger than 1.5 nm from a screw dislocation and 2 nm (up to 4 nm in the glide plane) from the edge dislocation. Atomistic kinetic Monte Carlo simulations performed at T = 300 K and additional analysis based on the activation energies obtained by both methods show that they are in good qualitative agreement, despite some important quantitative discrepancies due to the large absolute errors found near the dislocation cores.

  5. Nanostructure evolution under irradiation in FeMnNi alloys: A “grey alloy” object kinetic Monte Carlo model

    Energy Technology Data Exchange (ETDEWEB)

    Chiapetto, M., E-mail: mchiapet@sckcen.be [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, B-2400 Mol (Belgium); Unité Matériaux Et Transformations (UMET), UMR 8207, Université de Lille 1, ENSCL, F-59600 Villeneuve d’Ascq Cedex (France); Malerba, L. [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, B-2400 Mol (Belgium); Becquart, C.S. [Unité Matériaux Et Transformations (UMET), UMR 8207, Université de Lille 1, ENSCL, F-59600 Villeneuve d’Ascq Cedex (France)

    2015-07-15

    This work extends the object kinetic Monte Carlo model for neutron irradiation-induced nanostructure evolution in Fe–C binary alloys developed in [1], introducing the effects of substitutional solutes like Mn and Ni. The objective is to develop a model able to describe the nanostructural evolution of both vacancy and self-interstitial atom (SIA) defect cluster populations in Fe(C)MnNi neutron-irradiated model alloys at the operational temperature of light water reactors (∼300 °C), by simulating specific reference irradiation experiments. To do this, the effects of the substitutional solutes of interest are introduced, under simplifying assumptions, using a “grey alloy” scheme. Mn and Ni solute atoms are not explicitly introduced in the model, which therefore cannot describe their redistribution under irradiation, but their effect is introduced by modifying the parameters that govern the mobility of both SIA and vacancy clusters. In particular, the reduction of the mobility of point-defect clusters as a consequence of the presence of solutes proved to be key to explain the experimentally observed disappearance of detectable defect clusters with increasing solute content. Solute concentration is explicitly taken into account in the model as a variable determining the slowing down of self-interstitial clusters; small vacancy clusters, on the other hand, are assumed to be significantly slowed down by the presence of solutes, while for clusters bigger than 10 vacancies their complete immobility is postulated. The model, which is fully based on physical considerations and only uses a few parameters for calibration, is found to be capable of reproducing the experimental trends in terms of density and size distribution of the irradiation-induced defect populations with dose, as compared to the reference experiment, thereby providing insight into the physical mechanisms that influence the nanostructural evolution undergone by this material during irradiation.

  6. Mo-Bi系丙烯氨氧化催化剂上氨分解反应动力学的Monte Carlo模拟%Monte Carlo Simulation of Kinetics of Ammonia Oxidative Decomposition over the Commercial Propylene Ammoxidation Catalyst (Mo-Bi)

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 詹晓力; 陈丰秋; 阳永荣

    2003-01-01

    Monte Carlo method is applied to investigate the kinetics of ammonia oxidative decomposition overthe commercial propylene ammoxidation catalyst(Mo-Bi). The simulation is quite in agreement with experimentalresults. Monte Carlo simulation proves that the process of ammonia oxidation decomposition is a two-step reaction.

  7. Atomistic Properties of Solids

    CERN Document Server

    Sirdeshmukh, Dinker B; Subhadra, K G

    2011-01-01

    The book deals with atomistic properties of solids which are determined by the crystal structure, interatomic forces and atomic displacements influenced by the effects of temperature, stress and electric fields. The book gives equal importance to experimental details and theory. There are full chapters dedicated to the tensor nature of physical properties, mechanical properties, lattice vibrations, crystal structure determination and ferroelectricity. The other crystalline states like nano-, poly-, liquid- and quasi crystals are discussed. Several new topics like nonlinear optics and the Rietveld method are presented in the book. The book lays emphasis on the role of symmetry in crystal properties. Comprehensiveness is the strength of the book; this allows users at different levels a choice of chapters according to their requirements.

  8. Study of photo-oxidative reactivity of sunscreening agents based on photo-oxidation of uric acid by kinetic Monte Carlo simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moradmand Jalali, Hamed; Bashiri, Hadis, E-mail: hbashiri@kashanu.ac.ir; Rasa, Hossein

    2015-05-01

    In the present study, the mechanism of free radical production by light-reflective agents in sunscreens (TiO{sub 2}, ZnO and ZrO{sub 2}) was obtained by applying kinetic Monte Carlo simulation. The values of the rate constants for each step of the suggested mechanism have been obtained by simulation. The effect of the initial concentration of mineral oxides and uric acid on the rate of uric acid photo-oxidation by irradiation of some sun care agents has been studied. The kinetic Monte Carlo simulation results agree qualitatively with the existing experimental data for the production of free radicals by sun care agents. - Highlights: • The mechanism and kinetics of uric acid photo-oxidation by irradiation of sun care agents has been obtained by simulation. • The mechanism has been used for free radical production of TiO{sub 2} (rutile and anatase), ZnO and ZrO{sub 2}. • The ratios of photo-activity of ZnO to anastase, rutile and ZrO have been obtained. • By doubling the initial concentrations of mineral oxide, the rate of reaction was doubled. • The optimum ratio of initial concentration of mineral oxides to uric acid has been obtained.

  9. Multiscale atomistic simulation of metal-oxygen surface interactions: Methodological development, theoretical investigation, and correlation with experiment

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Judith C. [Univ. of Pittsburgh, Pittsburgh, PA (United States)

    2015-01-09

    The purpose of this grant is to develop the multi-scale theoretical methods to describe the nanoscale oxidation of metal thin films, as the PI (Yang) extensive previous experience in the experimental elucidation of the initial stages of Cu oxidation by primarily in situ transmission electron microscopy methods. Through the use and development of computational tools at varying length (and time) scales, from atomistic quantum mechanical calculation, force field mesoscale simulations, to large scale Kinetic Monte Carlo (KMC) modeling, the fundamental underpinings of the initial stages of Cu oxidation have been elucidated. The development of computational modeling tools allows for accelerated materials discovery. The theoretical tools developed from this program impact a wide range of technologies that depend on surface reactions, including corrosion, catalysis, and nanomaterials fabrication.

  10. Understanding materials behavior from atomistic simulations: Case study of al-containing high entropy alloys and thermally grown aluminum oxide

    Science.gov (United States)

    Yinkai Lei

    Atomistic simulation refers to a set of simulation methods that model the materials on the atomistic scale. These simulation methods are faster and cheaper alternative approaches to investigate thermodynamics and kinetics of materials compared to experiments. In this dissertation, atomistic simulation methods have been used to study the thermodynamic and kinetic properties of two material systems, i.e. the entropy of Al-containing high entropy alloys (HEAs) and the vacancy migration energy of thermally grown aluminum oxide. (Abstract shortened by ProQuest.).

  11. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    Science.gov (United States)

    2014-03-28

    Approved for Public Release; Distribution Unlimited Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic...non peer-reviewed journals: Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration" Report Title In... nanoscience of multifunctional materials: atomistic exploration” PI:Inna Ponomareva We have accomplished the following. 1. We have developed a set of

  12. Validation of a Monte Carlo method using a joint PDF of the composition and an ILDM kinetic model for the prediction of turbulent flames

    Energy Technology Data Exchange (ETDEWEB)

    Zurbach, S.; Garreton, D.; Kanniche, M.

    1997-09-01

    The resolution of the joint probability density function (PDF) of the composition and its application to the calculation of turbulent diffusion flames is presented. The numerical method is based on an Eulerian Monte-Carlo solver coupled with the CFD code Hades; an ILDM kinetic model allows the calculation of the chemical source terms. Two configurations are studied: the Masri-Bilger-Dibble flame and the Delft flame. The first turbulent diffusion flame is close to extinction and is a good test for the prediction of the interactions between the turbulence and the chemicals scales. The second one enables the validation of the prediction of an intermediate species taking a super-equilibrium concentration, the OH radical. (author) 9 refs.

  13. Simulation of nanostructural evolution under irradiation in Fe-9%CrC alloys: An object kinetic Monte Carlo study of the effect of temperature and dose-rate

    Directory of Open Access Journals (Sweden)

    M. Chiapetto

    2016-12-01

    Full Text Available This work explores the effects of both temperature and dose-rate on the nanostructural evolution under irradiation of the Fe-9%CrC alloy, model material for high-Cr ferritic/martensitic steels. Starting from an object kinetic Monte Carlo model validated at 563K, we investigate here the accumulation of radiation damage as a function of temperature and dose-rate, attempting to highlight its connection with low-temperature radiation-induced hardening. The results show that the defect cluster mobility becomes high enough to partially counteract the material hardening process only above ∼290°C, while high fluxes are responsible for higher densities of defects, so that an increase of the hardening process with increasing dose-rates may be expected.

  14. Influence of CH3SiCl3 Consistency on Growth Process of SiC Film by Kinetic Monte Carlo Method

    Institute of Scientific and Technical Information of China (English)

    LIU Cuixia; YANG Yanqing; LUO Xian

    2012-01-01

    CH3SiCl3 (MTS)-H2-Ar system has been applied to prepare SiC film with chemical vapor deposition (CVD) method in this paper.For three facets of SiC film,some significant influence on growth rate,surface roughness,thickness and relative density brought by MTS consistency has been mainly discussed with kinetic monte carlo (KMC) method.The simulation results show that there is a certain scale for mol ratio of H2 to MTS (H2/MTS) with different deposition temperature.When MTS consistency increases,growth rate and surface roughness of three facets all increase,which manifests approximate linearity relationship.Thickness of three facets also increases while increasing trend of three facets thickness is different obviously.Although relative density of three facets all increases,increasing trend shows a little difference with MTS consistency increasing.

  15. Atomic-Scale Kinetic Monte Carlo Simulation of {100}-Oriented Diamond Film Growth in C-H and C-H-Cl Systems by Chemical Vapour Deposition

    Institute of Scientific and Technical Information of China (English)

    安希忠; 张禹; 刘国权; 秦湘阁; 王辅忠; 刘胜新

    2002-01-01

    We simulate the { 100}-oriented diamond film growth of chemical vapour deposition (CVD) under different modelsin C-H and C-H-CI systems in an atomic scale by using the revised kinetic Monte Carlo method. The sirnulationresults show that: (1) the CVD diamond flm growth in the C-H system is suitable for high substrate temperature,and the flm surface roughness is very coarse; (2) the CVD diamond film can grow in the C-H-C1 system eitherat high temperature or at low temperature, and the film quality is outstanding; (3) atomic CI takes ala activerole for the growth of diamond film, especially at low temperatures. The concentration of atomic C1 should becontrolled in a proper range.

  16. Influence of free surfaces on microstructure evolution of radiation damage in Fe from molecular dynamics and object kinetic Monte Carlo calculations

    Energy Technology Data Exchange (ETDEWEB)

    Aliaga, Maria J.; Caturla, Maria J. [Facultad de Ciencias, Department Fisica Aplicada, Fase II, Universidad de Alicante, 03690, Alicante (Spain); Dopico, Ignacio; Martin-Bragado, Ignacio [IMDEA Materials Institute, C/Eric Kandel 2, 28906, Getafe, Madrid (Spain)

    2016-11-15

    The influence of surfaces on the evolution of damage of irradiated Fe is studied using object kinetic Monte Carlo with input from molecular dynamics simulations and ab initio calculations. Two effects are analysed: the influence of traps and the initial distribution of damage in the cascade. These simulations show that for a trap concentration of around 100 appm, there are no significant differences between defect concentrations in bulk and thin films. However, the initial distribution of defects plays an important role not only on total defect concentration but also on defect type, for the model used in this study. Damage produced by a 100 keV Fe ion impinging a Fe thin film. Blue (dark) spheres are self-interstitials, red (light) spheres are vacancies. (copyright 2016 The Authors/Employers. Phys. Status Solidi A published by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. Effects of pressure, temperature and atomic exchanges on phase separation dynamics in Au/Ni(111) surface alloy: Kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Zvejnieks, G. [Institute for Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga (Latvia); Ibenskas, A., E-mail: ibenskas@pfi.lt [Center for Physical Sciences and Technology, Semiconductor Physics Institute, Gostauto 11, LT-01108 Vilnius (Lithuania); Tornau, E.E. [Center for Physical Sciences and Technology, Semiconductor Physics Institute, Gostauto 11, LT-01108 Vilnius (Lithuania)

    2015-11-15

    Instability of the Au/Ni(111) surface alloy is studied in different CO gas pressure, p, and temperature limits using kinetic Monte Carlo simulations. We analyze the reaction front dynamics and formation of Au clusters using the model which takes into account surface adatom pair and three-body interactions, CO adsorption and desorption, catalytic carbonyl formation reaction, Au and Ni adatom diffusion and their concerted exchange. Variation of interaction parameters allows us to identify three possible reaction front propagation limits with different pressure dependencies: (i) slow channel-like flow in agreement with experimental data [1] (step flow rate, R, increases with p), (ii) intermediate regime (weak p–dependence), and (iii) fast homogeneous flow (R decreases with p). We find that only Au–Ni exchange, contrary to both Ni–CO and Au–CO exchanges, significantly reduces the number of screened Ni atoms inside the Au clusters and stimulates the occurrence of Ni-free Au clusters. The size of Au islands depends on both pressure and temperature. At a fixed temperature it decreases with pressure due to an increased step flow rate. In the high temperature limit, despite the step flow rate exponential increase with temperature, the cluster size increases due to an enhanced Au mobility. - Highlights: • Kinetic Monte Carlo study of Au–Ni surface alloy instability to CO pressure and temperature. • Three reaction front propagation regimes. • In channel-like regime, the step flow rate increases with CO pressure as in experiment. • Ni-free Au islands are obtained when Au-Ni adatom exchange mechanism is considered. • The size of Au islands decreases with pressure and increases with temperature.

  18. Calculation of Reactor Kinetic Parameters with Monte Carlo Method%反应堆动态参数的蒙特卡罗计算研究

    Institute of Scientific and Technical Information of China (English)

    王冠博; 刘汉刚; 王侃; 刘永康; 曾和荣; 杨鑫

    2012-01-01

    Basic conceptions of kinetic parameters, including effective delayed neutron fraction (βeff), effective neutron generation time (Aeff) and a eigenvalue, and Monte Carlo calculation methods for these values are systematically introduced in this paper. Βeff is obtained with a "Prompt Method". Perturbation method is chosen to obtain Aeff. And then a eigenvalue is obtained by two ways, (I) prompt neutron density attenuation, in other words "direct simulation of time evolvement", (ii) indirect method using the result of kp and neutron generation time. Linear fitting is used to get the critical ac eigenvalues which match well with experimental ones. And uncertainties of kinetic parameters with different methods using Monte Carlo method are also analyzed.%介绍缓发中子有效份额(βeff)、有效中子代时间(∧eff)和α本征值的概念及其蒙特卡罗程序计算方法.采用Prompt Method方法计算得到βeff;微扰法得到∧eff;采用瞬发中子密度衰减直接拟合法和间接求解法得到α本征值;将各种反应性状态下的α拟合得到临界α本征值,并与实验测量的α,值进行比对,结果符合很好;并对动态参数蒙特卡罗程序计算的各种方法进行不确定度分析.

  19. Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Wijesinghe, S; Hornung, R; Garcia, A; Hadjiconstantinou, N

    2004-04-15

    We present an adaptive mesh and algorithmic refinement (AMAR) scheme for modeling multi-scale hydrodynamics. The AMAR approach extends standard conservative adaptive mesh refinement (AMR) algorithms by providing a robust flux-based method for coupling an atomistic fluid representation to a continuum model. The atomistic model is applied locally in regions where the continuum description is invalid or inaccurate, such as near strong flow gradients and at fluid interfaces, or when the continuum grid is refined to the molecular scale. The need for such ''hybrid'' methods arises from the fact that hydrodynamics modeled by continuum representations are often under-resolved or inaccurate while solutions generated using molecular resolution globally are not feasible. In the implementation described herein, Direct Simulation Monte Carlo (DSMC) provides an atomistic description of the flow and the compressible two-fluid Euler equations serve as our continuum-scale model. The AMR methodology provides local grid refinement while the algorithm refinement feature allows the transition to DSMC where needed. The continuum and atomistic representations are coupled by matching fluxes at the continuum-atomistic interfaces and by proper averaging and interpolation of data between scales. Our AMAR application code is implemented in C++ and is built upon the SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) framework developed at Lawrence Livermore National Laboratory. SAMRAI provides the parallel adaptive gridding algorithm and enables the coupling between the continuum and atomistic methods.

  20. Material fields in atomistics as pull-backs of spatial distributions

    Science.gov (United States)

    Chandra Admal, Nikhil; Tadmor, Ellad B.

    2016-04-01

    The various fields defined in continuum mechanics have both a material and a spatial description that are related through the deformation mapping. In contrast, continuum fields defined for atomistic systems using the Irving-Kirkwood or Murdoch-Hardy procedures correspond to a spatial description. It is uncommon to define atomistic fields in the reference configuration due to the lack of a unique definition for the deformation mapping in atomistic systems. In this paper, we construct referential atomistic distributions as pull-backs of the spatial distributions obtained in the Murdoch-Hardy procedure with respect to a postulated deformation mapping that tracks particles. We then show that some of these referential distributions are independent of the choice of the deformation mapping and only depend on the reference and current configuration of particles. Therefore, the fields obtained from these distributions can be calculated without explicitly constructing a deformation map, and by construction they satisfy the balance equations. In particular, we obtain definitions for the first and second atomistic Piola-Kirchhoff stress tensors. We demonstrate the validity of these definitions through a numerical example involving finite deformation of a slab containing a notch under tension. An interesting feature of the atomistic first Piola-Kirchhoff stress tensor is the absence of a kinetic part, which in the atomistic Cauchy stress tensor accounts for thermal fluctuations. We show that this effect is implicitly included in the atomistic first Piola-Kirchhoff stress tensor through the motion of the particles. An open source program to compute the atomistic Cauchy and first Piola-Kirchhoff stress fields called MDStressLab is available online at

  1. A study on the morphology and catalytic activity of gold nanoparticles by the kinetic Monte Carlo simulation

    Science.gov (United States)

    He, Xiang; Chen, Zhao-Xu

    2016-05-01

    We studied the thermal-stability of supported Au nanoparticles on the substrates of different binding strength to gold by Monte Carlo simulations. It has been revealed that the stable Au morphology is determined by the temperature and the binding strength. When heated on the strongly-binding substrates, the Au nanoparticles would wet the substrate completely and form monolayer. The stable Au layered structure of few layers can be formed by the incomplete wetting of clusters on the intermediate-binding substrates. The simulation results are in good agreement with pertinent experimental and theoretical results. Based on the simulation results and experimental observations, we find the strong linkage between the top edge sites and the activity TOF of low-temperature CO oxidation. We conclude that the top edges sites of Au layered structures are possible reactive sites. This study may provide new perspective for controlling morphology and understanding catalytic activity of supported metallic clusters.

  2. Atomistic Simulations of Bicelle Mixtures

    OpenAIRE

    Jiang, Yong; Wang, Hao; Kindt, James T.

    2010-01-01

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironmen...

  3. Kinetic Monte Carlo simulations of one-dimensional and two-dimensional traffic flows: Comparison of two look-ahead rules

    Science.gov (United States)

    Sun, Yi; Timofeyev, Ilya

    2014-05-01

    We employ an efficient list-based kinetic Monte Carlo (KMC) method to study traffic flow models on one-dimensional (1D) and two-dimensional (2D) lattices based on the exclusion principle and Arrhenius microscopic dynamics. This model implements stochastic rules for cars' movements based on the configuration of the traffic ahead of each car. In particular, we compare two different look-ahead rules: one is based on the distance from the car under consideration to the car in front of it, and the other one is based on the density of cars ahead. The 1D numerical results of these two rules suggest different coarse-grained macroscopic limits in the form of integro-differential Burgers equations. The 2D results of both rules exhibit a sharp phase transition from freely flowing to fully jammed, as a function of the initial density of cars. However, the look-ahead rule based on the density of the traffic produces more realistic results. The KMC simulations reported in this paper are compared with those from other well-known traffic flow models and the corresponding empirical results from real traffic.

  4. Organic Field-Effect Transistors: A 3D Kinetic Monte Carlo Simulation of the Current Characteristics in Micrometer-Sized Devices

    KAUST Repository

    Li, Haoyuan

    2017-01-16

    The electrical properties of organic field-effect transistors (OFETs) are usually characterized by applying models initially developed for inorganic-based devices, which often implies the use of approximations that might be inappropriate for organic semiconductors. These approximations have brought limitations to the understanding of the device physics associated with organic materials. A strategy to overcome this issue is to establish straightforward connections between the macroscopic current characteristics and microscopic charge transport in OFETs. Here, a 3D kinetic Monte Carlo model is developed that goes beyond both the conventional assumption of zero channel thickness and the gradual channel approximation to simulate carrier transport and current. Using parallel computing and a new algorithm that significantly improves the evaluation of electric potential within the device, this methodology allows the simulation of micrometer-sized OFETs. The current characteristics of representative OFET devices are well reproduced, which provides insight into the validity of the gradual channel approximation in the case of OFETs, the impact of the channel thickness, and the nature of microscopic charge transport.

  5. Atomistic Simulations of Nanotube Fracture

    CERN Document Server

    Belytschko, T; Schatz, G; Ruoff, R S

    2002-01-01

    The fracture of carbon nanotubes is studied by atomistic simulations. The fracture behavior is found to be almost independent of the separation energy and to depend primarily on the inflection point in the interatomic potential. The rangle of fracture strians compares well with experimental results, but predicted range of fracture stresses is marketly higher than observed. Various plausible small-scale defects do not suffice to bring the failure stresses into agreement with available experimental results. As in the experiments, the fracture of carbon nanotubes is predicted to be brittle. The results show moderate dependence of fracture strength on chirality.

  6. Atomistic properties of γ uranium.

    Science.gov (United States)

    Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

    2012-02-22

    The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

  7. Kinetic Monte Carlo simulation of the efficiency roll-off, emission color, and degradation of organic light-emitting diodes (Presentation Recording)

    Science.gov (United States)

    Coehoorn, Reinder; van Eersel, Harm; Bobbert, Peter A.; Janssen, Rene A. J.

    2015-10-01

    The performance of Organic Light Emitting Diodes (OLEDs) is determined by a complex interplay of the charge transport and excitonic processes in the active layer stack. We have developed a three-dimensional kinetic Monte Carlo (kMC) OLED simulation method which includes all these processes in an integral manner. The method employs a physically transparent mechanistic approach, and is based on measurable parameters. All processes can be followed with molecular-scale spatial resolution and with sub-nanosecond time resolution, for any layer structure and any mixture of materials. In the talk, applications to the efficiency roll-off, emission color and lifetime of white and monochrome phosphorescent OLEDs [1,2] are demonstrated, and a comparison with experimental results is given. The simulations show to which extent the triplet-polaron quenching (TPQ) and triplet-triplet-annihilation (TTA) contribute to the roll-off, and how the microscopic parameters describing these processes can be deduced properly from dedicated experiments. Degradation is treated as a result of the (accelerated) conversion of emitter molecules to non-emissive sites upon a triplet-polaron quenching (TPQ) process. The degradation rate, and hence the device lifetime, is shown to depend on the emitter concentration and on the precise type of TPQ process. Results for both single-doped and co-doped OLEDs are presented, revealing that the kMC simulations enable efficient simulation-assisted layer stack development. [1] H. van Eersel et al., Appl. Phys. Lett. 105, 143303 (2014). [2] R. Coehoorn et al., Adv. Funct. Mater. (2015), publ. online (DOI: 10.1002/adfm.201402532)

  8. Evaluation of Interindividual Human Variation in Bioactivation and DNA Adduct Formation of Estragole in Liver Predicted by Physiologically Based Kinetic/Dynamic and Monte Carlo Modeling.

    Science.gov (United States)

    Punt, Ans; Paini, Alicia; Spenkelink, Albertus; Scholz, Gabriele; Schilter, Benoit; van Bladeren, Peter J; Rietjens, Ivonne M C M

    2016-04-18

    Estragole is a known hepatocarcinogen in rodents at high doses following metabolic conversion to the DNA-reactive metabolite 1'-sulfooxyestragole. The aim of the present study was to model possible levels of DNA adduct formation in (individual) humans upon exposure to estragole. This was done by extending a previously defined PBK model for estragole in humans to include (i) new data on interindividual variation in the kinetics for the major PBK model parameters influencing the formation of 1'-sulfooxyestragole, (ii) an equation describing the relationship between 1'-sulfooxyestragole and DNA adduct formation, (iii) Monte Carlo modeling to simulate interindividual human variation in DNA adduct formation in the population, and (iv) a comparison of the predictions made to human data on DNA adduct formation for the related alkenylbenzene methyleugenol. Adequate model predictions could be made, with the predicted DNA adduct levels at the estimated daily intake of estragole of 0.01 mg/kg bw ranging between 1.6 and 8.8 adducts in 10(8) nucleotides (nts) (50th and 99th percentiles, respectively). This is somewhat lower than values reported in the literature for the related alkenylbenzene methyleugenol in surgical human liver samples. The predicted levels seem to be below DNA adduct levels that are linked with tumor formation by alkenylbenzenes in rodents, which were estimated to amount to 188-500 adducts per 10(8) nts at the BMD10 values of estragole and methyleugenol. Although this does not seem to point to a significant health concern for human dietary exposure, drawing firm conclusions may have to await further validation of the model's predictions.

  9. Atomistic stimulation of defective oxides

    CERN Document Server

    Minervini, L

    2000-01-01

    defect processes. The predominant intrinsic disorder reaction and the mechanism by which excess oxygen is accommodated are established. Furthermore, the most favourable migration mechanism and pathway for oxygen ions is predicted. Chapters 7 and 8 investigate pyrochlore oxides. These materials are candidates for solid oxide fuel cell components and as actinide host phases. Such applications require a detailed understanding of the defect processes. The defect energies, displayed as contour maps, are able to account for structure stability and, given an appropriate partial charge potential model, to accurately determine the oxygen positional parameter. In particular, the dependence of the positional parameter on intrinsic disorder is predicted. It is demonstrated, by radiation damage experiments, that these results are able to predict the radiation performance of pyrochlore oxides. Atomistic simulation calculations based on energy minimization techniques and classical pair potentials are used to study several i...

  10. Atomistic simulation of static magnetic properties of bit patterned media

    Science.gov (United States)

    Arbeláez-Echeverri, O. D.; Agudelo-Giraldo, J. D.; Restrepo-Parra, E.

    2016-09-01

    In this work we present a new design of Co based bit pattern media with out-of-plane uni-axial anisotropy induced by interface effects. Our model features the inclusion of magnetic impurities in the non-magnetic matrix. After the material model was refined during three iterations using Monte Carlo simulations, further simulations were performed using an atomistic integrator of Landau-Lifshitz-Gilbert equation with Langevin dynamics to study the behavior of the system paying special attention to the super-paramagnetic limit. Our model system exhibits three magnetic phase transitions, one due to the magnetically doped matrix material and the weak magnetic interaction between the nano-structures in the system. The different magnetic phases of the system as well as the features of its phase diagram are explained.

  11. Atomistic simulations of dislocation processes in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Jacobsen, K.W.

    2002-01-01

    We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example, the sta......We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example...

  12. Shape evolution of nanostructures by thermal and ion beam processing. Modeling and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Roentzsch, L.

    2007-07-01

    Single-crystalline nanostructures often exhibit gradients of surface (and/or interface) curvature that emerge from fabrication and growth processes or from thermal fluctuations. Thus, the system-inherent capillary force can initiate morphological transformations during further processing steps or during operation at elevated temperature. Therefore and because of the ongoing miniaturization of functional structures which causes a general rise in surface-to-volume ratios, solid-state capillary phenomena will become increasingly important: On the one hand diffusion-mediated capillary processes can be of practical use in view of non-conventional nanostructure fabrication methods based on self-organization mechanisms, on the other hand they can destroy the integrity of nanostructures which can go along with the failure of functionality. Additionally, capillarity-induced shape transformations are effected and can thereby be controlled by applied fields and forces (guided or driven evolution). With these prospects and challenges at hand, formation and shape transformation of single-crystalline nanostructures due to the system-inherent capillary force in combination with external fields or forces are investigated in the frame of this dissertation by means of atomistic computer simulations. For the exploration (search, description, and prediction) of reaction pathways of nanostructure shape transformations, kinetic Monte Carlo (KMC) simulations are the method of choice. Since the employed KMC code is founded on a cellular automaton principle, the spatio-temporal development of lattice-based N-particle systems (N up to several million) can be followed for time spans of several orders of magnitude, while considering local phenomena due to atomic-scale effects like diffusion, nucleation, dissociation, or ballistic displacements. In this work, the main emphasis is put on nanostructures which have a cylindrical geometry, for example, nanowires (NWs), nanorods, nanotubes etc

  13. Atomistic modeling of dropwise condensation

    Science.gov (United States)

    Sikarwar, B. S.; Singh, P. L.; Muralidhar, K.; Khandekar, S.

    2016-05-01

    The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smaller sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.

  14. Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

    OpenAIRE

    Lipp, Vladimir

    2015-01-01

    In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First...

  15. Atomistic computer simulations a practical guide

    CERN Document Server

    Brazdova, Veronika

    2013-01-01

    Many books explain the theory of atomistic computer simulations; this book teaches you how to run them This introductory ""how to"" title enables readers to understand, plan, run, and analyze their own independent atomistic simulations, and decide which method to use and which questions to ask in their research project. It is written in a clear and precise language, focusing on a thorough understanding of the concepts behind the equations and how these are used in the simulations. As a result, readers will learn how to design the computational model and which parameters o

  16. Atomistic Processes of Catalyst Degradation

    Energy Technology Data Exchange (ETDEWEB)

    None

    2004-11-27

    The purpose of this cooperative research and development agreement (CRADA) between Sasol North America, Inc., and the oak Ridge National Laboratory (ORNL) was to improve the stability of alumina-based industrial catalysts through the combination of aberration-corrected scanning transmission electron microscopy (STEM) at ORNL and innovative sample preparation techniques at Sasol. Outstanding progress has been made in task 1, 'Atomistic processes of La stabilization'. STEM investigations provided structural information with single-atom precision, showing the lattice location of La dopant atoms, thus enabling first-principles calculations of binding energies, which were performed in collaboration with Vanderbilt University. The stabilization mechanism turns out to be entirely due to a particularly strong binding energy of the La tom to the {gamma}-alumina surface. The large size of the La atom precludes incorporation of La into the bulk alumina and also strains the surface, thus preventing any clustering of La atoms. Thus highly disperse distribution is achieved and confirmed by STEM images. la also affects relative stability of the exposed surfaces of {gamma}-alumina, making the 100 surface more stable for the doped case, unlike the 110 surface for pure {gamma}-alumina. From the first-principles calculations, they can estimate the increase in transition temperature for the 3% loading of La used commercially, and it is in excellent agreement with experiment. This task was further pursued aiming to generate useable recommendations for the optimization of the preparation techniques for La-doped aluminas. The effort was primarily concentrated on the connection between the boehmitre-{gamma}-Al{sub 2}O{sub 3} phase transition (i.e. catalyst preparation) and the resulting dispersion of La on the {gamma}-Al{sub 2}O{sub 3} surface. It was determined that the La distribution on boehmite was non-uniform and different from that on the {gamma}-Al{sub 2}O{sub 3} and thus

  17. Monte Carlo Simulation to relate primary and final fragments mass and kinetic energy distribution from low energy fission of $^{234}U$

    CERN Document Server

    Montoya, M; Lobato, I

    2008-01-01

    The kinetic energy distribution as a function of mass of final fragments (m) from low energy fission of $^{234}U$, measured with the Lohengrin spectrometer by Belhafaf et al. presents a peak around m=108 and another around m = 122. The authors attribute the first peak to the evaporation of a large number of neutrons around the corresponding mass number; and the second peak to the distribution of the primary fragment kinetic energy. Nevertheless, the theoretical calculations related to primary distribution made by Faust et al. do not result in a peak around m = 122. In order to clarify this apparent controversy, we have made a numerical experiment in which the masses and the kinetic energy of final fragments are calculated, assuming an initial distribution of the kinetic energy without peaks on the standard deviation as function of fragment mass. As a result we obtain a pronounced peak on the standard deviation of the kinetic energy distribution around m = 109, a depletion from m = 121 to m = 129, and an small...

  18. Prediction of La0.6Sr0.4Co0.2Fe0.8O3 cathode microstructures during sintering: Kinetic Monte Carlo (KMC) simulations calibrated by artificial neural networks

    Science.gov (United States)

    Yan, Zilin; Kim, Yongtae; Hara, Shotaro; Shikazono, Naoki

    2017-04-01

    The Potts Kinetic Monte Carlo (KMC) model, proven to be a robust tool to study all stages of sintering process, is an ideal tool to analyze the microstructure evolution of electrodes in solid oxide fuel cells (SOFCs). Due to the nature of this model, the input parameters of KMC simulations such as simulation temperatures and attempt frequencies are difficult to identify. We propose a rigorous and efficient approach to facilitate the input parameter calibration process using artificial neural networks (ANNs). The trained ANN reduces drastically the number of trial-and-error of KMC simulations. The KMC simulation using the calibrated input parameters predicts the microstructures of a La0.6Sr0.4Co0.2Fe0.8O3 cathode material during sintering, showing both qualitative and quantitative congruence with real 3D microstructures obtained by focused ion beam scanning electron microscopy (FIB-SEM) reconstruction.

  19. Atomistic modeling of H absorption in Pd nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Ruda, M., E-mail: ruda@cab.cnea.gov.a [Centro Atomico Bariloche, 8400 Bariloche (Argentina); Centro Regional Universitario Bariloche, U.N. Comahue (Argentina); Crespo, E.A., E-mail: crespo@uncoma.edu.a [Depto. de Fisica, Fac. de Ingenieria, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquen (Argentina); Debiaggi, S. Ramos de, E-mail: ramos@uncoma.edu.a [Depto. de Fisica, Fac. de Ingenieria, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquen (Argentina); CONICET (Argentina)

    2010-04-16

    Size affects the properties of absorption of H in Palladium nanoparticles. Because of their higher proportion of surface atoms compared to the bulk, the pressure-composition (P-C) isotherms of the nanoparticles are modified. We performed atomistic simulations for different-sized Pd nanoparticles and for the bulk at different H concentrations using the Monte Carlo technique in the TP{mu}N ensemble to calculate the P-C isotherms. The Pd-H interatomic potentials are of the Embedded Atom (EAM) type and have been recently developed by Zhou et al. . From the related van't Hoff equation we obtained |{Delta}H{sup o}| = (28 {+-} 7) kJ/0.5 mol of H{sub 2} and |{Delta}S{sup o}| = (71 {+-} 19) J/0.5 mol of H{sub 2}.K for the PdH formation in the bulk. For Pd nanoparticles previous simulations results based on a different set of EAM potentials showed that H was absorbed primarily in the surface before diffusing into the inside of small Pd clusters . Considering the better performance of Zhou's potentials for the bulk, in this work we analyzed the evolution of the equilibrium microstructure of Pd nanoparticles as a function of their size and H concentration. Our simulations predict enhanced hydrogen solubilities and vanishing plateaux when compared to the bulk and that H is absorbed in the subsurface of the nanoparticles.

  20. Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

    Science.gov (United States)

    Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean-François; Brommer, Peter; Mousseau, Normand

    2015-06-01

    We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion paths and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. This study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.

  1. Atomistic deformation mechanisms in twinned copper nanospheres.

    Science.gov (United States)

    Bian, Jianjun; Niu, Xinrui; Zhang, Hao; Wang, Gangfeng

    2014-01-01

    In the present study, we perform molecular dynamic simulations to investigate the compression response and atomistic deformation mechanisms of twinned nanospheres. The relationship between load and compression depth is calculated for various twin spacing and loading directions. Then, the overall elastic properties and the underlying plastic deformation mechanisms are illuminated. Twin boundaries (TBs) act as obstacles to dislocation motion and lead to strengthening. As the loading direction varies, the plastic deformation transfers from dislocations intersecting with TBs, slipping parallel to TBs, and then to being restrained by TBs. The strengthening of TBs depends strongly on the twin spacing.

  2. Atomistic Mechanisms of Fatigue in Nanocrystalline Metals

    Science.gov (United States)

    Farkas, D.; Willemann, M.; Hyde, B.

    2005-04-01

    We investigate the mechanisms of fatigue behavior in nanocrystalline metals at the atomic scale using empirical force laws and molecular level simulations. A combination of molecular statics and molecular dynamics was used to deal with the time scale limitations of molecular dynamics. We show that the main atomistic mechanism of fatigue crack propagation in these materials is the formation of nanovoids ahead of the main crack. The results obtained for crack advance as a function of stress intensity amplitude are consistent with experimental studies and a Paris law exponent of about 2.

  3. Dislocation climb models from atomistic scheme to dislocation dynamics

    Science.gov (United States)

    Niu, Xiaohua; Luo, Tao; Lu, Jianfeng; Xiang, Yang

    2017-02-01

    We develop a mesoscopic dislocation dynamics model for vacancy-assisted dislocation climb by upscalings from a stochastic model on the atomistic scale. Our models incorporate microscopic mechanisms of (i) bulk diffusion of vacancies, (ii) vacancy exchange dynamics between bulk and dislocation core, (iii) vacancy pipe diffusion along the dislocation core, and (iv) vacancy attachment-detachment kinetics at jogs leading to the motion of jogs. Our mesoscopic model consists of the vacancy bulk diffusion equation and a dislocation climb velocity formula. The effects of these microscopic mechanisms are incorporated by a Robin boundary condition near the dislocations for the bulk diffusion equation and a new contribution in the dislocation climb velocity due to vacancy pipe diffusion driven by the stress variation along the dislocation. Our climb formulation is able to quantitatively describe the translation of prismatic loops at low temperatures when the bulk diffusion is negligible. Using this new formulation, we derive analytical formulas for the climb velocity of a straight edge dislocation and a prismatic circular loop. Our dislocation climb formulation can be implemented in dislocation dynamics simulations to incorporate all the above four microscopic mechanisms of dislocation climb.

  4. Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

    Energy Technology Data Exchange (ETDEWEB)

    Ogawa, Hiroshi, E-mail: h.ogawa@aist.go.jp

    2015-10-05

    Highlights: • Hydrogen–dislocation interaction was simulated by molecular dynamics method. • Different distribution of H atoms were observed at edge and screw dislocation. • Planner distribution of hydrogen may be caused by partialized edge dislocation. • Hydrogen diffusivity was reduced in both edge and screw dislocation models. • Pipe diffusion was observed for edge dislocation but not for screw dislocation. - Abstract: Kinetics of interstitial hydrogen atoms near dislocation cores were analyzed by atomistic simulation. Classical molecular dynamics method was applied to model structures of edge and screw dislocations in α-phase vanadium hydride. Simulation showed that hydrogen atoms aggregate near dislocation cores. The spatial distribution of hydrogen has a planner shape at edge dislocation due to dislocation partialization, and a cylindrical shape at screw dislocation. Simulated self-diffusion coefficients of hydrogen atoms in dislocation models were a half- to one-order lower than that of dislocation-free model. Arrhenius plot of self-diffusivity showed slightly different activation energies for edge and screw dislocations. Directional dependency of hydrogen diffusion near dislocation showed high and low diffusivity along edge and screw dislocation lines, respectively, hence so called ‘pipe diffusion’ possibly occur at edge dislocation but does not at screw dislocation.

  5. Bridging Atomistic/Continuum Scales in Solids with Moving Dislocations

    Institute of Scientific and Technical Information of China (English)

    TANG Shao-Qiang; LIU Wing K.; KARPOV Eduard G.; HOU Thomas Y.

    2007-01-01

    @@ We propose a multiscale method for simulating solids with moving dislocations. Away from atomistic subdomains where the atomistic dynamics are fully resolved, a dislocation is represented by a localized jump profile, superposed on a defect-free field. We assign a thin relay zone around an atomistic subdomain to detect the dislocation profile and its propagation speed at a selected relay time. The detection technique utilizes a lattice time history integral treatment. After the relay, an atomistic computation is performed only for the defect-free field. The method allows one to effectively absorb the fine scale fluctuations and the dynamic dislocations at the interface between the atomistic and continuum domains. In the surrounding region, a coarse grid computation is adequate.

  6. Atomistic simulations of nanoscale electrokinetic transport

    Science.gov (United States)

    Liu, Jin; Wang, Moran; Chen, Shiyi; Robbins, Mark

    2011-11-01

    An efficient and accurate algorithm for atomistic simulations of nanoscale electrokinetic transport will be described. The long-range interactions between charged molecules are treated using the Particle-Particle Particle-Mesh method and the Poisson equation for the electric potential is solved using an efficient multi-grid method in physical space. Using this method, we investigate two important applications in electrokinetic transport: electroosmotic flow in rough channels and electowetting on dielectric (EWOD). Simulations of electroosmotic and pressure driven flow in exactly the same geometries show that surface roughness has a much more pronounced effect on electroosmotic flow. Analysis of local quantities shows that this is because the driving force in electroosmotic flow is localized near the wall where the charge density is high. In atomistic simulations of EWOD, we find the contact angle follows the continuum theory at low voltages and always saturates at high voltages. Based on our results, a new mechanism for saturation is identified and possible techniques for controlling saturation are proposed. This work is supported by the National Science Foundation under Grant No. CMMI 0709187.

  7. Scalable Atomistic Simulation Algorithms for Materials Research

    Directory of Open Access Journals (Sweden)

    Aiichiro Nakano

    2002-01-01

    Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

  8. Study of the diffusion of points defects in crystalline silicon using the kinetic ART method

    Science.gov (United States)

    Trochet, Mickael; Brommer, Peter; Beland, Laurent-Karim; Joly, Jean-Francois; Mousseau, Normand

    2013-03-01

    Because of the long-time scale involved, the activated diffusion of point defects is often studied in standard molecular dynamics at high temperatures only, making it more difficult to characterize complex diffusion mechanisms. Here, we turn to the study of point defect diffusion in crystalline silicon using kinetic ART (kART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building based on the activation-relaxation technique (ART nouveau). By generating catalogs of diffusion mechanisms and fully incorporating elastic and off-lattice effects, kART is a unique tool for characterizing this problem. More precisely, using kART with the standard Stillinger-Weber potential we consider the evolution of crystalline cells with 1 to 4 vacancies and 1 to 4 interstitials at various temperatures and to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics in addition to identifying special configurations such as a 2-interstitial super-diffuser.

  9. An atomistic vision of the Mass Action Law: Prediction of carbon/oxygen defects in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Brenet, G.; Timerkaeva, D.; Caliste, D.; Pochet, P. [CEA, INAC-SP2M, Atomistic Simulation Laboratory, F-38000 Grenoble (France); Univ. Grenoble Alpes, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Sgourou, E. N.; Londos, C. A. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece)

    2015-09-28

    We introduce an atomistic description of the kinetic Mass Action Law to predict concentrations of defects and complexes. We demonstrate in this paper that this approach accurately predicts carbon/oxygen related defect concentrations in silicon upon annealing. The model requires binding and migration energies of the impurities and complexes, here obtained from density functional theory (DFT) calculations. Vacancy-oxygen complex kinetics are studied as a model system during both isochronal and isothermal annealing. Results are in good agreement with experimental data, confirming the success of the methodology. More importantly, it gives access to the sequence of chain reactions by which oxygen and carbon related complexes are created in silicon. Beside the case of silicon, the understanding of such intricate reactions is a key to develop point defect engineering strategies to control defects and thus semiconductors properties.

  10. Kinetics of niobium carbide precipitation in ferrite; Cinetiques de precipitation du carbure de niobium dans la ferrite

    Energy Technology Data Exchange (ETDEWEB)

    Gendt, D

    2001-07-01

    The aim of this study is to develop a NbC precipitation modelling in ferrite. This theoretical study is motivated by the fact it considers a ternary system and focus on the concurrence of two different diffusion mechanisms. An experimental study with TEP, SANS and Vickers micro-hardening measurements allows a description of the NbC precipitation kinetics. The mean radius of the precipitates is characterized by TEM observations. To focus on the nucleation stage, we use the Tomographic Atom Probe that analyses, at an atomistic scale, the position of the solute atoms in the matrix. A first model based on the classical nucleation theory and the diffusion-limited growth describes the precipitation of spherical precipitates. To solve the set of equations, we use a numerical algorithm that furnishes an evaluation of the precipitated fraction, the mean radius and the whole size distribution of the particles. The parameters that are the interface energy, the solubility product and the diffusion coefficients are fitted with the data available in the literature and our experimental results. It allows a satisfactory agreement as regards to the simplicity of the model. Monte Carlo simulations are used to describe the evolution of a ternary alloy Fe-Nb-C on a cubic centred rigid lattice with vacancy and interstitial mechanisms. This is realized with an atomistic description of the atoms jumps and their related frequencies. The model parameters are fitted with phase diagrams and diffusion coefficients. For the sake of simplicity, we consider that the precipitation of NbC is totally coherent and we neglect any elastic strain effect. We can observe different kinetic paths: for low supersaturations, we find an expected precipitation of NbC but for higher supersaturations, the very fast diffusivity of carbon atoms conducts to the nucleation of iron carbide particles. We establish that the occurrence of this second phenomenon depends on the vacancy arrival kinetics and can be related

  11. Atomistic and continuums modeling of cluster migration and coagulation in precipitation reactions.

    Science.gov (United States)

    Warczok, Piotr; Ženíšek, Jaroslav; Kozeschnik, Ernst

    2012-07-01

    The influence of vacancy preference towards one of the constituents in a binary system on the formation of precipitates was investigated by atomistic and continuums modeling techniques. In case of vacancy preference towards the solute atoms, we find that the mobility of individual clusters as well as entire atom clusters is significantly altered compared to the case of vacancy preference towards the solvent atoms. The increased cluster mobility leads to pronounced cluster collisions, providing a precipitate growth and coarsening mechanism competitive to that of pure solute evaporation and adsorption considered in conventional diffusional growth and Ostwald ripening. A modification of a numerical Kampmann-Wagner type continuum model for precipitate growth is proposed, which incorporates the influence of both mechanisms. The prognoses of the modified model are validated against the growth laws obtained with lattice Monte Carlo simulations and a growth simulation considering solely the coalescence mechanism.

  12. Cell-veto Monte Carlo algorithm for long-range systems

    Science.gov (United States)

    Kapfer, Sebastian C.; Krauth, Werner

    2016-09-01

    We present a rigorous efficient event-chain Monte Carlo algorithm for long-range interacting particle systems. Using a cell-veto scheme within the factorized Metropolis algorithm, we compute each single-particle move with a fixed number of operations. For slowly decaying potentials such as Coulomb interactions, screening line charges allow us to take into account periodic boundary conditions. We discuss the performance of the cell-veto Monte Carlo algorithm for general inverse-power-law potentials, and illustrate how it provides a new outlook on one of the prominent bottlenecks in large-scale atomistic Monte Carlo simulations.

  13. Atomistic simulation of damage accumulation and amorphization in Ge

    Energy Technology Data Exchange (ETDEWEB)

    Gomez-Selles, Jose L., E-mail: joseluis.gomezselles@imdea.org; Martin-Bragado, Ignacio [IMDEA Materials Institute, Eric Kandel 2, 28906 Getafe, Madrid (Spain); Claverie, Alain [CEMES/CNRS, 29 rue J. Marvig, 31055 Toulouse Cedex (France); Sklenard, Benoit [CEA, LETI, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Benistant, Francis [GLOBALFOUNDRIES Singapore Pte Ltd., 60 Woodlands Industrial Park D Street 2, Singapore 738406 (Singapore)

    2015-02-07

    Damage accumulation and amorphization mechanisms by means of ion implantation in Ge are studied using Kinetic Monte Carlo and Binary Collision Approximation techniques. Such mechanisms are investigated through different stages of damage accumulation taking place in the implantation process: from point defect generation and cluster formation up to full amorphization of Ge layers. We propose a damage concentration amorphization threshold for Ge of ∼1.3 × 10{sup 22} cm{sup −3} which is independent on the implantation conditions. Recombination energy barriers depending on amorphous pocket sizes are provided. This leads to an explanation of the reported distinct behavior of the damage generated by different ions. We have also observed that the dissolution of clusters plays an important role for relatively high temperatures and fluences. The model is able to explain and predict different damage generation regimes, amount of generated damage, and extension of amorphous layers in Ge for different ions and implantation conditions.

  14. NiTi superelasticity via atomistic simulations

    Science.gov (United States)

    Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin

    2015-12-01

    The NiTi shape memory alloys (SMAs) are promising candidates for the next-generation multifunctional materials. These materials are superelastic i.e. they can fully recover their original shape even after fairly large inelastic deformations once the mechanical forces are removed. The superelasticity reportedly stems from atomic scale crystal transformations. However, very few computer simulations have emerged, elucidating the transformation mechanisms at the discrete lattice level, which underlie the extraordinary strain recoverability. Here, we conduct breakthrough molecular dynamics modelling on the superelastic behaviour of the NiTi single crystals, and unravel the atomistic genesis thereof. The deformation recovery is clearly traced to the reversible transformation between austenite and martensite crystals through simulations. We examine the mechanistic origin of the tension-compression asymmetries and the effects of pressure/temperature/strain rate variation isolatedly. Hence, this work essentially brings a new dimension to probing the NiTi performance based on the mesoscale physics under more complicated thermo-mechanical loading scenarios.

  15. Strain Functionals for Characterizing Atomistic Geometries

    Science.gov (United States)

    Kober, Edward; Rudin, Sven

    The development of a set of strain tensor functionals that are capable of characterizing arbitrarily ordered atomistic structures is described. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the moments of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. Other methods used to characterize atomic structures, such as the Steinhardt parameters or the centrosymmetry metric, can be derived from this more general approach. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. They allow material phases, deformations, and a large number of defect structures to be readily identified and classified. Applications to the analysis of shock-loaded samples of Cu, Ta and Ti will be presented. This strain functional basis can also then be used for developing interatomic potential functions, and an initial application to Cu will be presented.

  16. Stress in titania nanoparticles: An atomistic study

    Energy Technology Data Exchange (ETDEWEB)

    Darkins, Robert; Sushko, Maria L.; Liu, Jun; Duffy, Dorothy M.

    2014-04-24

    Stress engineering is becoming an increasingly important method for controlling electronic, optical, and magnetic properties of nanostructures, although the concept of stress is poorly defined at the nanoscale. We outline a methodology for computing bulk and surface stress in nanoparticles using atomistic simulation. The method is applicable to ionic and non- ionic materials alike and may be extended to other nanostructures. We apply it to spherical anatase nanoparticles ranging from 2 to 6 nm in diameter and obtain a surface stress of 0.89 N/m, in agreement with experimental measurements. Based on the extent that stress inhomogeneities at the surface are transmitted into the bulk, two characteristic length-scales are identified: below 3 nm bulk and surface regions cannot be defined and the available analytic theories for stress are not applicable, and above about 5 nm the stress becomes well-described by the theoretical Young-Laplace equation. The effect of a net surface charge on the bulk stress is also investigated. It is found that moderate surface charges can induce significant bulk stresses, on the order of 100 MPa, in nanoparticles within this size range.

  17. Atomistic Simulation of Non-Equilibrium Phenomena in Hypersonic Flows

    Science.gov (United States)

    Norman, Paul Erik

    The goal of this work is to model the heterogeneous recombination of atomic oxygen on silica surfaces, which is of interest for accurately predicting the heating on vehicles traveling at hypersonic speeds. This is accomplished by creating a finite rate catalytic model, which describes recombination with a set of elementary gas-surface reactions. Fundamental to a description of surface catalytic reactions are the in situ chemical structures on the surface where recombination can occur. Using molecular dynamics simulations with the Reax GSISiO potential, we find that the chemical sites active in direct gas-phase reactions on silica surfaces consist of a small number of specific structures (or defects). The existence of these defects on real silica surfaces is supported by experimental results and the structure and energetics of these defects have been verified with quantum chemical calculations. The reactions in the finite rate catalytic model are based on the interaction of molecular and atomic oxygen with these defects. Trajectory calculations are used to find the parameters in the forward rate equations, while a combination of detailed balance and transition state theory are used to find the parameters in the reverse rate equations. The rate model predicts that the oxygen recombination coefficient is relatively constant at T (300-1000 K), in agreement with experimental results. At T > 1000 K the rate model predicts a drop off in the oxygen recombination coefficient, in disagreement with experimental results, which predict that the oxygen recombination coefficient increases with temperature. A discussion of the possible reasons for this disagreement, including non-adiabatic collision dynamics, variable surface site concentrations, and additional recombination mechanisms is presented. This thesis also describes atomistic simulations with Classical Trajectory Calculation Direction Simulation Monte Carlo (CTC-DSMC), a particle based method for modeling non

  18. Atomistic simulation of Voronoi-based coated nanoporous metals

    Science.gov (United States)

    Onur Yildiz, Yunus; Kirca, Mesut

    2017-02-01

    In this study, a new method developed for the generation of periodic atomistic models of coated and uncoated nanoporous metals (NPMs) is presented by examining the thermodynamic stability of coated nanoporous structures. The proposed method is mainly based on the Voronoi tessellation technique, which provides the ability to control cross-sectional dimension and slenderness of ligaments as well as the thickness of coating. By the utilization of the method, molecular dynamic (MD) simulations of randomly structured NPMs with coating can be performed efficiently in order to investigate their physical characteristics. In this context, for the purpose of demonstrating the functionality of the method, sample atomistic models of Au/Pt NPMs are generated and the effects of coating and porosity on the thermodynamic stability are investigated by using MD simulations. In addition to that, uniaxial tensile loading simulations are performed via MD technique to validate the nanoporous models by comparing the effective Young’s modulus values with the results from literature. Based on the results, while it is demonstrated that coating the nanoporous structures slightly decreases the structural stability causing atomistic configurational changes, it is also shown that the stability of the atomistic models is higher at lower porosities. Furthermore, adaptive common neighbour analysis is also performed to identify the stabilized atomistic structure after the coating process, which provides direct foresights for the mechanical behaviour of coated nanoporous structures.

  19. A robust, coupled approach for atomistic-continuum simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Aubry, Sylvie; Webb, Edmund Blackburn, III (Sandia National Laboratories, Albuquerque, NM); Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John (Sandia National Laboratories, Albuquerque, NM); Kimmer, Christopher J.

    2004-09-01

    This report is a collection of documents written by the group members of the Engineering Sciences Research Foundation (ESRF), Laboratory Directed Research and Development (LDRD) project titled 'A Robust, Coupled Approach to Atomistic-Continuum Simulation'. Presented in this document is the development of a formulation for performing quasistatic, coupled, atomistic-continuum simulation that includes cross terms in the equilibrium equations that arise due to kinematic coupling and corrections used for the calculation of system potential energy to account for continuum elements that overlap regions containing atomic bonds, evaluations of thermo-mechanical continuum quantities calculated within atomistic simulations including measures of stress, temperature and heat flux, calculation used to determine the appropriate spatial and time averaging necessary to enable these atomistically-defined expressions to have the same physical meaning as their continuum counterparts, and a formulation to quantify a continuum 'temperature field', the first step towards constructing a coupled atomistic-continuum approach capable of finite temperature and dynamic analyses.

  20. Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics

    Energy Technology Data Exchange (ETDEWEB)

    Amani, Ehsan, E-mail: eamani@aut.ac.ir; Movahed, Saeid, E-mail: smovahed@aut.ac.ir

    2016-06-07

    In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. - Highlights: • A hybrid continuum-atomistic model is proposed for electrokinetics in nanochannels. • The model is validated by molecular dynamics. • This is a promising approach to model more complicated geometries and physics.

  1. Atomistic Modelling of Si Nanoparticles Synthesis

    Directory of Open Access Journals (Sweden)

    Giovanni Barcaro

    2017-02-01

    Full Text Available Silicon remains the most important material for electronic technology. Presently, some efforts are focused on the use of Si nanoparticles—not only for saving material, but also for improving the efficiency of optical and electronic devices, for instance, in the case of solar cells coated with a film of Si nanoparticles. The synthesis by a bottom-up approach based on condensation from low temperature plasma is a promising technique for the massive production of such nanoparticles, but the knowledge of the basic processes occurring at the atomistic level is still very limited. In this perspective, numerical simulations can provide fundamental information of the nucleation and growth mechanisms ruling the bottom-up formation of Si nanoclusters. We propose to model the low temperature plasma by classical molecular dynamics by using the reactive force field (ReaxFF proposed by van Duin, which can properly describe bond forming and breaking. In our approach, first-principles quantum calculations are used on a set of small Si clusters in order to collect all the necessary energetic and structural information to optimize the parameters of the reactive force-field for the present application. We describe in detail the procedure used for the determination of the force field and the following molecular dynamics simulations of model systems of Si gas at temperatures in the range 2000–3000 K. The results of the dynamics provide valuable information on nucleation rate, nanoparticle size distribution, and growth rate that are the basic quantities for developing a following mesoscale model.

  2. Method of Tallying Adjoint Fluence and Calculating Kinetics Parameters in Monte Carlo Codes%在蒙特卡罗程序中统计共轭通量并计算中子动力学参数的方法

    Institute of Scientific and Technical Information of China (English)

    汪量子; 姚栋; 王侃

    2012-01-01

    A method of using iterated fission probability to estimate the adjoint fluence during particles simulation, and using it as the weighting function to calculate kinetics parameters βell and A in Monte Carlo codes, was introduced in this paper. Implements of this method in continuous energy Monte Carlo code MCNP and multi-group Monte Carlo code MCMG are both elaborated. Verification results show that, with regardless additional computing cost, using this method, the adjoint fluence accounted by MCMG matches well with the result computed by ANISN, and the kinetics parameters calculated by MCNP agree very well with benchmarks. This method is proved to be reliable, and the function of calculating kinetics parameters in Monte Carlo codes is carried out effectively, which could be the basement for Monte Carlo codes' utility in the analysis of nuclear reactors' transient behavior.%文章介绍了在蒙特卡罗程序中,使用反复裂变几率的统计结果作为共轭通量的估计,并作为权重函数计算动力学参数βeff和Λ的方法,阐释了在连续能量蒙特卡罗程序MCNP和多群蒙特卡罗程序MCMG中实现这种方法的过程.数值校验结果表明:在几乎不带来附加计算量的同时,在MCMG中使用该方法统计得到的共轭通量与ANISN的共轭通量计算结果符合较好,在MCNP中使用该方法计算得到的中子动力学参数与基准测量结果符合较好.在蒙特卡罗程序中实现了高效率计算中子动力学参数的功能,为蒙特卡罗程序进一步用于反应堆动态行为的分析奠定了基础.

  3. Atomistic Method Applied to Computational Modeling of Surface Alloys

    Science.gov (United States)

    Bozzolo, Guillermo H.; Abel, Phillip B.

    2000-01-01

    The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on

  4. Atomistic Study on Size Effects in Thermally Induced Martensitic Phase Transformation of NiTi

    Directory of Open Access Journals (Sweden)

    Sourav Gur

    2016-01-01

    Full Text Available The atomistic study shows strong size effects in thermally induced martensitic phase transformation evolution kinetics of equiatomic NiTi shape memory alloys (SMAs. It is shown that size effects are closely related to the presence of free surfaces; thus, NiTi thin films and nanopillars are studied. Quasi-static molecular dynamics simulations for several cell sizes at various (constant temperatures are performed by employing well-established interatomic potentials for NiTi. The study shows that size plays a crucial role in the evolution of martensite phase fraction and, importantly, can significantly change the phase transformation temperatures, which can be used for the design of NiTi based sensors, actuators, or devices at nano- to microscales. Interestingly, it is found that, at the nanometer scale, Richard’s equation describes very well the martensite phase fraction evolution in NiTi thin films and nanopillars as a function of temperature.

  5. An object oriented Python interface for atomistic simulations

    Science.gov (United States)

    Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

    2016-01-01

    Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

  6. Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

    Science.gov (United States)

    2014-10-01

    of these networks, the specific volume and the coefficient of volumetric thermal expansion (CVTE), are shown in Fig. 4. Specific volume is...CVTE values are somewhat lower than expected from experimental measurements of the coefficient of linear thermal expansion ,27 which can be...coefficient of volumetric thermal expansion db equilibrium bond length DCPD dicyclopentadiene GAFF general AMBER force field ID identification K

  7. Linear grain growth kinetics and rotation in nanocrystalline Ni

    OpenAIRE

    Farkas, Diana; Mohanty, S.; Monk, J.

    2007-01-01

    We report three-dimensional atomistic molecular dynamics studies of grain growth kinetics in nanocrystalline Ni. The results show the grain size increasing linearly with time, contrary to the square root of the time kinetics observed in coarse-grained structures. The average grain boundary energy per unit area decreases simultaneously with the decrease in total grain boundary area associated with grain growth. The average mobility of the boundaries increases as the grain size increases. The r...

  8. Extended Ensemble Monte Carlo

    OpenAIRE

    Iba, Yukito

    2000-01-01

    ``Extended Ensemble Monte Carlo''is a generic term that indicates a set of algorithms which are now popular in a variety of fields in physics and statistical information processing. Exchange Monte Carlo (Metropolis-Coupled Chain, Parallel Tempering), Simulated Tempering (Expanded Ensemble Monte Carlo), and Multicanonical Monte Carlo (Adaptive Umbrella Sampling) are typical members of this family. Here we give a cross-disciplinary survey of these algorithms with special emphasis on the great f...

  9. Definition and detection of contact in atomistic simulations

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    2015-01-01

    In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

  10. Adaptive resolution simulation of an atomistic protein in MARTINI water

    NARCIS (Netherlands)

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-01-01

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coa

  11. Atomistic Determination of Cross-Slip Pathway and Energetics

    DEFF Research Database (Denmark)

    Rasmussen, Torben; Jacobsen, Karsten Wedel; Leffers, Torben;

    1997-01-01

    The mechanism for cross slip of a screw dislocation in Cu is determined by atomistic simulations that only presume the initial and final states of the process. The dissociated dislocation constricts in the primary plane and redissociates into the cross-slip plane while still partly in the primary...

  12. Atomistic simulations of jog migration on extended screw dislocations

    DEFF Research Database (Denmark)

    Vegge, T.; Leffers, T.; Pedersen, O.B.;

    2001-01-01

    We have performed large-scale atomistic simulations of the migration of elementary jogs on dissociated screw dislocations in Cu. The local crystalline configurations, transition paths. effective masses. and migration barriers for the jogs are determined using an interatomic potential based on the...

  13. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

    Science.gov (United States)

    Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

    2016-12-01

    The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

  14. Using atomistic simulations to model cadmium telluride thin film growth

    Science.gov (United States)

    Yu, Miao; Kenny, Steven D.

    2016-03-01

    Cadmium telluride (CdTe) is an excellent material for low-cost, high efficiency thin film solar cells. It is important to conduct research on how defects are formed during the growth process, since defects lower the efficiency of solar cells. In this work we use computer simulation to predict the growth of a sputter deposited CdTe thin film. On-the-fly kinetic Monte Carlo technique is used to simulate the CdTe thin film growth on the (1 1 1) surfaces. The results show that on the (1 1 1) surfaces the growth mechanisms on surfaces which are terminated by Cd or Te are quite different, regardless of the deposition energy (0.1∼ 10 eV). On the Te-terminated (1 1 1) surface the deposited clusters first form a single mixed species layer, then the Te atoms in the mixed layer moved up to form a new layer. Whilst on the Cd-terminated (1 1 1) surface the new Cd and Te layers are formed at the same time. Such differences are probably caused by stronger bonding between ad-atoms and surface atoms on the Te layer than on the Cd layer.

  15. Atomistic Modeling of the Negative Thermal Expansion in δ- Plutonium  Based on the Two-State Description

    Directory of Open Access Journals (Sweden)

    Steven M. Valone

    2012-06-01

    Full Text Available The δ phase  of plutonium with the fcc structure exhibits an unusual negative thermal expansion (NTE over its narrow  temperature range of stability, 593–736 K. An accurate description  of the anomalous high-temperature volume effect of plutonium  goes beyond the current capability  of electronic-structure  calculations.  We propose an atomistic scheme to model the thermodynamic properties of δ-Pu based on the two-state model of Weiss for the Invar alloys, inspired by the simple free-energy analysis previously conducted by Lawson et al. The two-state mechanism is incorporated into the atomistic description of a many-body  interacting  system.  Two modified  embedded atom method potentials are employed to represent the binding energies of two competing  electronic  states in δ-Pu. We demonstrate how the NTE takes place in δ-Pu by means of Monte Carlo simulations implemented with the two-state mechanism.

  16. Long-time atomistic simulations with the Parallel Replica Dynamics method

    Science.gov (United States)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  17. Adhesive contact:from atomistic model to continuum model

    Institute of Scientific and Technical Information of China (English)

    Fan Kang-Qi; Jia Jian-Yuan; Zhu Ying-Min; Zhang Xiu-Yan

    2011-01-01

    Two types of Lennard-Jones potential are widely used in modeling adhesive contacts. However, the relationships between the parameters of the two types of Lennard-Jones potential are not well defined. This paper employs a selfconsistent method to derive the Lennard-Jones surface force law from the interatomic Lennard-Jones potential with emphasis on the relationships between the parameters. The effect of using correct parameters in the adhesion models is demonstrated in single sphere-flat contact via continuum models and an atomistic model. Furthermore, the adhesion hysteresis behaviour is investigated, and the S-shaped force-distance relation is revealed by the atomistic model. It shows that the adhesion hysteresis loop is generated by the jump-to-contact and jump-off-contact, which are illustrated by the S-shaped force-distance curve.

  18. Atomistic aspects of crack propagation along high angle grain boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1997-12-31

    The author presents atomistic simulations of the crack tip configuration near a high angle {Sigma} = 5 [001](210) symmetrical tilt grain boundary in NiAl. The simulations were carried out using molecular statics and embedded atom (EAM) potentials. The cracks are stabilized near a Griffith condition involving the cohesive energy of the grain boundary. The atomistic configurations of the tip region are different in the presence of the high angle grain boundary than in the bulk. Three different configurations of the grain boundary were studied corresponding to different local compositions. It was found that in ordered NiAl, cracks along symmetrical tilt boundaries show a more brittle behavior for Al rich boundaries than for Ni-rich boundaries. Lattice trapping effects in grain boundary fracture were found to be more significant than in the bulk.

  19. The notion of a plastic material spin in atomistic simulations

    Science.gov (United States)

    Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

    2016-12-01

    A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

  20. Atomistic modeling of carbon Cottrell atmospheres in bcc iron

    Science.gov (United States)

    Veiga, R. G. A.; Perez, M.; Becquart, C. S.; Domain, C.

    2013-01-01

    Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

  1. Monte Carlo methods

    OpenAIRE

    Bardenet, R.

    2012-01-01

    ISBN:978-2-7598-1032-1; International audience; Bayesian inference often requires integrating some function with respect to a posterior distribution. Monte Carlo methods are sampling algorithms that allow to compute these integrals numerically when they are not analytically tractable. We review here the basic principles and the most common Monte Carlo algorithms, among which rejection sampling, importance sampling and Monte Carlo Markov chain (MCMC) methods. We give intuition on the theoretic...

  2. Predicting dislocation climb: Classical modeling versus atomistic simulations

    OpenAIRE

    Clouet, Emmanuel

    2011-01-01

    International audience; The classical modeling of dislocation climb based on a continuous description of vacancy diffusion is compared to recent atomistic simulations of dislocation climb in body-centered cubic iron under vacancy supersaturation [Phys. Rev. Lett. 105 095501 (2010)]. A quantitative agreement is obtained, showing the ability of the classical approach to describe dislocation climb. The analytical model is then used to extrapolate dislocation climb velocities to lower dislocation...

  3. Redox reactions with empirical potentials: Atomistic battery discharge simulations

    OpenAIRE

    Dapp, Wolf B.; Müser, Martin H.

    2013-01-01

    Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each ...

  4. The atomistic representation of first strain-gradient elastic tensors

    Science.gov (United States)

    Admal, Nikhil Chandra; Marian, Jaime; Po, Giacomo

    2017-02-01

    We derive the atomistic representations of the elastic tensors appearing in the linearized theory of first strain-gradient elasticity for an arbitrary multi-lattice. In addition to the classical (2nd-Piola) stress and elastic moduli tensors, these include the rank-three double-stress tensor, the rank-five tensor of mixed elastic moduli, and the rank-six tensor of strain-gradient elastic moduli. The atomistic representations are closed-form analytical expressions in terms of the first and second derivatives of the interatomic potential with respect to interatomic distances, and dyadic products of relative atomic positions. Moreover, all expressions are local, in the sense that they depend only on the atomic neighborhood of a lattice site. Our results emanate from the condition of energetic equivalence between continuum and atomistic representations of a crystal, when the kinematics of the latter is governed by the Cauchy-Born rule. Using the derived expressions, we prove that the odd-order tensors vanish if the lattice basis admits central-symmetry. The analytical expressions are implemented as a KIM compliant algorithm to compute the strain gradient elastic tensors for various materials. Numerical results are presented to compare representative interatomic potentials used in the literature for cubic crystals, including simple lattices and multi-lattices. We observe that central potentials exhibit generalized Cauchy relations for the rank-six tensor of strain-gradient elastic moduli. In addition, this tensor is found to be indefinite for many potentials. We discuss the relationship between indefiniteness and material stability. Finally, the atomistic representations are specialized to central potentials in simple lattices. These expressions are used with analytical potentials to study the sensitivity of the elastic tensors to the choice of the cutoff radius.

  5. Modeling micelle-templated mesoporous material SBA-15: atomistic model and gas adsorption studies.

    Science.gov (United States)

    Bhattacharya, Supriyo; Coasne, Benoit; Hung, Francisco R; Gubbins, Keith E

    2009-05-19

    We report the development of a realistic molecular model for mesoporous silica SBA-15, which includes both the large cylindrical mesopores and the smaller micropores in the pore walls. The methodology for modeling the SBA-15 structure involves molecular and mesoscale simulations combined with geometrical interpolation techniques. First, a mesoscale model is prepared by mimicking the synthesis process using lattice Monte Carlo simulations. The main physical features of this mesoscale pore model are then carved out of an atomistic silica block; both the mesopores and the micropores are incorporated from the mimetic simulations. The calculated pore size distribution, surface area, and simulated TEM images of the model structure are in good agreement with those obtained from experimental samples of SBA-15. We then investigate the adsorption of argon in this structure using Grand Canonical Monte Carlo (GCMC) simulations. The adsorption results for our SBA-15 model are compared with those for a similar model that does not include the micropores; we also compare with results obtained in a regular cylindrical pore. The simulated adsorption isotherm for the SBA-15 model shows semiquantitative agreement with the experimental isotherm for a SBA-15 sample having a similar pore size. We observe that the presence of the micropores leads to increased adsorption at low pressure compared to the case of a model without micropores in the pore walls. At higher pressures, for all models, the filling proceeds via the monolayer-multilayer adsorption on the mesopore surface followed by capillary condensation, which is mainly controlled by the mesopore diameter and is not influenced by the presence of the micropores.

  6. Exploring Monte Carlo methods

    CERN Document Server

    Dunn, William L

    2012-01-01

    Exploring Monte Carlo Methods is a basic text that describes the numerical methods that have come to be known as "Monte Carlo." The book treats the subject generically through the first eight chapters and, thus, should be of use to anyone who wants to learn to use Monte Carlo. The next two chapters focus on applications in nuclear engineering, which are illustrative of uses in other fields. Five appendices are included, which provide useful information on probability distributions, general-purpose Monte Carlo codes for radiation transport, and other matters. The famous "Buffon's needle proble

  7. A dynamic atomistic-continuum method for the simulation of crystalline materials

    CERN Document Server

    Huang Zhon Gy

    2002-01-01

    We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics in crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away from defects and interfaces. We propose a new class of matching conditions between the atomistic and the continuum regions. These conditions ensure the accurate passage of large-scale information between the atomistic and the continuum regions and at the same time minimize the reflection of phonons at the atomistic-continuum interface. They can be made adaptive by choosing appropriate weight functions. We present applications to dislocation dynamics, friction between two-dimensional crystal surfaces, and fracture dynamics. We compare results of the coupled method and of the detailed atomistic model.

  8. MORSE Monte Carlo code

    Energy Technology Data Exchange (ETDEWEB)

    Cramer, S.N.

    1984-01-01

    The MORSE code is a large general-use multigroup Monte Carlo code system. Although no claims can be made regarding its superiority in either theoretical details or Monte Carlo techniques, MORSE has been, since its inception at ORNL in the late 1960s, the most widely used Monte Carlo radiation transport code. The principal reason for this popularity is that MORSE is relatively easy to use, independent of any installation or distribution center, and it can be easily customized to fit almost any specific need. Features of the MORSE code are described.

  9. Atomistic simulation of the structural and elastic properties of magnesite

    Indian Academy of Sciences (India)

    ZI-JIANG LIU; XIAO-WEI SUN; TING SONG; YUAN GUO; CAI-RONG ZHANG; ZHENG-RONG ZHANG

    2016-09-01

    Atomistic simulation was carried out to study the structural and elastic properties of MgCO$_3$ magnesite within the pressure range of the Earth’s mantle based on a novel force field. The lattice parameters and elasticconstants as a function of pressure up to 150 GPa are calculated. The results are in good agreement with the available experimental data and previous theoretical results, showing no phase transition over the pressure range of interest. We also found that magnesite exhibits a strong anisotropy throughout the lower mantle and that the nature of the anisotropy changes significantly with depth.

  10. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable...

  11. Interfacial Phenomena: Linking Atomistic and Molecular Level Processes

    Energy Technology Data Exchange (ETDEWEB)

    Jay A Brandes

    2009-09-23

    This was a grant to support travel for scientists to present data and interact with others in their field. Specifically, speakers presented their data in a session entitled “Interfacial Phenomena: Linking Atomistic and Macroscopic Properties: Theoretical and Experimental Studies of the Structure and Reactivity of Mineral Surfaces”. The session ran across three ½ day periods, March 30-31 2004. The session’s organizers were David J. Wesolowski andGordon E. Brown Jr. There were a total of 30 talks presented.

  12. Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

    Science.gov (United States)

    Tvaroška, Igor

    2015-02-11

    Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed.

  13. Control of density fluctuations in atomistic-continuum simulations of dense liquids

    DEFF Research Database (Denmark)

    Kotsalis, E.M.; Walther, Jens Honore; Koumoutsakos, P.

    2007-01-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a co...

  14. Going Backward : A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

    NARCIS (Netherlands)

    Wassenaar, Tsjerk A.; Pluhackova, Kristyna; Böckmann, Rainer A.; Marrink, Siewert J.; Tieleman, D. Peter

    2014-01-01

    The conversion of coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations. For this process, called backmapping or reverse transformation, several tools are available, but these commonly require libraries of molecul

  15. Atomistic simulation for deforming complex alloys with application toward TWIP steel and associated physical insights

    Science.gov (United States)

    Wang, Peng; Xu, Shaofeng; Liu, Jiabin; Li, Xiaoyan; Wei, Yujie; Wang, Hongtao; Gao, Huajian; Yang, Wei

    2017-01-01

    The interest in promoting deformation twinning for plasticity is mounting for advanced materials. In contrast to disordered grain boundaries, highly organized twin boundaries are beneficial to promoting strength-ductility combination. Twinning deformation typically involves the kinetics of stacking faults, its interplay with dislocations, as well as the interactions between dislocations and twin boundaries. While the latter has been intensively studied, the dynamics of stacking faults has been rarely touched upon. In this work, we report new physical insights on the stacking fault dynamics in twin induced plasticity (TWIP) steels. The atomistic simulation is made possible by a newly introduced approach: meta-atom molecular dynamics simulation. The simulation suggests that the stacking fault interactions are dominated by dislocation reactions that take place spontaneously, different from the existing mechanisms. Whether to generate a single stacking fault, or a twinning partial and a trailing partial dislocation, depends upon a unique parameter, namely the stacking fault energy. The latter in turn determines the deformation twinning characteristics. The complex twin-slip and twin-dislocation interactions demonstrate the dual role of deformation twins as both the dislocation barrier and dislocation storage. This duality contributes to the high strength and high ductility of TWIP steels.

  16. Atomistic Studies of Cation Transport in Tetragonal ZrO2 During Zirconium Corrosion

    Energy Technology Data Exchange (ETDEWEB)

    Xian-Ming Bai; Yongfeng Zhang; Michael R. Tonks

    2013-10-01

    Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is one of the major degradation mechanisms of these alloys. During corrosion the transport of oxidizing species in zirconium dioxide (ZrO2) determines the corrosion kinetics. Previously it has been argued that the outward diffusion of cation ions is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO2 is studied with temperature accelerated dynamics and molecular dynamics simulations. The results show that Zr interstitials have anisotropic diffusion and migrate preferentially along the [001] or c direction in tetragonal ZrO2. The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration barriers of some defect clusters can be much lower than those of point defects. The migration of Zr interstitials at some special grain boundaries is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed.

  17. Atomistic modelling and prediction of glass forming ability in bulk metallic glasses

    Science.gov (United States)

    Sedighi, Sina

    Atomistic modeling (via molecular dynamics with EAM interaction potentials) was conducted for the detailed investigation of kinetics, thermodynamics, structure, and bonding in Ni-Al and Cu-Zr metallic glasses. This work correlates GFA with the nature of atomic-level bonding and vibrational properties, with results potentially extensible to the Transition Metal -- Transition Metal and Transition Metal -- Metalloid alloy classes in general. As a first step in the development of a liquid-only GFA tuning approach, an automated tool has also been created for the broad compositional sampling of liquid and glassy phase properties in multicomponent (binary, ternary, quaternary) alloy systems. Its application to the Cu-Zr alloy system shows promising results, including the successful identification of the two highest GFA compositions, Cu50Zr50 and Cu64Zr 36. Combined, the findings of this work highlight the critical importance of incorporating more complex alloy-specific information regarding the nature of bonding and ordering at the atomic level into such an approach.

  18. Quantum Monte Carlo simulation

    OpenAIRE

    Wang, Yazhen

    2011-01-01

    Contemporary scientific studies often rely on the understanding of complex quantum systems via computer simulation. This paper initiates the statistical study of quantum simulation and proposes a Monte Carlo method for estimating analytically intractable quantities. We derive the bias and variance for the proposed Monte Carlo quantum simulation estimator and establish the asymptotic theory for the estimator. The theory is used to design a computational scheme for minimizing the mean square er...

  19. Monte Carlo transition probabilities

    OpenAIRE

    Lucy, L. B.

    2001-01-01

    Transition probabilities governing the interaction of energy packets and matter are derived that allow Monte Carlo NLTE transfer codes to be constructed without simplifying the treatment of line formation. These probabilities are such that the Monte Carlo calculation asymptotically recovers the local emissivity of a gas in statistical equilibrium. Numerical experiments with one-point statistical equilibrium problems for Fe II and Hydrogen confirm this asymptotic behaviour. In addition, the re...

  20. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si{sub 3}N

    Energy Technology Data Exchange (ETDEWEB)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-20

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  1. Quantum transport in RTD and atomistic modeling of nanostructures

    Science.gov (United States)

    Jiang, Zhengping

    As devices are scaled down to nanometer scale, new materials and device structures are introduced to extend Moore's law beyond Si devices. In this length scale, carrier transport moves from classical transport to quantum transport; material granularity has more and more impacts on performance. Computer Aided Design (CAD) becomes essential for both industrial and educational purposes. First part focuses on physical models and numerical issues in nano-scale devices modeling. Resonance Tunneling Diode (RTD) is simulated and used to illustrate phenomena in carrier transport. Non-Equilibrium Green's Function (NEGF) formulism is employed in quantum transport simulation. Inhomogeneous energy grid is used in energy integration, which is critical to capture essential physics in RTD simulation. All simulation results could be reproduced by developed simulators RTDNEGF and NEMO5. In nanostructures, device length becomes comparable to material granularity; it is not proper to consider materials as continuous in many situations. Second part of this work resolves this problem by introducing atomistic modeling method. Valley degeneracy in Si (110) QW is investigated. Inconsistency of experimental observations is resolved by introducing miscut in surface. Impacts of strain and electric field on electronic bandstructure are studied. Research of SiGe barrier disorder effects on valley splitting in Si (100) QW is then conducted. Behaviors of valley splitting in different well widths under electric field are predicted by atomistic simulation. Nearest neighbor empirical tight-binding method is used in electronic calculation and VFF Keating model is used in strain relaxation.

  2. Atomistic interpretation of solid solution hardening from spectral analysis.

    Science.gov (United States)

    Plendl, J N

    1971-05-01

    From analysis of a series of vibrational spectra of ir energy absorption and laser Raman, an attempt is made to interpret solid solution hardening from an atomistic point of view for the system CaF(2)/SrF(2). It is shown to be caused by the combined action of three atomic characteristics, i.e., their changes as a function of composition. They are deformation of the atomic coordination polyhedrons, overlap of the outer electron shells of the atom pairs, and the ratio of the ionic to covalent share of binding. A striking nonlinear behavior of the three characteristics, as a function of composition, gives maximum atomic bond strength to the 55/45 position of the system CaF(2)/SrF(2), in agreement with the measured data of the solid solution hardening. The curve for atomic bond strength, derived from the three characteristics, is almost identical to the curve for measured microhardness data. This result suggests that the atomistic interpretation, put forward in this paper, is correct.

  3. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2007-01-12

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process. We also discuss a technique for optimizing the calculation of fine-scale information on the fly for use in a coarse-scale simulation, and discuss the specific case of a fine-scale model that calculates void growth explicitly feeding into a coarse-scale mechanics model to study damage localization.

  4. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2005-12-31

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process.

  5. Adaptive resolution simulation of an atomistic protein in MARTINI water

    Science.gov (United States)

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-02-01

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

  6. 3d visualization of atomistic simulations on every desktop

    Science.gov (United States)

    Peled, Dan; Silverman, Amihai; Adler, Joan

    2013-08-01

    Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

  7. Application of Bayesian population physiologically based pharmacokinetic (PBPK) modeling and Markov chain Monte Carlo simulations to pesticide kinetics studies in protected marine mammals: DDT, DDE, and DDD in harbor porpoises.

    Science.gov (United States)

    Weijs, Liesbeth; Yang, Raymond S H; Das, Krishna; Covaci, Adrian; Blust, Ronny

    2013-05-01

    Physiologically based pharmacokinetic (PBPK) modeling in marine mammals is a challenge because of the lack of parameter information and the ban on exposure experiments. To minimize uncertainty and variability, parameter estimation methods are required for the development of reliable PBPK models. The present study is the first to develop PBPK models for the lifetime bioaccumulation of p,p'-DDT, p,p'-DDE, and p,p'-DDD in harbor porpoises. In addition, this study is also the first to apply the Bayesian approach executed with Markov chain Monte Carlo simulations using two data sets of harbor porpoises from the Black and North Seas. Parameters from the literature were used as priors for the first "model update" using the Black Sea data set, the resulting posterior parameters were then used as priors for the second "model update" using the North Sea data set. As such, PBPK models with parameters specific for harbor porpoises could be strengthened with more robust probability distributions. As the science and biomonitoring effort progress in this area, more data sets will become available to further strengthen and update the parameters in the PBPK models for harbor porpoises as a species anywhere in the world. Further, such an approach could very well be extended to other protected marine mammals.

  8. Degenerate Ising model for atomistic simulation of crystal-melt interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Schebarchov, D., E-mail: Dmitri.Schebarchov@gmail.com [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Schulze, T. P., E-mail: schulze@math.utk.edu [Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996-1300 (United States); Hendy, S. C. [The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140 (New Zealand); Department of Physics, University of Auckland, Auckland 1010 (New Zealand)

    2014-02-21

    One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level.

  9. Monte-carlo calculations for some problems of quantum mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Novoselov, A. A., E-mail: novoselov@goa.bog.msu.ru; Pavlovsky, O. V.; Ulybyshev, M. V. [Moscow State University (Russian Federation)

    2012-09-15

    The Monte-Carlo technique for the calculations of functional integral in two one-dimensional quantum-mechanical problems had been applied. The energies of the bound states in some potential wells were obtained using this method. Also some peculiarities in the calculation of the kinetic energy in the ground state had been studied.

  10. Kinetic Actviation Relaxation Technique

    CERN Document Server

    Béland, Laurent Karim; El-Mellouhi, Fedwa; Joly, Jean-François; Mousseau, Normand

    2011-01-01

    We present a detailed description of the kinetic Activation-Relaxation Technique (k-ART), an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search. Combining a topological classification for local environments and event generation with ART nouveau, an efficient unbiased sampling method for finding transition states, k-ART can be applied to complex materials with atoms in off-lattice positions or with elastic deformations that cannot be handled with standard KMC approaches. In addition to presenting the various elements of the algorithm, we demonstrate the general character of k-ART by applying the algorithm to three challenging systems: self-defect annihilation in c-Si, self-interstitial diffusion in Fe and structural relaxation in amorphous silicon.

  11. Amp: A modular approach to machine learning in atomistic simulations

    Science.gov (United States)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

    Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which

  12. Modeling and Monte Carlo simulation of nucleation and growth of UV/low-temperature-induced nanostructures

    Science.gov (United States)

    Flicstein, Jean; Pata, S.; Chun, L. S. H. K.; Palmier, Jean F.; Courant, J. L.

    1998-05-01

    A model for ultraviolet induced chemical vapor deposition (UV CVD) for a-SiN:H is described. In the simulation of UV CVD process, activate charged centers creation, species incorporation, surface diffusion, and desorption are considered as elementary steps for the photonucleation and photodeposition mechanisms. The process is characterized by two surface sticking coefficients. Surface diffusion of species is modeled with a gaussian distribution. A real time Monte Carlo method is used to determine photonucleation and photodeposition rates in nanostructures. Comparison of experimental versus simulation results for a-SiN:H is shown to predict the morphology temporal evolution under operating conditions down to atomistic resolution.

  13. Atomistic Structure, Strength, and Kinetic Properties of Intergranular Films in Ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Garofalini, Stephen H

    2015-01-08

    Intergranular films (IGFs) present in polycrystalline oxide and nitride ceramics provide an excellent example of nanoconfined glasses that occupy only a small volume percentage of the bulk ceramic, but can significantly influence various mechanical, thermal, chemical, and optical properties. By employing molecular dynamics computer simulations, we have been able to predict structures and the locations of atoms at the crystal/IGF interface that were subsequently verified with the newest electron microscopies. Modification of the chemistry of the crystal surface in the simulations provided the necessary mechanism for adsorption of specific rare earth ions from the IGF in the liquid state to the crystal surface. Such results had eluded other computational approaches such as ab-initio calculations because of the need to include not only the modified chemistry of the crystal surfaces but also an accurate description of the adjoining glassy IGF. This segregation of certain ions from the IGF to the crystal caused changes in the local chemistry of the IGF that affected fracture behavior in the simulations. Additional work with the rare earth ions La and Lu in the silicon oxynitride IGFs showed the mechanisms for their different affects on crystal growth, even though both types of ions are seen adhering to a bounding crystal surface that would normally imply equivalent affects on grain growth.

  14. The Virtual Monte Carlo

    CERN Document Server

    Hrivnacova, I; Berejnov, V V; Brun, R; Carminati, F; Fassò, A; Futo, E; Gheata, A; Caballero, I G; Morsch, Andreas

    2003-01-01

    The concept of Virtual Monte Carlo (VMC) has been developed by the ALICE Software Project to allow different Monte Carlo simulation programs to run without changing the user code, such as the geometry definition, the detector response simulation or input and output formats. Recently, the VMC classes have been integrated into the ROOT framework, and the other relevant packages have been separated from the AliRoot framework and can be used individually by any other HEP project. The general concept of the VMC and its set of base classes provided in ROOT will be presented. Existing implementations for Geant3, Geant4 and FLUKA and simple examples of usage will be described.

  15. Kinetic Typography

    DEFF Research Database (Denmark)

    van Leeuwen, Theo; Djonov, Emilia

    2014-01-01

    After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images.......After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images....

  16. Atomistic Hydrodynamics and the Dynamical Hydrophobic Effect in Porous Graphene.

    Science.gov (United States)

    Strong, Steven E; Eaves, Joel D

    2016-05-19

    Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For numerical simulation to play a predictive and descriptive role, one must have theoretically sound methods that span orders of magnitude in physical scales, from the atomistic motions of particles inside the channels to the large-scale hydrodynamic gradients that drive transport. Here, we use constraint dynamics to derive a nonequilibrium molecular dynamics method for simulating steady-state mass flow of a fluid moving through the nanoscopic spaces of a porous solid. After validating our method on a model system, we use it to study the hydrophobic effect of water moving through pores of electrically doped single-layer graphene. The trend in permeability that we calculate does not follow the hydrophobicity of the membrane but is instead governed by a crossover between two competing molecular transport mechanisms.

  17. Quantum-based Atomistic Simulation of Transition Metals

    Energy Technology Data Exchange (ETDEWEB)

    Moriarty, J A; Benedict, L X; Glosli, J N; Hood, R Q; Orlikowski, D A; Patel, M V; Soderlind, P; Streitz, F H; Tang, M; Yang, L H

    2005-08-29

    First-principles generalized pseudopotential theory (GPT) provides a fundamental basis for transferable multi-ion interatomic potentials in d-electron transition metals within density-functional quantum mechanics. In mid-period bcc metals, where multi-ion angular forces are important to structural properties, simplified model GPT or MGPT potentials have been developed based on canonical d bands to allow analytic forms and large-scale atomistic simulations. Robust, advanced-generation MGPT potentials have now been obtained for Ta and Mo and successfully applied to a wide range of structural, thermodynamic, defect and mechanical properties at both ambient and extreme conditions of pressure and temperature. Recent algorithm improvements have also led to a more general matrix representation of MGPT beyond canonical bands allowing increased accuracy and extension to f-electron actinide metals, an order of magnitude increase in computational speed, and the current development of temperature-dependent potentials.

  18. Shock Hugoniot behavior of single crystal titanium using atomistic simulations

    Science.gov (United States)

    Mackenchery, Karoon; Dongare, Avinash

    2017-01-01

    Atomistic shock simulations are performed for single crystal titanium using four different interatomic potentials at impact velocities ranging from 0.5 km/s to 2.0 km/s. These potentials comprise of three parameterizations in the formulation of the embedded atom method and one formulation of the modified embedded atom method. The capability of the potentials to model the shock deformation and failure behavior is investigated by computing the shock hugoniot response of titanium and comparing to existing experimental data. In addition, the capability to reproduce the shock induced alpha (α) to omega (ω) phase transformation seen in Ti is investigated. The shock wave structure is discussed and the velocities for the elastic, plastic and the α-ω phase transformation waves are calculated for all the interatomic potentials considered.

  19. Effective Transparency: A Test of Atomistic Laser-Cluster Models

    CERN Document Server

    Pandit, Rishi; Teague, Thomas; Hartwick, Zachary; Bigaouette, Nicolas; Ramunno, Lora; Ackad, Edward

    2016-01-01

    The effective transparency of rare-gas clusters, post-interaction with an extreme ultraviolet (XUV) pump pulse, is studied by using an atomistic hybrid quantum-classical molecular dynamics model. We find there is an intensity range in which an XUV probe pulse has no lasting effect on the average charge state of a cluster after being saturated by an XUV pump pulse: the cluster is effectively transparent to the probe pulse. The range of this phenomena increases with the size of the cluster and thus provides an excellent candidate for an experimental test of the effective transparency effect. We present predictions for the clusters at the peak of the laser pulse as well as the experimental time-of-flight signal expected along with trends which can be compared with. Significant deviations from these predictions would provide evidence for enhanced photoionization mechanism(s).

  20. Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann-Molecular Dynamics Simulations of Dense Fluids

    Science.gov (United States)

    Dupuis, A.; Koumoutsakos, P.

    We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.

  1. Control of density fluctuations in atomistic-continuum simulations of dense liquids

    Science.gov (United States)

    Kotsalis, E. M.; Walther, J. H.; Koumoutsakos, P.

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation. We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

  2. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

    Science.gov (United States)

    Rzepiela, Andrzej J; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J

    2011-06-14

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1:1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein

  3. Atomistic study of crack propagation and dislocation emission in Cu-Ni multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Clinedinst, J.; Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1997-09-01

    The authors present atomistic simulations of the crack tip configuration in multilayered Cu-Ni materials. The simulations were carried out using molecular statics and EAM potentials. The atomistic structure of the interface was studied first for a totally coherent structure. Cracks were simulated near a Griffith condition in different possible configurations of the crack plane and front with respect to the axis of the layers. Results show that interface effects predominantly control the mechanical behavior of the system studied.

  4. Calculation of the effect of macromolecular architecture on structure and thermodynamic properties of linear-tri-arm polyethylene blends from Monte Carlo simulation

    DEFF Research Database (Denmark)

    Rissanou, Anastassia N.; Peristeras, Loukas D.; Economou, Ioannis

    2007-01-01

    A Monte Carlo simulation formalism proposed recently [Peristeras et al. Macromolecules 2007;40:2904-14] is applied here to linear-tri-arm polyethylene blends using atomistic models. Elementary Monte Carlo moves for long chain and branched molecules are used and shown to result in efficient...... relaxation of long chains. The effect of chain and arm molecular weight and of temperature on the structure and thermodynamic properties of blends is examined. Chemical potential versus composition diagrams are drawn in order to assess the non-ideality of mixing that may lead to phase separation. All...

  5. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  6. An atomistically informed mesoscale model for growth and coarsening during discharge in lithium-oxygen batteries

    Energy Technology Data Exchange (ETDEWEB)

    Welland, Michael J.; Lau, Kah Chun; Redfern, Paul C.; Wolf, Dieter; Curtiss, Larry A., E-mail: curtiss@anl.gov [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Liang, Linyun [Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Zhai, Denyun [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2015-12-14

    An atomistically informed mesoscale model is developed for the deposition of a discharge product in a Li-O{sub 2} battery. This mescocale model includes particle growth and coarsening as well as a simplified nucleation model. The model involves LiO{sub 2} formation through reaction of O{sub 2}{sup −} and Li{sup +} in the electrolyte, which deposits on the cathode surface when the LiO{sub 2} concentration reaches supersaturation in the electrolyte. A reaction-diffusion (rate-equation) model is used to describe the processes occurring in the electrolyte and a phase-field model is used to capture microstructural evolution. This model predicts that coarsening, in which large particles grow and small ones disappear, has a substantial effect on the size distribution of the LiO{sub 2} particles during the discharge process. The size evolution during discharge is the result of the interplay between this coarsening process and particle growth. The growth through continued deposition of LiO{sub 2} has the effect of causing large particles to grow ever faster while delaying the dissolution of small particles. The predicted size evolution is consistent with experimental results for a previously reported cathode material based on activated carbon during discharge and when it is at rest, although kinetic factors need to be included. The approach described in this paper synergistically combines models on different length scales with experimental observations and should have applications in studying other related discharge processes, such as Li{sub 2}O{sub 2} deposition, in Li-O{sub 2} batteries and nucleation and growth in Li-S batteries.

  7. An atomistically informed mesoscale model for growth and coarsening during discharge in lithium-oxygen batteries

    Energy Technology Data Exchange (ETDEWEB)

    Welland, Michael J. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Lau, Kah Chun [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Redfern, Paul C. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Liang, Linyun [Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439, USA; Zhai, Denyun [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Wolf, Dieter [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Curtiss, Larry A. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA

    2015-12-14

    An atomistically informed mesoscale model is developed for the deposition of a discharge product in a Li-O-2 battery. This mescocale model includes particle growth and coarsening as well as a simplified nucleation model. The model involves LiO2 formation through reaction of O-2(-) and Li+ in the electrolyte, which deposits on the cathode surface when the LiO2 concentration reaches supersaturation in the electrolyte. A reaction-diffusion (rate-equation) model is used to describe the processes occurring in the electrolyte and a phase-field model is used to capture microstructural evolution. This model predicts that coarsening, in which large particles grow and small ones disappear, has a substantial effect on the size distribution of the LiO2 particles during the discharge process. The size evolution during discharge is the result of the interplay between this coarsening process and particle growth. The growth through continued deposition of LiO2 has the effect of causing large particles to grow ever faster while delaying the dissolution of small particles. The predicted size evolution is consistent with experimental results for a previously reported cathode material based on activated carbon during discharge and when it is at rest, although kinetic factors need to be included. The approach described in this paper synergistically combines models on different length scales with experimental observations and should have applications in studying other related discharge processes, such as Li2O2 deposition, in Li-O-2 batteries and nucleation and growth in Li-S batteries.

  8. Nano sculpt: A methodology for generating complex realistic configurations for atomistic simulations.

    Science.gov (United States)

    Prakash, A; Hummel, M; Schmauder, S; Bitzek, E

    2016-01-01

    Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nano sculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data.

  9. Diffusion Quantum Monte Carlo Study of Martensitic Phase Transition: The Case of Phosphorene

    CERN Document Server

    Reeves, Kyle G; Kanai, Yosuke

    2016-01-01

    Recent technical advances in dealing with finite-size errors make quantum Monte Carlo methods quite appealing for treating extended systems in electronic structure calculations, especially when commonly-used density functional theory (DFT) methods might not be satisfactory. We present a theoretical study of martensitic phase transition of a two-dimensional phosphorene by employing diffusion Monte Carlo (DMC) approach to investigate the energetics of this phase transition. The DMC calculation supports DFT prediction of having a rather diffusive barrier that is characterized by having two transition states, in addition to confirming that the so-called black and blue phases of phosphorene are essentially degenerate. At the same time, the calculation shows the importance of treating correlation energy accurately for describing the energy changes in the martensitic phase transition, as is already widely appreciated for chemical bond formation/dissociation. Building on the atomistic characterization of the phase tr...

  10. Physically representative atomistic modeling of atomic-scale friction

    Science.gov (United States)

    Dong, Yalin

    Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the

  11. Quantum Monte Carlo Calculations of Neutron Matter

    CERN Document Server

    Carlson, J; Ravenhall, D G

    2003-01-01

    Uniform neutron matter is approximated by a cubic box containing a finite number of neutrons, with periodic boundary conditions. We report variational and Green's function Monte Carlo calculations of the ground state of fourteen neutrons in a periodic box using the Argonne $\\vep $ two-nucleon interaction at densities up to one and half times the nuclear matter density. The effects of the finite box size are estimated using variational wave functions together with cluster expansion and chain summation techniques. They are small at subnuclear densities. We discuss the expansion of the energy of low-density neutron gas in powers of its Fermi momentum. This expansion is strongly modified by the large nn scattering length, and does not begin with the Fermi-gas kinetic energy as assumed in both Skyrme and relativistic mean field theories. The leading term of neutron gas energy is ~ half the Fermi-gas kinetic energy. The quantum Monte Carlo results are also used to calibrate the accuracy of variational calculations ...

  12. On the time scale associated with Monte Carlo simulations.

    Science.gov (United States)

    Bal, Kristof M; Neyts, Erik C

    2014-11-28

    Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general.

  13. On the time scale associated with Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bal, Kristof M., E-mail: kristof.bal@uantwerpen.be; Neyts, Erik C. [Department of Chemistry, University of Antwerp, Research Group PLASMANT, Universiteitsplein 1, 2610 Wilrijk, Antwerp (Belgium)

    2014-11-28

    Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general.

  14. Monte Carlo and nonlinearities

    CERN Document Server

    Dauchet, Jérémi; Blanco, Stéphane; Caliot, Cyril; Charon, Julien; Coustet, Christophe; Hafi, Mouna El; Eymet, Vincent; Farges, Olivier; Forest, Vincent; Fournier, Richard; Galtier, Mathieu; Gautrais, Jacques; Khuong, Anaïs; Pelissier, Lionel; Piaud, Benjamin; Roger, Maxime; Terrée, Guillaume; Weitz, Sebastian

    2016-01-01

    The Monte Carlo method is widely used to numerically predict systems behaviour. However, its powerful incremental design assumes a strong premise which has severely limited application so far: the estimation process must combine linearly over dimensions. Here we show that this premise can be alleviated by projecting nonlinearities on a polynomial basis and increasing the configuration-space dimension. Considering phytoplankton growth in light-limited environments, radiative transfer in planetary atmospheres, electromagnetic scattering by particles and concentrated-solar-power-plant productions, we prove the real world usability of this advance on four test-cases that were so far regarded as impracticable by Monte Carlo approaches. We also illustrate an outstanding feature of our method when applied to sharp problems with interacting particles: handling rare events is now straightforward. Overall, our extension preserves the features that made the method popular: addressing nonlinearities does not compromise o...

  15. Atomistic modeling of electronic structure and transport in disordered nanostructures

    Science.gov (United States)

    Kharche, Neerav

    As the Si-CMOS technology approaches the end of the International Technology Roadmap for Semiconductors (ITRS), the semiconductor industry faces a formidable challenge to continue the transistor scaling according to Moore's law. To continue the scaling of classical devices, alternative channel materials such as SiGe, carbon nanotubes, nanowires, and III-V based materials are being investigated along with novel 3D device geometries. Researchers are also investigating radically new quantum computing devices, which are expected to perform calculations faster than the existing classical Si-CMOS based structures. Atomic scale disorders such as interface roughness, alloy randomness, non-uniform strain, and dopant fluctuations are routinely present in the experimental realization of such devices. These disorders now play an increasingly important role in determining the electronic structure and transport properties as device sizes enter the nanometer regime. This work employs the atomistic tight-binding technique, which is ideally suited for modeling systems with local disorders on an atomic scale. High-precision multi-million atom electronic structure calculations of (111) Si surface quantum wells and (100) SiGe/Si/SiGe heterostructure quantum wells are performed to investigate the modulation of valley splitting induced by atomic scale disorders. The calculations presented here resolve the existing discrepancies between theoretically predicted and experimentally measured valley splitting, which is an important design parameter in quantum computing devices. Supercell calculations and the zone-unfolding method are used to compute the bandstructures of inhomogeneous nanowires made of AlGaAs and SiGe and their connection with the transmission coefficients computed using non-equilibrium Green's function method is established. A unified picture of alloy nanowires emerges, in which the nanodevice (transmission) and nanomaterials (bandstructure) viewpoints complement each other

  16. Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized System Dynamics

    Science.gov (United States)

    Ho, Phay; Knight, Christopher; Bostedt, Christoph; Young, Linda; Tegze, Miklos; Faigel, Gyula

    2016-05-01

    We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  17. Atomistic MD simulations reveal the protective role of cholesterol in dimeric beta-amyloid induced disruptions in neuronal membrane mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Cheng, Sara; Chou, George; Vaughn, Mark; Cheng, K.

    2011-10-01

    Interactions of oligomeric beta-amyloid peptides with neuronal membranes have been linked to the pathogenesis of Alzheimer's disease (AD). The molecular details of the interactions of different lipid components, particularly cholesterol (CHOL), of the membranes with the peptides are not clear. Using an atomistic MD simulations approach, the water permeability barrier, structural geometry and order parameters of binary phosphatidylcholine (PC) and PC/CHOL lipid bilayers were examined from various 200 ns-simulation replicates. Our results suggest that the longer length dimer (2 x 42 residues) perturbs the membrane more than the shorter one (2 x 40 residues). In addition, we discovered a significant protective role of cholesterol in protein-induced disruptions of the membranes. The use of a new Monte-Carlo method in characterizing the structures of the conformal annular lipids in close proximity with the proteins will be introduced. We propose that the neurotoxicity of beta-amyloid peptide may be associated with the nanodomain or raft-like structures of the neuronal membranes in-vivo in the development of AD.

  18. Fundamentals of Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Wollaber, Allan Benton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-06-16

    This is a powerpoint presentation which serves as lecture material for the Parallel Computing summer school. It goes over the fundamentals of the Monte Carlo calculation method. The material is presented according to the following outline: Introduction (background, a simple example: estimating π), Why does this even work? (The Law of Large Numbers, The Central Limit Theorem), How to sample (inverse transform sampling, rejection), and An example from particle transport.

  19. Optimization Algorithms in Optimal Predictions of Atomistic Properties by Kriging.

    Science.gov (United States)

    Di Pasquale, Nicodemo; Davie, Stuart J; Popelier, Paul L A

    2016-04-12

    The machine learning method kriging is an attractive tool to construct next-generation force fields. Kriging can accurately predict atomistic properties, which involves optimization of the so-called concentrated log-likelihood function (i.e., fitness function). The difficulty of this optimization problem quickly escalates in response to an increase in either the number of dimensions of the system considered or the size of the training set. In this article, we demonstrate and compare the use of two search algorithms, namely, particle swarm optimization (PSO) and differential evolution (DE), to rapidly obtain the maximum of this fitness function. The ability of these two algorithms to find a stationary point is assessed by using the first derivative of the fitness function. Finally, the converged position obtained by PSO and DE is refined through the limited-memory Broyden-Fletcher-Goldfarb-Shanno bounded (L-BFGS-B) algorithm, which belongs to the class of quasi-Newton algorithms. We show that both PSO and DE are able to come close to the stationary point, even in high-dimensional problems. They do so in a reasonable amount of time, compared to that with the Newton and quasi-Newton algorithms, regardless of the starting position in the search space of kriging hyperparameters. The refinement through L-BFGS-B is able to give the position of the maximum with whichever precision is desired.

  20. Transistor roadmap projection using predictive full-band atomistic modeling

    Energy Technology Data Exchange (ETDEWEB)

    Salmani-Jelodar, M., E-mail: m.salmani@gmail.com; Klimeck, G. [Network for Computational Nanotechnology and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Kim, S. [Intel Corporation, 2501 Northwest 229th Avenue, Hillsboro, Oregon 97124 (United States); Ng, K. [Semiconductor Research Corporation (SRC), 1101 Slater Rd, Durham, North Carolina 27703 (United States)

    2014-08-25

    In this letter, a full band atomistic quantum transport tool is used to predict the performance of double gate metal-oxide-semiconductor field-effect transistors (MOSFETs) over the next 15 years for International Technology Roadmap for Semiconductors (ITRS). As MOSFET channel lengths scale below 20 nm, the number of atoms in the device cross-sections becomes finite. At this scale, quantum mechanical effects play an important role in determining the device characteristics. These quantum effects can be captured with the quantum transport tool. Critical results show the ON-current degradation as a result of geometry scaling, which is in contrast to previous ITRS compact model calculations. Geometric scaling has significant effects on the ON-current by increasing source-to-drain (S/D) tunneling and altering the electronic band structure. By shortening the device gate length from 20 nm to 5.1 nm, the ratio of S/D tunneling current to the overall subthreshold OFF-current increases from 18% to 98%. Despite this ON-current degradation by scaling, the intrinsic device speed is projected to increase at a rate of at least 8% per year as a result of the reduction of the quantum capacitance.

  1. Scoring multipole electrostatics in condensed-phase atomistic simulations.

    Science.gov (United States)

    Bereau, Tristan; Kramer, Christian; Monnard, Fabien W; Nogueira, Elisa S; Ward, Thomas R; Meuwly, Markus

    2013-05-09

    Permanent multipoles (MTPs) embody a natural extension to common point-charge (PC) representations in atomistic simulations. In this work, we propose an alternative to the computationally expensive MTP molecular dynamics simulations by running a simple PC simulation and later reevaluate-"score''-all energies using the more detailed MTP force field. The method, which relies on the assumption that the PC and MTP force fields generate closely related phase spaces, is accomplished by enforcing identical sets of monopoles between the two force fields-effectively highlighting the higher MTP terms as a correction to the PC approximation. We first detail our consistent parametrization of the electrostatics and van der Waals interactions for the two force fields. We then validate the method by comparing the accuracy of protein-ligand binding free energies from both PC and MTP-scored representations with experimentally determined binding constants obtained by us. Specifically, we study the binding of several arylsulfonamide ligands to human carbonic anhydrase II. We find that both representations yield an accuracy of 1 kcal/mol with respect to experiment. Finally, we apply the method to rank the energetic contributions of individual atomic MTP coefficients for molecules solvated in water. All in all, MTP scoring is a computationally appealing method that can provide insight into the multipolar electrostatic interactions of condensed-phase systems.

  2. Atomistic Simulations of Uranium Incorporation into Iron (Hydr)Oxides

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Felmy, Andrew R.; Ilton, Eugene S.

    2011-04-29

    Atomistic simulations were carried out to characterize the coordination environments of U incorporated in three Fe-(hydr)oxide minerals: goethite, magnetite, and hematite. The simulations provided information on U-O and U-Fe distances, coordination numbers, and lattice distortion for U incorporated in different sites (e.g., unoccupied versus occupied sites, octahedral versus tetrahedral) as a function of the oxidation state of U and charge compensation mechanisms (i.e., deprotonation, vacancy formation, or reduction of Fe(III) to Fe(II)). For goethite, deprotonation of first shell hydroxyls enables substitution of U for Fe(III) with a minimal amount of lattice distortion, whereas substitution in unoccupied octahedral sites induced appreciable distortion to 7-fold coordination regardless of U oxidation states and charge compensation mechanisms. Importantly, U-Fe distances of ~3.6 Å were associated with structural incorporation of U and cannot be considered diagnostic of simple adsorption to goethite surfaces. For magnetite, the octahedral site accommodates U(V) or U(VI) with little lattice distortion. U substituted for Fe(III) in hematite maintained octahedral coordination in most cases. In general, comparison of the simulations with available experimental data provides further evidence for the structural incorporation of U in iron (hydr)oxide minerals.

  3. Atomistic modeling of phonon transport in turbostratic graphitic structures

    Science.gov (United States)

    Mao, Rui; Chen, Yifeng; Kim, Ki Wook

    2016-05-01

    Thermal transport in turbostratic graphitic systems is investigated by using an atomistic analytical model based on the 4th-nearest-neighbor force constant approximation and a registry-dependent interlayer potential. The developed model is shown to produce an excellent agreement with the experimental data and ab initio results in the calculation of bulk properties. Subsequent analysis of phonon transport in combination with the Green's function method illustrates the significant dependence of key characteristics on the misorientation angle, clearly indicating the importance of this degree of freedom in multi-stacked structures. Selecting three angles with the smallest commensurate unit cells, the thermal resistance is evaluated at the twisted interface between two AB stacked graphite. The resulting values in the range of 35 × 10-10 K m2/W to 116 × 10-10 K m2/W are as large as those between two dissimilar material systems such as a metal and graphene. The strong rotational effect on the cross-plane thermal transport may offer an effective means of phonon engineering for applications such as thermoelectric materials.

  4. Atomistic Molecular Dynamics Simulations of Shock Compressed Quartz

    CERN Document Server

    Farrow, Matthew R

    2011-01-01

    Atomistic non-equilibrium molecular dynamics (NEMD) simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer and van Santen to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geom- etry optimised system of a polar slab in a 3-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under repres...

  5. Spectrum of Radiation-Induced Clustered Non-DSB Damage - A Monte Carlo Track Structure Modeling and Calculations.

    Science.gov (United States)

    Watanabe, Ritsuko; Rahmanian, Shirin; Nikjoo, Hooshang

    2015-05-01

    The aim of this report is to present the spectrum of initial radiation-induced cellular DNA damage [with particular focus on non-double-strand break (DSB) damage] generated by computer simulations. The radiation types modeled in this study were monoenergetic electrons (100 eV-1.5 keV), ultrasoft X-ray photons Ck, AlK and TiK, as well as some selected ions including 3.2 MeV/u proton; 0.74 and 2.4 MeV/u helium ions; 29 MeV/u nitrogen ions and 950 MeV/u iron ions. Monte Carlo track structure methods were used to simulate damage induction by these radiation types in a cell-mimetic condition from a single-track action. The simulations took into account the action of direct energy deposition events and the reaction of hydroxyl radicals on atomistic linear B-DNA segments of a few helical turns including the water of hydration. Our results permitted the following conclusions: a. The absolute levels of different types of damage [base damage, simple and complex single-strand breaks (SSBs) and DSBs] vary depending on the radiation type; b. Within each damage class, the relative proportions of simple and complex damage vary with radiation type, the latter being higher with high-LET radiations; c. Overall, for both low- and high-LET radiations, the ratios of the yields of base damage to SSBs are similar, being about 3.0 ± 0.2; d. Base damage contributes more to the complexity of both SSBs and DSBs, than additional SSB damage and this is true for both low- and high-LET radiations; and e. The average SSB/DSB ratio for low-LET radiations is about 18, which is about 5 times higher than that for high-LET radiations. The hypothesis that clustered DNA damage is more difficult for cells to repair has gained currency among radiobiologists. However, as yet, there is no direct in vivo experimental method to validate the dependence of kinetics of DNA repair on DNA damage complexity (both DSB and non-DSB types). The data on the detailed spectrum of DNA damage presented here, in particular

  6. Parallelization of Kinetic Theory Simulations

    CERN Document Server

    Howell, Jim; Colbry, Dirk; Pickett, Rodney; Staber, Alec; Sagert, Irina; Strother, Terrance

    2013-01-01

    Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a kinetic Monte Carlo code for astrophysical simulations such as core-collapse supernovae. Our goal is to attain a flexible program that scales well with the architecture of modern supercomputers. This approach requires a hybrid model of programming that combines a message passing interface (MPI) with a multithreading model (OpenMP) in C++. We report on our approach to implement the hybrid design into the kinetic code and show first results which demonstrate a significant gain in performance when many processors are applied.

  7. Monts Jura Jazz Festival

    CERN Multimedia

    2012-01-01

    The 5th edition of the "Monts Jura Jazz Festival" will take place at the Esplanade du Lac in Divonne-les-Bains, France on September 21 and 22. This festival organized by the CERN Jazz Club and supported by the CERN Staff Association is becoming a major musical event in the Geneva region. International Jazz artists like Didier Lockwood and David Reinhardt are part of this year outstanding program. Full program and e-tickets are available on the festival website. Don't miss this great festival!

  8. Monts Jura Jazz Festival

    CERN Multimedia

    Jazz Club

    2012-01-01

    The 5th edition of the "Monts Jura Jazz Festival" that will take place on September 21st and 22nd 2012 at the Esplanade du Lac in Divonne-les-Bains. This festival is organized by the "CERN Jazz Club" with the support of the "CERN Staff Association". This festival is a major musical event in the French/Swiss area and proposes a world class program with jazz artists such as D.Lockwood and D.Reinhardt. More information on http://www.jurajazz.com.

  9. Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.

    Energy Technology Data Exchange (ETDEWEB)

    Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

    2010-09-01

    This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and

  10. Atomistic Mechanisms for Viscoelastic Damping in Inorganic Solids

    Science.gov (United States)

    Ranganathan, Raghavan

    Viscoelasticity, a ubiquitous material property, can be tuned to engineer a wide range of fascinating applications such as mechanical dampers, artificial tissues, functional foams and optoelectronics, among others. Traditionally, soft matter such as polymers and polymer composites have been used extensively for viscoelastic damping applications, owing to the inherent viscous nature of interactions between polymer chains. Although this leads to good damping characteristics, the stiffness in these materials is low, which in turn leads to limitations. In this context, hard inorganic materials and composites are promising candidates for enhanced damping, owing to their large stiffness and, in some cases large loss modulus. Viscoelasticity in these materials has been relatively unexplored and atomistic mechanisms responsible for damping are not apparent. Therefore, the overarching goal of this work is to understand mechanisms for viscoelastic damping in various classes of inorganic composites and alloys at an atomistic level from molecular dynamics simulations. We show that oscillatory shear deformation serves as a powerful probe to explain mechanisms for exceptional damping in hitherto unexplored systems. The first class of inorganic materials consists of crystalline phases of a stiff inclusion in a soft matrix. The two crystals within the composite, namely the soft and a stiff phase, individually show a highly elastic behavior and a very small loss modulus. On the other hand, a composite with the two phases is seen to exhibit damping that is about 20 times larger than predicted theoretical bounds. The primary reason for the damping is due to large anharmonicity in phonon-phonon coupling, resulting from the composite microstructure. A concomitant effect is the distribution of shear strain, which is observed to be highly inhomogeneous and mostly concentrated in the soft phase. Interestingly, the shear frequency at which the damping is greatest is observed to scale with

  11. Atomistic study of the buckling of gold nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, Paer A.T., E-mail: par.olsson@mek.lth.se [Division of Mechanics, Lund University, PO Box 118, SE-221 00 Lund (Sweden); Park, Harold S., E-mail: parkhs@bu.edu [Department of Mechanical Engineering, Boston University, Boston, MA 02215 (United States)

    2011-06-15

    In this work, we present results from atomistic simulations of gold nanowires under axial compression, with a focus on examining the effects of both axial and surface orientation effects on the buckling behavior. This was accomplished by using molecular statics simulations while considering three different crystallographic systems: <1 0 0>/{l_brace}1 0 0{r_brace}, <1 0 0>/{l_brace}1 1 0{r_brace} and <1 1 0>/{l_brace}1 1 0{r_brace}{l_brace}1 0 0{r_brace}, with aspect ratios spanning from 20 to 50 and cross-sectional dimensions ranging from 2.45 to 5.91 nm. The simulations indicate that there is a deviation from the inverse square length dependence of critical forces predicted from traditional linear elastic Bernoulli-Euler and Timoshenko beam theories, where the nature of the deviation from the perfect inverse square length behavior differs for different crystallographic systems. This variation is found to be strongly correlated to either stiffening or increased compliance of the tangential stiffness due to the influence of nonlinear elasticity, which leads to normalized critical forces that decrease with decreasing aspect ratio for the <1 0 0>/{l_brace}1 0 0{r_brace} and <1 0 0>/{l_brace}1 1 0{r_brace} systems, but increase with decreasing aspect ratio for the <1 1 0>/{l_brace}1 1 0{r_brace}{l_brace}1 0 0{r_brace} system. In contrast, it was found that the critical strains are all lower than their bulk counterparts, and that the critical strains decrease with decreasing cross-sectional dimensions; the lower strains may be an effect emanating from the presence of the surfaces, which are all more elastically compliant than the bulk and thus give rise to a more compliant flexural rigidity.

  12. Linking Atomistic and Mesoscale Simulations of Water Soluble Polymers

    Science.gov (United States)

    Jones, J. L.

    2003-03-01

    There exist a range of techniques for studying surfactants and polymers in the mesoscale regime. One of the challenges is to link mesoscale theories and simulations to other calculation methods which address different length scales of the system. We introduce some mesoscale methods of calculation for polymers and surfactants and then present a case study of where mesoscale modelling is used for mechanistic understanding, by linking the method to high throughput in-silico screening methods. We look at the adsorption onto silica of ethylene oxide (EO)/ propylene oxide (PO) block copolymers (lutrols) which have been modified by end-grafting of short, cationic dimethylamino ethyl methacrylate (DMAEMA)chains. Given that the silica surface is negatively charged, it is remarkable that in some circumstances, polymers with longercationic chains have a lower adsorption. The effect is attributed to a competition between strong adsorption of the cationic DMAEMA groups driven by electrostatics, and weaker adsorption of the more numerous EO groups. This then raises the question of how we produce the values for the mesoscale parameters in these models and in the second part of the talk we describe a calculation method for doing this for water soluble polymers. The most promising route, but notoriously costly, is based on free energy calculations at the atomistic level. Free energy calculations are computationally intensive in general, but in an aqueous system one is also faced with the additional problem of using complex continuum models and/or accurate interaction potentials for water. Here we show how potential of mean force (PMF)calculations offer a practical alternative which avoids these drawbacks, though one is still faced with extremely long simulations.

  13. Megasonic cleaning, cavitation, and substrate damage: an atomistic approach

    Science.gov (United States)

    Kapila, Vivek; Deymier, Pierre A.; Shende, Hrishikesh; Pandit, Viraj; Raghavan, Srini; Eschbach, Florence O.

    2006-05-01

    Megasonic cleaning has been a traditional approach for the cleaning of photomasks. Its feasibility as a damage free approach to sub 50 nm particulate removal is under investigation for the cleaning of optical and EUV photomasks. Two major mechanisms are active in a megasonic system, namely, acoustic streaming and acoustic cavitation. Acoustic streaming is instrumental in contaminant removal via application of drag force and rolling of particles, while cavitation may dislodge particles by the release of large energy during cavity implosion or by acting as a secondary source of microstreaming. Often times, the structures (substrates with or without patterns) subjected to megasonic cleaning show evidence of damage. This is one of the impediments in the implementation of megasonic technology for 45 nm and future technology nodes. Prior work suggests that acoustic streaming does not lead to sufficiently strong forces to cause damage to the substrates or patterns. However, current knowledge of the effects of cavitation on cleaning and damage can be described, at best, as speculative. Recent experiments suggest existence of a cavity size and energy distributions in megasonic systems that may be responsible for cleaning and damage. In the current work, we develop a two-dimensional atomistic model to study such multibubble cavitation phenomena. The model consists of a Lennard-Jones liquid which is subjected to sinusoidal pressure changes leading to the formation of cavitation bubbles. The current work reports on the effects of pressure amplitude (megasonic power) and frequency on cavity size distributions in vaporous and gaseous cavitation. The findings of the work highlight the role of multibubble cavitation as cleaning and damage mechanism in megasonic cleaning.

  14. A fully atomistic model of the Cx32 connexon.

    Directory of Open Access Journals (Sweden)

    Sergio Pantano

    Full Text Available Connexins are plasma membrane proteins that associate in hexameric complexes to form channels named connexons. Two connexons in neighboring cells may dock to form a "gap junction" channel, i.e. an intercellular conduit that permits the direct exchange of solutes between the cytoplasm of adjacent cells and thus mediate cell-cell ion and metabolic signaling. The lack of high resolution data for connexon structures has hampered so far the study of the structure-function relationships that link molecular effects of disease-causing mutations with their observed phenotypes. Here we present a combination of modeling techniques and molecular dynamics (MD to infer side chain positions starting from low resolution structures containing only C alpha atoms. We validated this procedure on the structure of the KcsA potassium channel, which is solved at atomic resolution. We then produced a fully atomistic model of a homotypic Cx32 connexon starting from a published model of the C alpha carbons arrangement for the connexin transmembrane helices, to which we added extracellular and cytoplasmic loops. To achieve structural relaxation within a realistic environment, we used MD simulations inserted in an explicit solvent-membrane context and we subsequently checked predictions of putative side chain positions and interactions in the Cx32 connexon against a vast body of experimental reports. Our results provide new mechanistic insights into the effects of numerous spontaneous mutations and their implication in connexin-related pathologies. This model constitutes a step forward towards a structurally detailed description of the gap junction architecture and provides a structural platform to plan new biochemical and biophysical experiments aimed at elucidating the structure of connexin channels and hemichannels.

  15. Kinetic Interface

    DEFF Research Database (Denmark)

    2009-01-01

    A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises.......A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises....

  16. Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical Theory with Generalized Quantum Master Equations.

    Science.gov (United States)

    Pfalzgraff, William C; Kelly, Aaron; Markland, Thomas E

    2015-12-03

    The development of methods that can efficiently and accurately treat nonadiabatic dynamics in quantum systems coupled to arbitrary atomistic environments remains a significant challenge in problems ranging from exciton transport in photovoltaic materials to electron and proton transfer in catalysis. Here we show that our recently introduced MF-GQME approach, which combines Ehrenfest mean field theory with the generalized quantum master equation framework, is able to yield quantitative accuracy over a wide range of charge-transfer regimes in fully atomistic environments. This is accompanied by computational speed-ups of up to 3 orders of magnitude over a direct application of Ehrenfest theory. This development offers the opportunity to efficiently investigate the atomistic details of nonadiabatic quantum relaxation processes in regimes where obtaining accurate results has previously been elusive.

  17. Accelerating a hybrid continuum-atomistic fluidic model with on-the-fly machine learning

    CERN Document Server

    Stephenson, David; Lockerby, Duncan A

    2016-01-01

    We present a hybrid continuum-atomistic scheme which combines molecular dynamics (MD) simulations with on-the-fly machine learning techniques for the accurate and efficient prediction of multiscale fluidic systems. By using a Gaussian process as a surrogate model for the computationally expensive MD simulations, we use Bayesian inference to predict the system behaviour at the atomistic scale, purely by consideration of the macroscopic inputs and outputs. Whenever the uncertainty of this prediction is greater than a predetermined acceptable threshold, a new MD simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial enhancement to the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging-diverging channel, and make comparisons between the new s...

  18. Local stress and heat flux in atomistic systems involving three-body forces.

    Science.gov (United States)

    Chen, Youping

    2006-02-01

    Local densities of fundamental physical quantities, including stress and heat flux fields, are formulated for atomistic systems involving three-body forces. The obtained formulas are calculable within an atomistic simulation, in consistent with the conservation equations of thermodynamics of continuum, and can be applied to systems with general two- and three-body interaction forces. It is hoped that this work may correct some misuse of inappropriate formulas of stress and heat flux in the literature, may clarify the definition of site energy of many-body potentials, and may serve as an analytical link between an atomistic model and a continuum theory. Physical meanings of the obtained formulas, their relation with virial theorem and heat theorem, and the applicability are discussed.

  19. An atomistic modelling of the porosity impact on UO{sub 2} matrix macroscopic properties

    Energy Technology Data Exchange (ETDEWEB)

    Jelea, A., E-mail: andrei.jelea@irsn.fr [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Institute of Physical Chemistry Ilie Murgulescu, Romanian Academy, 202 Spl Independentei St., 060021 Bucharest-12 (Romania); Colbert, M. [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Ribeiro, F. [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Treglia, G. [Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Pellenq, R.J.-M. [Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States)

    2011-08-15

    Highlights: > The porosity impact on the UO{sub 2} matrix thermomechanical properties was investigated. > Atomistic simulation techniques were used in this study. > The UO{sub 2} thermal expansion coefficient is modified due to the pore surface effects. > The elastic moduli at 0 K and at finite temperature decrease linearly with porosity. - Abstract: The porosity impact on the UO{sub 2} matrix thermomechanical properties was investigated using atomistic simulation techniques. The porosity modifies the thermal expansion coefficient and this is attributed to pore surface effects. The elastic moduli at 0 K and at finite temperature decrease with porosity, this variation being well approximated using affine functions. These results agree with other mesoscale model predictions and experimental data, showing the ability of the semiempirical potential atomistic simulations to give an overall good description of the porous UO{sub 2}. However, the surface effects are incompletely described.

  20. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. I. Structural modeling

    Science.gov (United States)

    Kim, Nayong; Kim, Yongman; Tsotsis, Theodore T.; Sahimi, Muhammad

    2005-06-01

    An atomistic model of layered double hydroxides, an important class of nanoporous materials, is presented. These materials have wide applications, ranging from adsorbents for gases and liquid ions to nanoporous membranes and catalysts. They consist of two types of metallic cations that are accommodated by a close-packed configuration of OH- and other anions in a positively charged brucitelike layer. Water and various anions are distributed in the interlayer space for charge compensation. A modified form of the consistent-valence force field, together with energy minimization and molecular dynamics simulations, is utilized for developing an atomistic model of the materials. To test the accuracy of the model, we compare the vibrational frequencies, x-ray diffraction patterns, and the basal spacing of the material, computed using the atomistic model, with our experimental data over a wide range of temperature. Good agreement is found between the computed and measured quantities.

  1. Origin of unrealistic blunting during atomistic fracture simulations based on MEAM potentials

    Science.gov (United States)

    Ko, Won-Seok; Lee, Byeong-Joo

    2014-06-01

    Atomistic simulations based on interatomic potentials have frequently failed to correctly reproduce the brittle fracture of materials, showing an unrealistic blunting. We analyse the origin of the unrealistic blunting during atomistic simulations by modified embedded-atom method (MEAM) potentials for experimentally well-known brittle materials such as bcc tungsten and diamond silicon. The radial cut-off which has been thought to give no influence on MEAM calculations is found to have a decisive effect on the crack propagation behaviour. Extending both cut-off distance and truncation range can prevent the unrealistic blunting, reproducing many well-known fracture behaviour which have been difficult to reproduce. The result provides a guideline for future atomistic simulations that focus on various fracture-related phenomena including the failure of metallic-covalent bonding material systems using MEAM potentials.

  2. MCMini: Monte Carlo on GPGPU

    Energy Technology Data Exchange (ETDEWEB)

    Marcus, Ryan C. [Los Alamos National Laboratory

    2012-07-25

    MCMini is a proof of concept that demonstrates the possibility for Monte Carlo neutron transport using OpenCL with a focus on performance. This implementation, written in C, shows that tracing particles and calculating reactions on a 3D mesh can be done in a highly scalable fashion. These results demonstrate a potential path forward for MCNP or other Monte Carlo codes.

  3. Amyloid protein unfolding and insertion kinetics on neuronal membrane mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Vaughn, Mark; Cheng, Kwan

    2010-03-01

    Atomistic details of beta-amyloid (Aβ ) protein unfolding and lipid interaction kinetics mediated by the neuronal membrane surface are important for developing new therapeutic strategies to prevent and cure Alzheimer's disease. Using all-atom MD simulations, we explored the early unfolding and insertion kinetics of 40 and 42 residue long Aβ in binary lipid mixtures with and without cholesterol that mimic the cholesterol-depleted and cholesterol-enriched lipid nanodomains of neurons. The protein conformational transition kinetics was evaluated from the secondary structure profile versus simulation time plot. The extent of membrane disruption was examined by the calculated order parameters of lipid acyl chains and cholesterol fused rings as well as the density profiles of water and lipid headgroups at defined regions across the lipid bilayer from our simulations. Our results revealed that both the cholesterol content and the length of the protein affect the protein-insertion and membrane stability in our model lipid bilayer systems.

  4. Phase separation in H2O:N2 mixture - molecular dynamics simulations using atomistic force fields

    Energy Technology Data Exchange (ETDEWEB)

    Maiti, A; Gee, R; Bastea, S; Fried, L

    2006-09-25

    A class II atomistic force field with Lennard-Jones 6-9 nonbond interactions is used to investigate equations of state (EOS) for important high explosive detonation products N{sub 2} and H{sub 2}O in the temperature range 700-2500 K and pressure range 0.1-10 GPa. A standard 6th order parameter-mixing scheme is then employed to study a 2:1 (molar) H{sub 2}O:N{sub 2} mixture, to investigate in particular the possibility of phase-separation under detonation conditions. The simulations demonstrate several important results, including: (1) the accuracy of computed EOS for both N{sub 2} and H{sub 2}O over the entire range of temperature and pressure considered; (2) accurate mixing-demixing phase boundary as compared to experimental data; and (3) the departure of mixing free energy from that predicted by ideal mixing law. The results provide comparison and guidance to state-of-the-art chemical kinetic models.

  5. Atomistic simulation studies on the dynamics and thermodynamics of nonpolar molecules within the zeolite imidazolate framework-8.

    Science.gov (United States)

    Pantatosaki, Evangelia; Pazzona, Federico G; Megariotis, Gregory; Papadopoulos, George K

    2010-02-25

    Statistical-mechanics-based simulation studies at the atomistic level of argon (Ar), methane (CH(4)), and hydrogen (H(2)) sorbed in the zeolite imidazolate framework-8 (ZIF-8) are reported. ZIF-8 is a product of a special kind of chemical process, recently termed as reticular synthesis, which has generated a class of materials of critical importance as molecular binders. In this work, we explore the mechanisms that govern the sorption thermodynamics and kinetics of nonpolar sorbates possessing different sizes and strength of interactions with the metal-organic framework to understand the outstanding properties of this novel class of sorbents, as revealed by experiments published elsewhere. For this purpose, we have developed an in-house modeling procedure involving calculations of sorption isotherms, partial internal energies, various probability density functions, and molecular dynamics for the simulation of the sorbed phase over a wide range of occupancies and temperatures within a digitally reconstructed unit cell of ZIF-8. The results showed that sorbates perceive a marked energetic inhomogeneity within the atomic framework of the metal-organic material under study, resulting in free energy barriers that give rise to inflections in the sorption isotherms and guide the dynamics of guest molecules.

  6. Atomistic Simulations of Chemical Reactivity of TATB Under Thermal and Shock Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Manaa, M R; Reed, E J; Fried, L E

    2009-09-23

    The study of chemical transformations that occur at the reactive shock front of energetic materials provides important information for the development of predictive models at the grain-and continuum scales. A major shortcoming of current high explosives models is the lack of chemical kinetics data of the reacting explosive in the high pressure and temperature regimes. In the absence of experimental data, long-time scale atomistic molecular dynamics simulations with reactive chemistry become a viable recourse to provide an insight into the decomposition mechanism of explosives, and to obtain effective reaction rate laws. These rates can then be incorporated into thermo-chemical-hydro codes (such as Cheetah linked to ALE3D) for accurate description of the grain and macro scales dynamics of reacting explosives. In this talk, I will present quantum simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystals under thermal decomposition (high density and temperature) and shock compression conditions. This is the first time that condensed phase quantum methods have been used to study the chemistry of insensitive high explosives. We used the quantum-based, self-consistent charge density functional tight binding method (SCC{_}DFTB) to calculate the interatomic forces for reliable predictions of chemical reactions, and to examine electronic properties at detonation conditions for a relatively long time-scale on the order of several hundreds of picoseconds. For thermal decomposition of TATB, we conducted constant volume-temperature simulations, ranging from 0.35 to 2 nanoseconds, at {rho} = 2.87 g/cm{sup 3} at T = 3500, 3000, 2500, and 1500 K, and {rho} = 2.9 g/cm{sup 3} and 2.72 g/cm{sup 3}, at T = 3000 K. We also simulated crystal TATB's reactivity under steady overdriven shock compression using the multi-scale shock technique. We conducted shock simulations with specified shock speeds of 8, 9, and 10 km/s for up to 0.43 ns duration, enabling us to track the

  7. Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Paavilainen, S.; Rog, T.; Vattulainen, I.

    2011-01-01

    We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile, no sign......We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile......, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril....

  8. Hypercrosslinked polystyrene networks: An atomistic molecular dynamics simulation combined with a mapping/reverse mapping procedure

    Energy Technology Data Exchange (ETDEWEB)

    Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R. [A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova Str. 28, 119991 Moscow (Russian Federation)

    2014-04-07

    An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.

  9. Monte Carlo methods for electromagnetics

    CERN Document Server

    Sadiku, Matthew NO

    2009-01-01

    Until now, novices had to painstakingly dig through the literature to discover how to use Monte Carlo techniques for solving electromagnetic problems. Written by one of the foremost researchers in the field, Monte Carlo Methods for Electromagnetics provides a solid understanding of these methods and their applications in electromagnetic computation. Including much of his own work, the author brings together essential information from several different publications.Using a simple, clear writing style, the author begins with a historical background and review of electromagnetic theory. After addressing probability and statistics, he introduces the finite difference method as well as the fixed and floating random walk Monte Carlo methods. The text then applies the Exodus method to Laplace's and Poisson's equations and presents Monte Carlo techniques for handing Neumann problems. It also deals with whole field computation using the Markov chain, applies Monte Carlo methods to time-varying diffusion problems, and ...

  10. Monte Carlo exploration of warped Higgsless models

    Energy Technology Data Exchange (ETDEWEB)

    Hewett, JoAnne L.; Lillie, Benjamin; Rizzo, Thomas Gerard [Stanford Linear Accelerator Center, 2575 Sand Hill Rd., Menlo Park, CA, 94025 (United States)]. E-mail: rizzo@slac.stanford.edu

    2004-10-01

    We have performed a detailed Monte Carlo exploration of the parameter space for a warped Higgsless model of electroweak symmetry breaking in 5 dimensions. This model is based on the SU(2){sub L} x SU(2){sub R} x U(1){sub B-L} gauge group in an AdS{sub 5} bulk with arbitrary gauge kinetic terms on both the Planck and TeV branes. Constraints arising from precision electroweak measurements and collider data are found to be relatively easy to satisfy. We show, however, that the additional requirement of perturbative unitarity up to the cut-off, {approx_equal} 10 TeV, in W{sub L}{sup +}W{sub L}{sup -} elastic scattering in the absence of dangerous tachyons eliminates all models. If successful models of this class exist, they must be highly fine-tuned. (author)

  11. Monte Carlo Exploration of Warped Higgsless Models

    CERN Document Server

    Hewett, J L; Rizzo, T G

    2004-01-01

    We have performed a detailed Monte Carlo exploration of the parameter space for a warped Higgsless model of electroweak symmetry breaking in 5 dimensions. This model is based on the $SU(2)_L\\times SU(2)_R\\times U(1)_{B-L}$ gauge group in an AdS$_5$ bulk with arbitrary gauge kinetic terms on both the Planck and TeV branes. Constraints arising from precision electroweak measurements and collider data are found to be relatively easy to satisfy. We show, however, that the additional requirement of perturbative unitarity up to the cut-off, $\\simeq 10$ TeV, in $W_L^+W_L^-$ elastic scattering in the absence of dangerous tachyons eliminates all models. If successful models of this class exist, they must be highly fine-tuned.

  12. Scalable and portable visualization of large atomistic datasets

    Science.gov (United States)

    Sharma, Ashish; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2004-10-01

    A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data

  13. Metropolis Methods for Quantum Monte Carlo Simulations

    OpenAIRE

    Ceperley, D. M.

    2003-01-01

    Since its first description fifty years ago, the Metropolis Monte Carlo method has been used in a variety of different ways for the simulation of continuum quantum many-body systems. This paper will consider some of the generalizations of the Metropolis algorithm employed in quantum Monte Carlo: Variational Monte Carlo, dynamical methods for projector monte carlo ({\\it i.e.} diffusion Monte Carlo with rejection), multilevel sampling in path integral Monte Carlo, the sampling of permutations, ...

  14. Kinetics and

    Directory of Open Access Journals (Sweden)

    Mojtaba Ahmadi

    2016-11-01

    Full Text Available The aqueous degradation of Reactive Yellow 84 (RY84 by potassium peroxydisulfate (K2S2O8 has been studied in laboratory scale experiments. The effect of the initial concentrations of potassium peroxydisulfate and RY84, pH and temperature on RY84 degradation were also examined. Experimental data were analyzed using first and second-order kinetics. The degradation kinetics of RY84 of the potassium peroxydisulfate process followed the second-order reaction kinetics. These rate constants have an extreme values similar to of 9.493 mM−1min−1 at a peroxydisulfate dose of 4 mmol/L. Thermodynamic parameters such as activation (Ea and Gibbs free energy (ΔG° were also evaluated. The negative value of ΔGo and Ea shows the spontaneous reaction natural conditions and exothermic nature.

  15. Kinetic activation-relaxation technique

    Science.gov (United States)

    Béland, Laurent Karim; Brommer, Peter; El-Mellouhi, Fedwa; Joly, Jean-François; Mousseau, Normand

    2011-10-01

    We present a detailed description of the kinetic activation-relaxation technique (k-ART), an off-lattice, self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search. Combining a topological classification for local environments and event generation with ART nouveau, an efficient unbiased sampling method for finding transition states, k-ART can be applied to complex materials with atoms in off-lattice positions or with elastic deformations that cannot be handled with standard KMC approaches. In addition to presenting the various elements of the algorithm, we demonstrate the general character of k-ART by applying the algorithm to three challenging systems: self-defect annihilation in c-Si (crystalline silicon), self-interstitial diffusion in Fe, and structural relaxation in a-Si (amorphous silicon).

  16. Kinetic activation-relaxation technique.

    Science.gov (United States)

    Béland, Laurent Karim; Brommer, Peter; El-Mellouhi, Fedwa; Joly, Jean-François; Mousseau, Normand

    2011-10-01

    We present a detailed description of the kinetic activation-relaxation technique (k-ART), an off-lattice, self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search. Combining a topological classification for local environments and event generation with ART nouveau, an efficient unbiased sampling method for finding transition states, k-ART can be applied to complex materials with atoms in off-lattice positions or with elastic deformations that cannot be handled with standard KMC approaches. In addition to presenting the various elements of the algorithm, we demonstrate the general character of k-ART by applying the algorithm to three challenging systems: self-defect annihilation in c-Si (crystalline silicon), self-interstitial diffusion in Fe, and structural relaxation in a-Si (amorphous silicon).

  17. Atomistic simulation of laser ablation of gold : Effect of pressure relaxation

    NARCIS (Netherlands)

    Norman, G. E.; Starikov, S. V.; Stegailov, V. V.

    2012-01-01

    The process of ablation of a gold target by femto- and picosecond laser radiation pulses has been studied by numerical simulations using an atomistic model with allowance for the electron subsystem and the dependence of the ion-ion interaction potential on the electron temperature. Using this potent

  18. Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures

    NARCIS (Netherlands)

    Rzepiela, Andrzej J.; Schafer, Lars V.; Goga, Nicolae; Risselada, H. Jelger; De Vries, Alex H.; Marrink, Siewert J.

    2010-01-01

    We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which

  19. A Mathematical Analysis of Atomistic-to-Continuum (AtC) Multiscale Coupling Methods

    Energy Technology Data Exchange (ETDEWEB)

    Gunzburger, Max

    2013-11-13

    We have worked on several projects aimed at improving the efficiency and understanding of multiscale methods, especially those applicable to problems involving atomistic-to-continuum coupling. Activities include blending methods for AtC coupling and efficient quasi-continuum methods for problems with long-range interactions.

  20. Atomistic study on the FCC/BCC interface structure with {112}KS orientation

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Keonwook [Los Alamos National Laboratory; Beyerlein, Irene [Los Alamos National Laboratory

    2011-09-23

    In this study, atomistic simulation is used to explore the atomic interface structure, the intrinsic defect network, and mechanism of twin formation from the {112}KS Cu-Nb interface. The interface structure of different material systems AI-Fe and AI-Nb are also compared with Cu-Nb interface.

  1. Hybrid simulations : combining atomistic and coarse-grained force fields using virtual sites

    NARCIS (Netherlands)

    Rzepiela, Andrzej J.; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J.

    2011-01-01

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. I

  2. Monte Carlo integration on GPU

    OpenAIRE

    Kanzaki, J.

    2010-01-01

    We use a graphics processing unit (GPU) for fast computations of Monte Carlo integrations. Two widely used Monte Carlo integration programs, VEGAS and BASES, are parallelized on GPU. By using $W^{+}$ plus multi-gluon production processes at LHC, we test integrated cross sections and execution time for programs in FORTRAN and C on CPU and those on GPU. Integrated results agree with each other within statistical errors. Execution time of programs on GPU run about 50 times faster than those in C...

  3. Fundamental aspects of plasma chemical physics kinetics

    CERN Document Server

    Capitelli, Mario; Colonna, Gianpiero; Esposito, Fabrizio; Gorse, Claudine; Hassouni, Khaled; Laricchiuta, Annarita; Longo, Savino

    2016-01-01

    Describing non-equilibrium "cold" plasmas through a chemical physics approach, this book uses the state-to-state plasma kinetics, which considers each internal state as a new species with its own cross sections. Extended atomic and molecular master equations are coupled with Boltzmann and Monte Carlo methods to solve the electron energy distribution function. Selected examples in different applied fields, such as microelectronics, fusion, and aerospace, are presented and discussed including the self-consistent kinetics in RF parallel plate reactors, the optimization of negative ion sources and the expansion of high enthalpy flows through nozzles of different geometries. The book will cover the main aspects of the state-to-state kinetic approach for the description of nonequilibrium cold plasmas, illustrating the more recent achievements in the development of kinetic models including the self-consistent coupling of master equations and Boltzmann equation for electron dynamics. To give a complete portrayal, the...

  4. Kinetic Biochemistry

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2003-03-01

    Full Text Available Mathematics and computer programming have a major contribution to chemistry. Two directions can be identified: one that searches and tries (rich to explain the structural binding and shape of the chemical compounds [1] with major applications in QSPR/QSAR studies [2], and applied sciences such as engineering of materials or agriculture [3]; the second direction is to models the kinetic processes that are involved in chemical reactions [4]. Many such models are available here. The present paper describes three variants of well the known kinetic models and presents the mathematical equations associated with them. The differential equations are numerically solved and fitted with MathCad program. [1] Diudea M., Gutman I., Jäntschi L., Molecular Topology, Nova Science, Huntington, New York, 332 p., 2001, 2002. [2] Diudea M. V., Ed., QSPR / QSAR Studies by Molecular Descriptors, Nova Science, Huntington, New York, 438 p., 2001. [3] Jäntschi L., Microbiology and Toxicology. Phytochemistry Studies (in Romanian, Amici, Cluj-Napoca, 184 p., 2003. [4] Jäntschi L., Unguresan M., Physical Chemistry. Molecular Kinetic and Dynamic (in Romanian, Mediamira, Cluj-Napoca, 159 p., 2001.

  5. Physisorption kinetics

    CERN Document Server

    Kreuzer, Hans Jürgen

    1986-01-01

    This monograph deals with the kinetics of adsorption and desorption of molecules physisorbed on solid surfaces. Although frequent and detailed reference is made to experiment, it is mainly concerned with the theory of the subject. In this, we have attempted to present a unified picture based on the master equation approach. Physisorption kinetics is by no means a closed and mature subject; rather, in writing this monograph we intended to survey a field very much in flux, to assess its achievements so far, and to give a reasonable basis from which further developments can take off. For this reason we have included many papers in the bibliography that are not referred to in the text but are of relevance to physisorption. To keep this monograph to a reasonable size, and also to allow for some unity in the presentation of the material, we had to omit a number of topics related to physisorption kinetics. We have not covered to any extent the equilibrium properties of physisorbed layers such as structures, phase tr...

  6. Coupling-of-length-scale approach for multiscale atomistic-continuum simulations: Atomistically-induced stress distributions in Si/Si_3N4 nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George; Madhukar, Anupam

    2001-03-01

    A hybrid molecular-dynamics and finite-element simulation approach has been used to investigate stress distributions in Si(111) nanopixels covered with both crystalline and amorphous Si_3N4 thin films. Surfaces, lattice-mismatched interfaces, edges, and corners create stress fields on the order of 1 GPa inside the Si substrate with patterns that cannot be reproduced by a continuum approach alone. For these atomistically-induced inhomogeneouse stresses, the hybrid simulation approach provides an excellent agreement with the standard molecular dynamics, with considerably less computational costs.

  7. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si3N4 Nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-01

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  8. Subtle Monte Carlo Updates in Dense Molecular Systems

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Boomsma, Wouter; Johansson, Kristoffer E.;

    2012-01-01

    Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce...... as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results...... a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule...

  9. Multilevel sequential Monte Carlo samplers

    KAUST Repository

    Beskos, Alexandros

    2016-08-29

    In this article we consider the approximation of expectations w.r.t. probability distributions associated to the solution of partial differential equations (PDEs); this scenario appears routinely in Bayesian inverse problems. In practice, one often has to solve the associated PDE numerically, using, for instance finite element methods which depend on the step-size level . hL. In addition, the expectation cannot be computed analytically and one often resorts to Monte Carlo methods. In the context of this problem, it is known that the introduction of the multilevel Monte Carlo (MLMC) method can reduce the amount of computational effort to estimate expectations, for a given level of error. This is achieved via a telescoping identity associated to a Monte Carlo approximation of a sequence of probability distributions with discretization levels . ∞>h0>h1⋯>hL. In many practical problems of interest, one cannot achieve an i.i.d. sampling of the associated sequence and a sequential Monte Carlo (SMC) version of the MLMC method is introduced to deal with this problem. It is shown that under appropriate assumptions, the attractive property of a reduction of the amount of computational effort to estimate expectations, for a given level of error, can be maintained within the SMC context. That is, relative to exact sampling and Monte Carlo for the distribution at the finest level . hL. The approach is numerically illustrated on a Bayesian inverse problem. © 2016 Elsevier B.V.

  10. Symmetry Breaking and Fine Structure Splitting in Zincblende Quantum Dots: Atomistic Simulations of Long-Range Strain and Piezoelectric Field

    Science.gov (United States)

    Ahmed, Shaikh; Usman, Muhammad; Heitzinger, Clemens; Rahman, Rajib; Schliwa, Andrei; Klimeck, Gerhard

    2007-04-01

    Electrons and holes captured in self-assembled quantum dots (QDs) are subject to symmetry breaking that cannot be represented in with continuum material representations. Atomistic calculations reveal symmetry lowering due to effects of strain and piezo-electric fields. These effects are fundamentally based on the crystal topology in the quantum dots. This work studies these two competing effects and demonstrates the fine structure splitting that has been demonstrated experimentally can be attributed to the underlying atomistic structure of the quantum dots.

  11. Equilibrium Statistics: Monte Carlo Methods

    Science.gov (United States)

    Kröger, Martin

    Monte Carlo methods use random numbers, or ‘random’ sequences, to sample from a known shape of a distribution, or to extract distribution by other means. and, in the context of this book, to (i) generate representative equilibrated samples prior being subjected to external fields, or (ii) evaluate high-dimensional integrals. Recipes for both topics, and some more general methods, are summarized in this chapter. It is important to realize, that Monte Carlo should be as artificial as possible to be efficient and elegant. Advanced Monte Carlo ‘moves’, required to optimize the speed of algorithms for a particular problem at hand, are outside the scope of this brief introduction. One particular modern example is the wavelet-accelerated MC sampling of polymer chains [406].

  12. Nanoscale finite element models for vibrations of single-walled carbon nanotubes:atomistic versus continuum

    Institute of Scientific and Technical Information of China (English)

    R ANSARI; S ROUHI; M ARYAYI

    2013-01-01

    By the atomistic and continuum finite element models, the free vibration behavior of single-walled carbon nanotubes (SWCNTs) is studied. In the atomistic finite element model, the bonds and atoms are modeled by the beam and point mass elements, respectively. The molecular mechanics is linked to structural mechanics to determine the elastic properties of the mentioned beam elements. In the continuum finite element approach, by neglecting the discrete nature of the atomic structure of the nanotubes, they are modeled with shell elements. By both models, the natural frequencies of SWCNTs are computed, and the effects of the geometrical parameters, the atomic structure, and the boundary conditions are investigated. The accuracy of the utilized methods is verified in comparison with molecular dynamic simulations. The molecular structural model leads to more reliable results, especially for lower aspect ratios. The present analysis provides valuable information about application of continuum models in the investigation of the mechanical behaviors of nanotubes.

  13. Systematic study of grain boundary atomistic structures and related properties in cubic zirconia bicrystals

    Energy Technology Data Exchange (ETDEWEB)

    Shibata, N.; Ikuhara, Y. [Inst. of Engineering Innovation, Univ. of Tokyo, Tokyo (Japan); Oba, F. [Dept. of Materials Science and Engineering, Graduate School of Engineering, Kyoto Univ., Kyoto (Japan); Yamamoto, T. [Dept. of Advanced Materials Science, Graduate School of Frontier Science, Univ. of Tokyo, Kashiwa, Chiba (Japan)

    2005-02-01

    Systematic grain boundary study of cubic zirconia has been conducted by using bicrystals. It is clearly demonstrated that grain boundary atomistic structures dramatically change according to the misorientations and plane orientations of the boundaries, resulting in a dramatic change of excess energies and solute segregation behaviors. Combining with theoretical calculations, it is found that grain boundaries possess unique coordination-deficient cation sites at the cores, and their densities have a clear correlation with these properties in high-angle grain boundaries. This result indicates that grain boundary properties in ceramics are possibly determined by the accumulation of coordination-deficient sites. Thus, systematic grain boundary study using bicrystal offers fundamental understandings of the relationship between atomistic structures and properties in ceramic grain boundaries. (orig.)

  14. Atomistic electrodynamics simulations of bare and ligand-coated nanoparticles in the quantum size regime.

    Science.gov (United States)

    Chen, Xing; Moore, Justin E; Zekarias, Meserret; Jensen, Lasse

    2015-11-10

    The optical properties of metallic nanoparticles with nanometre dimensions exhibit features that cannot be described by classical electrodynamics. In this quantum size regime, the near-field properties are significantly modified and depend strongly on the geometric arrangements. However, simulating realistically sized systems while retaining the atomistic description remains computationally intractable for fully quantum mechanical approaches. Here we introduce an atomistic electrodynamics model where the traditional description of nanoparticles in terms of a macroscopic homogenous dielectric constant is replaced by an atomic representation with dielectric properties that depend on the local chemical environment. This model provides a unified description of bare and ligand-coated nanoparticles, as well as strongly interacting nanoparticle dimer systems. The non-local screening owing to an inhomogeneous ligand layer is shown to drastically modify the near-field properties. This will be important to consider in optimization of plasmonic nanostructures for near-field spectroscopy and sensing applications.

  15. Atomistic simulation of grain boundary structure in a series of B2 intermetallics

    Energy Technology Data Exchange (ETDEWEB)

    Mutasa, B. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Engineering; Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Engineering

    1996-08-01

    Using molecular statics and interatomic potentials of the embedded atom type, the relaxed atomistic grain boundary structures in B2 aluminides were investigated in order to study trends in a series of B2 compounds. The compounds studied: FeAl, NiAl and CoAl show increasing anti-phase boundary energies. The atomistic structure of the {Sigma}=5(310)[100] and {Sigma}=5(210)[100] symmetrical tilt grain boundaries in these compounds was studied considering possible variations of local chemical composition on grain boundary energetics. The structures obtained for the three alloys are very similar. A discussion of the trends in energetics across this series of compounds is entered into. (orig.)

  16. Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

    Science.gov (United States)

    Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

    2016-01-01

    Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

  17. Buprenorphine kinetics.

    Science.gov (United States)

    Bullingham, R E; McQuay, H J; Moore, A; Bennett, M R

    1980-11-01

    Buprenorphine kinetics was determined in surgical patients using radioimmunoassay. Buprenorphine was measured in the plasma of 24 patients who had received 0.3 mg buprenorphine intraoperatively. After 3 hr 10 of these patients then received a further 0.3 mg buprenorphine intravenously for postoperative pain relief, and 11 patients were given 0.3 mg intramuscularly; again, plasma levels were measured for 3 hr. The data fitted closely to a triexponential decay curve. There was a very fast initial phase, with a half-life (t1/2) of 2 min. The terminal t1/2 was slow, approximately 3 hr. Comparison of the kinetics of the same patient, awake and anesthetized, showed that the clearance was significantly lower in the anesthetized state. A notable feature of the drug given intramuscularly is rapid systemic availability, so that peaks are obtained in 2 to 5 min, and in 10 min the resulting levels are the same as for the intravenous and intramuscular routes.

  18. Monte Carlo Hamiltonian: Linear Potentials

    Institute of Scientific and Technical Information of China (English)

    LUO Xiang-Qian; LIU Jin-Jiang; HUANG Chun-Qing; JIANG Jun-Qin; Helmut KROGER

    2002-01-01

    We further study the validity of the Monte Carlo Hamiltonian method. The advantage of the method,in comparison with the standard Monte Carlo Lagrangian approach, is its capability to study the excited states. Weconsider two quantum mechanical models: a symmetric one V(x) = |x|/2; and an asymmetric one V(x) = ∞, forx < 0 and V(x) = x, for x ≥ 0. The results for the spectrum, wave functions and thermodynamical observables are inagreement with the analytical or Runge-Kutta calculations.

  19. Proton Upset Monte Carlo Simulation

    Science.gov (United States)

    O'Neill, Patrick M.; Kouba, Coy K.; Foster, Charles C.

    2009-01-01

    The Proton Upset Monte Carlo Simulation (PROPSET) program calculates the frequency of on-orbit upsets in computer chips (for given orbits such as Low Earth Orbit, Lunar Orbit, and the like) from proton bombardment based on the results of heavy ion testing alone. The software simulates the bombardment of modern microelectronic components (computer chips) with high-energy (.200 MeV) protons. The nuclear interaction of the proton with the silicon of the chip is modeled and nuclear fragments from this interaction are tracked using Monte Carlo techniques to produce statistically accurate predictions.

  20. Atomistic Failure Mechanism of Single Wall Carbon Nanotubes with Small Diameters

    Institute of Scientific and Technical Information of China (English)

    JI Dong; GAO Xiang; KONG Xiang-Yang; LI Jia-Ming

    2007-01-01

    @@ Single wall carbon nanotubes with small diameters (< 5.0 (A)) subjected to bending deformation are simulated by orthogonal tight-binding molecular dynamics approach. Based on the calculations of C-C bond stretching and breaking in the bending nanotubes, we elucidate the atomistic failure mechanisms of nanotube with small diameters. In the folding zone of bending nanotube, a large elongation of C-C bonds occurs, accounting for the superelastic behaviour.

  1. Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures

    Directory of Open Access Journals (Sweden)

    Aruna Prakash

    2017-01-01

    Full Text Available Single-crystal Ni-base superalloys, consisting of a two-phase γ/ γ ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/ γ ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ ′ particles with planar γ/ γ ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions.

  2. Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments.

    Science.gov (United States)

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  3. Atomistic insight into the minimum wear depth of Cu(111) surface

    OpenAIRE

    2013-01-01

    In the present work, we investigate the minimum wear depth of single crystalline Cu(111) under single asperity friction by means of molecular dynamics simulations. The atomistic mechanisms governing the incipient plasticity are elucidated by characterizing specific defect structures and are correlated to the observed mechanical and frictional responses of the material. Furthermore, the effect of probe radius on the friction process is studied. Our simulations indicate that the formation of we...

  4. Phase field crystal modelling of the order-to-disordered atomistic structure transition of metallic glasses

    Science.gov (United States)

    Zhang, W.; Mi, J.

    2016-03-01

    Bulk metallic glass composites are a new class of metallic alloy systems that have very high tensile strength, ductility and fracture toughness. This unique combination of mechanical properties is largely determined by the presence of crystalline phases uniformly distributed within the glassy matrix. However, there have been very limited reports on how the crystalline phases are nucleated in the super-cooled liquid and their growth dynamics, especially lack of information on the order-to-disordered atomistic structure transition across the crystalline-amorphous interface. In this paper, we use phase field crystal (PFC) method to study the nucleation and growth of the crystalline phases and the glass formation of the super cooled liquid of a binary alloy. The study is focused on understanding the order-to-disordered transition of atomistic configuration across the interface between the crystalline phases and amorphous matrix of different chemical compositions at different thermal conditions. The capability of using PFC to simulate the order-to-disorder atomistic transition in the bulk material or across the interface is discussed in details.

  5. State Representation Approach for Atomistic Time-Dependent Transport Calculations in Molecular Junctions.

    Science.gov (United States)

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

    We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville-von-Neumann equation approach of Sánchez et al. [J. Chem. Phys. 2006, 124, 214708] and Subotnik et al. [J. Chem. Phys. 2009, 130, 144105]. A key ingredient of our approach is a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to uniquely define the bias voltage across the system while maintaining a proper thermal electronic distribution within the finite lead models. Furthermore, it allows us to investigate complex molecular junctions, including multilead configurations. A heuristic derivation of our working equation leads to explicit expressions for the damping and driving terms, which serve as appropriate electron sources and sinks that effectively "open" the finite model system. Although the method does not forbid it, in practice we find neither violation of Pauli's exclusion principles nor deviation from density matrix positivity throughout our numerical simulations of various tight-binding model systems. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic molecular junction models.

  6. A study of conditions for dislocation nucleation in coarser-than-atomistic scale models

    Science.gov (United States)

    Garg, Akanksha; Acharya, Amit; Maloney, Craig E.

    2015-02-01

    We perform atomistic simulations of dislocation nucleation in defect free crystals in 2 and 3 dimensions during indentation with circular (2D) or spherical (3D) indenters. The kinematic structure of the theory of Field Dislocation Mechanics (FDM) is shown to allow the identification of a local feature of the atomistic velocity field in these simulations as indicative of dislocation nucleation. It predicts the precise location of the incipient spatially distributed dislocation field, as shown for the cases of the Embedded Atom Method potential for Al and the Lennard-Jones pair potential. We demonstrate the accuracy of this analysis for two crystallographic orientations in 2D and one in 3D. Apart from the accuracy in predicting the location of dislocation nucleation, the FDM based analysis also demonstrates superior performance than existing nucleation criteria in not persisting in time beyond the nucleation event, as well as differentiating between phase boundary/shear band and dislocation nucleation. Our analysis is meant to facilitate the modeling of dislocation nucleation in coarser-than-atomistic scale models of the mechanics of materials.

  7. The injection of a screw dislocation into a crystal: Atomistics vs. continuum elastodynamics

    Science.gov (United States)

    Verschueren, J.; Gurrutxaga-Lerma, B.; Balint, D. S.; Dini, D.; Sutton, A. P.

    2017-01-01

    The injection (creation) process of a straight screw dislocation is compared atomistically with elastodynamic continuum theory. A method for injecting quiescent screw dislocations into a crystal of tungsten is simulated using non-equilibrium molecular dynamics. The resulting stress fields are compared to the those of elastodynamic solutions for the injection of a quiescent screw dislocation. A number of differences are found: a plane wave emission is observed to emanate from the whole surface of the cut used to create the dislocation, affecting the displacement field along the dislocation line (z), and introducing displacement field components perpendicular to the line (along x and y). It is argued that, in part, this emission is the result of the finite time required to inject the dislocation, whereby the atoms in the cut surface must temporarily be displaced to unstable positions in order to produce the required slip. By modelling this process in the continuum it is shown that the displacements components normal to the dislocation line arise from transient displacements of atoms in the cut surface parallel to x and y. It is shown that once these displacements are included in the elastodynamic continuum formulation the plane wave emission in uz is correctly captured. A detailed comparison between the atomistic and continuum models is then offered, showing that the main atomistic features can also be captured in the continuum.

  8. MONTE CARLO SIMULATION OF SPIN-POLARIZED SECONDARY ELECTRONS FROM IRON

    Institute of Scientific and Technical Information of China (English)

    X. Sun; Z.J. Ding; H.M Li; K. Salma; Z.M. Zhang; W.S. Tan

    2005-01-01

    A Monte Carlo model considering the electron spin direction and spin asymmetry has been developed. The energy distribution of the secondary electron polarization and the primary energy dependence of the polarization from Fe are studied. The simulation results show that:(1) the intensity of the spin-up secondary electrons is larger thanvthat of thevspin-down secondary electrons, suggesting the secondary electrons are spin polarized; (2) the spin polarization of secondary electrons with nearly zero kinetic energy is higher than the average valance spin polarization, Pb=27% for Fe. With increasing kinetic energy, the spin polarization of the secondary electrons decreases to the value of Pb remaining constant at higher kinetic energies;(3) the spin polarization increases with an increase in the primary energy and reaches a saturation value at higher primary energy in both the Monte Carlo simulation and experimental results.

  9. Application of Uncertainty and Sensitivity Analysis to a Kinetic Model for Enzymatic Biodiesel Production

    DEFF Research Database (Denmark)

    Price, Jason Anthony; Nordblad, Mathias; Woodley, John

    2014-01-01

    This paper demonstrates the added benefits of using uncertainty and sensitivity analysis in the kinetics of enzymatic biodiesel production. For this study, a kinetic model by Fedosov and co-workers is used. For the uncertainty analysis the Monte Carlo procedure was used to statistically quantify...

  10. Kinetic buffers.

    Science.gov (United States)

    Alibrandi, Giuseppe; Fabbrizzi, Luigi; Licchelli, Maurizio; Puglisi, Antonio

    2015-01-12

    This paper proposes a new type of molecular device that is able to act as an inverse proton sponge to slowly decrease the pH inside a reaction vessel. This makes the automatic monitoring of the concentration of pH-sensitive systems possible. The device is a composite formed of an alkyl chloride, which kinetically produces acidity, and a buffer that thermodynamically modulates the variation in pH value. Profiles of pH versus time (pH-t plots) have been generated under various experimental conditions by computer simulation, and the device has been tested by carrying out automatic spectrophotometric titrations, without using an autoburette. To underline the wide variety of possible applications, this new system has been used to realize and monitor HCl uptake by a di-copper(II) bistren complex in a single run, in a completely automatic experiment.

  11. Monte Carlo Particle Lists: MCPL

    CERN Document Server

    Kittelmann, Thomas; Knudsen, Erik B; Willendrup, Peter; Cai, Xiao Xiao; Kanaki, Kalliopi

    2016-01-01

    A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community, along with converters and plugins for several popular simulation packages.

  12. Energy Conservation Tests of a Coupled Kinetic-kinetic Plasma-neutral Transport Code

    Energy Technology Data Exchange (ETDEWEB)

    Stotler, D. P.; Chang, C. S.; Ku, S. H.; Lang, J.; Park, G.

    2012-08-29

    A Monte Carlo neutral transport routine, based on DEGAS2, has been coupled to the guiding center ion-electron-neutral neoclassical PIC code XGC0 to provide a realistic treatment of neutral atoms and molecules in the tokamak edge plasma. The DEGAS2 routine allows detailed atomic physics and plasma-material interaction processes to be incorporated into these simulations. The spatial pro le of the neutral particle source used in the DEGAS2 routine is determined from the uxes of XGC0 ions to the material surfaces. The kinetic-kinetic plasma-neutral transport capability is demonstrated with example pedestal fueling simulations.

  13. Applications of Monte Carlo Methods in Calculus.

    Science.gov (United States)

    Gordon, Sheldon P.; Gordon, Florence S.

    1990-01-01

    Discusses the application of probabilistic ideas, especially Monte Carlo simulation, to calculus. Describes some applications using the Monte Carlo method: Riemann sums; maximizing and minimizing a function; mean value theorems; and testing conjectures. (YP)

  14. Monnte Carlo Simulation of Kinetics of Ammonia Oxidative Decomposition over the Commercial Propylene Ammoxidation Catalyst(Mo-Bi)

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 詹晓力; 等

    2003-01-01

    Monte Carlo method is applied to investigate the kinetics of ammonia oxidative decomposition over the commercial propylene ammoxidation catalyst(Mo-Bi).The simulation is quite in agreement with experimetal results.Monte Carlo simulation proves that the process of ammonia oxidation decomposition is a two-step reaction.

  15. A united event grand canonical Monte Carlo study of partially doped polyaniline

    Energy Technology Data Exchange (ETDEWEB)

    Byshkin, M. S., E-mail: mbyshkin@unisa.it, E-mail: gmilano@unisa.it; Correa, A. [Modeling Lab for Nanostructure and Catalysis, Dipartimento di Chimica e Biologia and NANOMATES, University of Salerno, 84084, via Ponte don Melillo, Fisciano Salerno (Italy); Buonocore, F. [ENEA Casaccia Research Center, Via Anguillarese 301, 00123 Rome (Italy); Di Matteo, A. [STMicroelectronics, Via Remo de Feo, 1 80022 Arzano, Naples (Italy); IMAST Scarl Piazza Bovio 22, 80133 Naples (Italy); Milano, G., E-mail: mbyshkin@unisa.it, E-mail: gmilano@unisa.it [Modeling Lab for Nanostructure and Catalysis, Dipartimento di Chimica e Biologia and NANOMATES, University of Salerno, 84084, via Ponte don Melillo, Fisciano Salerno (Italy); IMAST Scarl Piazza Bovio 22, 80133 Naples (Italy)

    2013-12-28

    A Grand Canonical Monte Carlo scheme, based on united events combining protonation/deprotonation and insertion/deletion of HCl molecules is proposed for the generation of polyaniline structures at intermediate doping levels between 0% (PANI EB) and 100% (PANI ES). A procedure based on this scheme and subsequent structure relaxations using molecular dynamics is described and validated. Using the proposed scheme and the corresponding procedure, atomistic models of amorphous PANI-HCl structures were generated and studied at different doping levels. Density, structure factors, and solubility parameters were calculated. Their values agree well with available experimental data. The interactions of HCl with PANI have been studied and distribution of their energies has been analyzed. The procedure has also been extended to the generation of PANI models including adsorbed water and the effect of inclusion of water molecules on PANI properties has also been modeled and discussed. The protocol described here is general and the proposed United Event Grand Canonical Monte Carlo scheme can be easily extended to similar polymeric materials used in gas sensing and to other systems involving adsorption and chemical reactions steps.

  16. Density matrix quantum Monte Carlo

    CERN Document Server

    Blunt, N S; Spencer, J S; Foulkes, W M C

    2013-01-01

    This paper describes a quantum Monte Carlo method capable of sampling the full density matrix of a many-particle system, thus granting access to arbitrary reduced density matrices and allowing expectation values of complicated non-local operators to be evaluated easily. The direct sampling of the density matrix also raises the possibility of calculating previously inaccessible entanglement measures. The algorithm closely resembles the recently introduced full configuration interaction quantum Monte Carlo method, but works all the way from infinite to zero temperature. We explain the theory underlying the method, describe the algorithm, and introduce an importance-sampling procedure to improve the stochastic efficiency. To demonstrate the potential of our approach, the energy and staggered magnetization of the isotropic antiferromagnetic Heisenberg model on small lattices and the concurrence of one-dimensional spin rings are compared to exact or well-established results. Finally, the nature of the sign problem...

  17. Adaptive Multilevel Monte Carlo Simulation

    KAUST Repository

    Hoel, H

    2011-08-23

    This work generalizes a multilevel forward Euler Monte Carlo method introduced in Michael B. Giles. (Michael Giles. Oper. Res. 56(3):607–617, 2008.) for the approximation of expected values depending on the solution to an Itô stochastic differential equation. The work (Michael Giles. Oper. Res. 56(3):607– 617, 2008.) proposed and analyzed a forward Euler multilevelMonte Carlo method based on a hierarchy of uniform time discretizations and control variates to reduce the computational effort required by a standard, single level, Forward Euler Monte Carlo method. This work introduces an adaptive hierarchy of non uniform time discretizations, generated by an adaptive algorithmintroduced in (AnnaDzougoutov et al. Raùl Tempone. Adaptive Monte Carlo algorithms for stopped diffusion. In Multiscale methods in science and engineering, volume 44 of Lect. Notes Comput. Sci. Eng., pages 59–88. Springer, Berlin, 2005; Kyoung-Sook Moon et al. Stoch. Anal. Appl. 23(3):511–558, 2005; Kyoung-Sook Moon et al. An adaptive algorithm for ordinary, stochastic and partial differential equations. In Recent advances in adaptive computation, volume 383 of Contemp. Math., pages 325–343. Amer. Math. Soc., Providence, RI, 2005.). This form of the adaptive algorithm generates stochastic, path dependent, time steps and is based on a posteriori error expansions first developed in (Anders Szepessy et al. Comm. Pure Appl. Math. 54(10):1169– 1214, 2001). Our numerical results for a stopped diffusion problem, exhibit savings in the computational cost to achieve an accuracy of ϑ(TOL),from(TOL−3), from using a single level version of the adaptive algorithm to ϑ(((TOL−1)log(TOL))2).

  18. Cholesterol-Induced Suppression of Membrane Elastic Fluctuations at the Atomistic Level

    Science.gov (United States)

    Molugu, Trivikram R.

    2017-01-01

    Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state 2H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C–2H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of 13C–1H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For 2H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes. PMID:27154600

  19. Cholesterol-induced suppression of membrane elastic fluctuations at the atomistic level.

    Science.gov (United States)

    Molugu, Trivikram R; Brown, Michael F

    2016-09-01

    Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state (2)H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C-(2)H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of (13)C-(1)H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For (2)H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes.

  20. Using a scalar parameter to trace dislocation evolution in atomistic modeling

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jinbo [ORNL; Zhang, Z F [Shenyang National Laboratory for Materials Science; Osetskiy, Yury N [ORNL; Stoller, Roger E [ORNL

    2015-01-01

    A scalar gamma-parameter is proposed from the Nye tensor. Its maximum value occurs along a dislocation line, either straight or curved, when the coordinate system is purposely chosen. This parameter can be easily obtained from the Nye tensor calculated at each atom in atomistic modeling. Using the gamma-parameter, a fully automated approach is developed to determine core atoms and the Burgers vectors of dislocations simultaneously. The approach is validated by revealing the smallest dislocation loop and by tracing the whole formation process of complicated dislocation networks on the fly.

  1. Electron and phonon transport in silicon nanowires: Atomistic approach to thermoelectric properties

    DEFF Research Database (Denmark)

    Markussen, Troels; Jauho, Antti-Pekka; Brandbyge, Mads

    2009-01-01

    We compute both electron and phonon transmissions in thin disordered silicon nanowires (SiNWs). Our atomistic approach is based on tight-binding and empirical potential descriptions of the electronic and phononic systems, respectively. Surface disorder is modeled by introducing surface silicon...... apply this averaging method to surface disordered SiNWs in the diameter range of 1–3 nm to compute the thermoelectric figure of merit ZT. It is found that the phonon transmission is affected more by the vacancies than the electronic transmission leading to an increased thermoelectric performance...

  2. Atomistic understanding of hydrogen loading phenomenon into palladium cathode: A simple nanocluster approach and electrochemical evidence

    Indian Academy of Sciences (India)

    Mohsen Lashgari; Davood Matloubi

    2015-03-01

    The inherent potency of palladium to sorb hydrogen atoms was examined empirically and theoretically through various electrochemical methods and high-level quantum chemical calculations (HSE06) based on cluster model (CM) and density functional theory (DFT). The CM-DFT approach using QZVP/cc-PV6Z basis sets revealed a strong attraction between Pd nanoclusters and H atoms that generates some charged entities. This atomistically justifies why the electrochemical impedance of the system becomes less by the loading phenomenon. It is concluded that hydrogen atoms enter the palladium subsurface through hollow and bridge sites by diffusing as proton-like species and get loaded predominantly in the octahedral voids.

  3. Methods for atomistic abrasion simulations of laterally periodic polycrystalline substrates with fractal surfaces

    Science.gov (United States)

    Eder, S. J.; Bianchi, D.; Cihak-Bayr, U.; Gkagkas, K.

    2017-03-01

    In this work we discuss a method to generate laterally periodic polycrystalline samples with fractal surfaces for use in molecular dynamics simulations of abrasion. We also describe a workflow that allows us to produce random lateral distributions of simple but realistically shaped hard abrasive particles with Gaussian size distribution and random particle orientations. We evaluate some on-the-fly analysis and visualization possibilities that may be applied during a molecular dynamics simulation to considerably reduce the post-processing effort. Finally, we elaborate on a parallelizable post-processing approach to evaluating and visualizing the surface topography, the grain structure and orientation, as well as the temperature distribution in large atomistic systems.

  4. Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    McCarty, Keven F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Zhou, Xiaowang [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ward, Donald K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schultz, Peter A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Foster, Michael E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bartelt, Norman Charles [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expand the number of potential types of graphene electronic devices.

  5. Atomistic Simulation of Intrinsic Defects and Trivalent and Tetravalent Ion Doping in Hydroxyapatite

    Directory of Open Access Journals (Sweden)

    Ricardo D. S. Santos

    2014-01-01

    Full Text Available Atomistic simulation techniques have been employed in order to investigate key issues related to intrinsic defects and a variety of dopants from trivalent and tetravalent ions. The most favorable intrinsic defect is determined to be a scheme involving calcium and hydroxyl vacancies. It is found that trivalent ions have an energetic preference for the Ca site, while tetravalent ions can enter P sites. Charge compensation is predicted to occur basically via three schemes. In general, the charge compensation via the formation of calcium vacancies is more favorable. Trivalent dopant ions are more stable than tetravalent dopants.

  6. Rotational viscosity of a liquid crystal mixture:a fully atomistic molecular dynamics study

    Institute of Scientific and Technical Information of China (English)

    Zhang Ran; Peng Zeng-Hui; Liu Yong-Gang; Zheng Zhi-Gang; Xuan Li

    2009-01-01

    Fully atomistic molecular dynamics(MD)simulations at 293, 303 and 313 K have been performed for the four. component liquid crystal mixture, E7, using the software package Material Studio. Order parameters and orientational time correlation functions(TCFs)were calculated from MD trajectories. The rotational viscosity coefficients(RVCs)of the mixture were ca]culated using the Nemtsov-Zakharov and Fialkowski methods based on statistical-mechanical approaches. Temperature dependences of RVC and density were discussed in detall. Reasonable agreement between the simulated and experimental values was found.

  7. Dislocation pinning effects on fracture behavior: Atomistic and dislocation dynamics simulations

    Science.gov (United States)

    Noronha, S. J.; Farkas, D.

    2002-10-01

    We introduce an approach in which results from atomistic simulations are combined with discrete dislocation dynamics simulations of crack-tip plasticity. The method is used to study the effects of dislocation pinning due to grain boundaries or secondary particles on the fracture behavior of aluminum. We find that the fracture resistance is reduced with decreasing pinning distance. The results show that the pinning of the dislocations causes a net decrease in the shear stress projected on the slip plane, preventing further dislocation emission. Semibrittle cleavage occurs after a certain number of dislocations is emitted.

  8. Investigations on the mechanical behavior of nanowires with twin boundaries by atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Xia, E-mail: tianxia@lsec.cc.ac.cn [College of Mechanics and Materials, HoHai University, Nanjing 210098 (China)

    2015-03-10

    Atomistic simulations are used to study the deformation behavior of twinned Cu nanowires with a <111> growth orientation under tension. Due to the existence of the twin boundaries, the strength of the twinned nanowires is higher than that of the twin-free nanowire and the yielding stress of twinned nanowires is inversely proportional to the spacings of the twin boundaries. Moreover, The ductility of the twin-free nanowire is the highest of all and it grows with the increasing spacings of the twin boundaries for twinned nanowires. Besides, we find that the twin boundaries can be served as dislocation sources as well as the free surfaces and grain boundaries.

  9. Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

    Science.gov (United States)

    Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

    2006-01-01

    A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

  10. Elastic behavior of amorphous-crystalline silicon nanocomposite: An atomistic view

    Science.gov (United States)

    Das, Suvankar; Dutta, Amlan

    2017-01-01

    In the context of mechanical properties, nanocomposites with homogeneous chemical composition throughout the matrix and the dispersed phase are of particular interest. In this study, the elastic moduli of amorphous-crystalline silicon nanocomposite have been estimated using atomistic simulations. A comparison with the theoretical model reveals that the elastic behavior is significantly influenced by the crystal-amorphous interphase. On observing the effect of volume-fraction of the crystalline phase, an anomalous trend for the bulk modulus is obtained. This phenomenon is attributed to the relaxation displacements of the amorphous atoms.

  11. Atomistic spin dynamic method with both damping and moment of inertia effects included from first principles.

    Science.gov (United States)

    Bhattacharjee, Satadeep; Nordström, Lars; Fransson, Jonas

    2012-02-03

    We consider spin dynamics for implementation in an atomistic framework and we address the feasibility of capturing processes in the femtosecond regime by inclusion of moment of inertia. In the spirit of an s-d-like interaction between the magnetization and electron spin, we derive a generalized equation of motion for the magnetization dynamics in the semiclassical limit, which is nonlocal in both space and time. Using this result we retain a generalized Landau-Lifshitz-Gilbert equation, also including the moment of inertia, and demonstrate how the exchange interaction, damping, and moment of inertia, all can be calculated from first principles.

  12. Atomistic formulas for local properties in systems with many-body interactions

    Science.gov (United States)

    Hardy, Robert J.

    2016-11-01

    Atomistic formulas are derived for the local densities and fluxes used in the continuum description of energy and momentum transport. Two general methods for the distribution of potential energy among a system's constituent particles are presented and analyzed. The resulting formulas for the heat flux and stress tensor and the equations for energy and momentum transport are exact consequences of the definitions of the densities and the equations of classical mechanics. The formulas and equations obtained are valid for systems with very general types of many-body interactions.

  13. AGU Chapman Conference Hydrogeologic Processes: Building and Testing Atomistic- to Basin-Scale Models

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, B. [American Geophysical Union, Washington, DC (United States)

    1994-12-31

    This report presents details of the Chapman Conference given on June 6--9, 1994 in Lincoln, New Hampshire. This conference covered the scale of processes involved in coupled hydrogeologic mass transport and a concept of modeling and testing from the atomistic- to the basin- scale. Other topics include; the testing of fundamental atomic level parameterizations in the laboratory and field studies of fluid flow and mass transport and the next generation of hydrogeologic models. Individual papers from this conference are processed separately for the database.

  14. Cold melting of beryllium: Atomistic view on Z-machine experiments

    Science.gov (United States)

    Dremov, V. V.; Rykounov, A. A.; Sapozhnikov, F. A.; Karavaev, A. V.; Yakovlev, S. V.; Ionov, G. V.; Ryzhkov, M. V.

    2015-07-01

    Analysis of phase diagram of beryllium at high pressures and temperatures obtained as a result of ab initio calculations and large scale classical molecular dynamics simulations of beryllium shock loading have shown that the so called cold melting takes place when shock wave propagates through polycrystalline samples. Comparison of ab initio calculation results on sound speed along the Hugoniot with experimental data obtained on Z-machine also evidences for possible manifestation of the cold melting. The last may explain the discrepancy between atomistic simulations and experimental data on the onset of the melting on the Hugoniot.

  15. Consistent Energy-Based Atomistic/Continuum Coupling for Two-Body Potential: 1D and 2D Case

    CERN Document Server

    Shapeev, Alexander V

    2010-01-01

    This paper concerns the problem of consistent energy-based coupling of atomistic and continuum models of materials, limited to zero-temperature statics of simple crystalline materials. It has been widely recognized that the most practical coupled methods exhibit finite errors on the atomistic/continuum interface (which are often attributed to spurious forces called "ghost forces"). There are only few existing works that propose a coupling which is sufficiently accurate near the interface under certain limitations. In this paper a novel coupling that is free from "ghost forces" is proposed for a two-body interaction potential under the assumptions of either (i) one spatial dimension, or (ii) two spatial dimensions and piecewise affine finite elements for describing the continuum deformation. The computational efficiency of the proposed coupling is demonstrated with numerical experiments. The coupling strategy is based on judiciously defining the contributions of the atomistic bonds to the discrete and the cont...

  16. Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.

    Science.gov (United States)

    Mittal, Anuradha; Lyle, Nicholas; Harmon, Tyler S; Pappu, Rohit V

    2014-08-12

    There is growing interest in the topic of intrinsically disordered proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations based on novel implicit solvation models have yielded useful insights regarding sequence-ensemble relationships for IDPs modeled as autonomous units. However, a majority of naturally occurring IDPs are tethered to ordered domains. Tethering introduces additional energy scales and this creates the challenge of broken ergodicity for standard MMC sampling or molecular dynamics that cannot be readily alleviated by using generalized tempering methods. We have designed, deployed, and tested our adaptation of the Nested Markov Chain Monte Carlo sampling algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis Monte Carlo (HS-MMC) sampling. In this method, transitions out of energetic traps are enabled by the introduction of an auxiliary Markov chain that draws conformations for the disordered region from a Boltzmann distribution that is governed by an alternative potential function that only includes short-range steric repulsions and conformational restraints on the ordered domain. We show using multiple, independent runs that the HS-MMC method yields conformational distributions that have similar and reproducible statistical properties, which is in direct contrast to standard MMC for equivalent amounts of sampling. The method is efficient and can be deployed for simulations of a range of biologically relevant disordered regions that are tethered to ordered domains.

  17. Combined atomistic-continuum model for simulation of laser interaction with metals: application in the calculation of melting thresholds in Ni targets of varying thickness

    Science.gov (United States)

    Ivanov, D. S.; Zhigilei, L. V.

    The threshold laser fluence for the onset of surface melting is calculated for Ni films of different thicknesses and for a bulk Ni target using a combined atomistic-continuum computational model. The model combines the classical molecular dynamics (MD) method for simulation of non-equilibrium processes of lattice superheating and fast phase transformations with a continuum description of the laser excitation and subsequent relaxation of the conduction band electrons based on the two-temperature model (TTM). In the hybrid TTM-MD method, MD substitutes the TTM equation for the lattice temperature, and the diffusion equation for the electron temperature is solved simultaneously with MD integration of the equations of motion of atoms. The dependence of the threshold fluence on the film thickness predicted in TTM-MD simulations qualitatively agrees with TTM calculations, while the values of the thresholds for thick films and bulk targets are 10% higher in TTM-MD. The quantitative differences between the predictions of TTM and TTM-MD demonstrate that the kinetics of laser melting as well as the energy partitioning between the thermal energy of atomic vibrations and energy of the collective atomic motion driven by the relaxation of the laser-induced pressure should be taken into account in interpretation of experimental results on surface melting.

  18. Coupled structural and magnetic properties of ferric fluoride nanostructures: Part II, a Monte Carlo-Heisenberg study

    Energy Technology Data Exchange (ETDEWEB)

    Fongang, Bernard [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France); Laboratoire de Sciences des Materiaux, Departement de Physique, Universite de Yaounde i, BP 812 Yaounde (Cameroon); Labaye, Yvan [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France); Calvayrac, Florent, E-mail: Florent.Calvayrac@univ-lemans.fr [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France); Zekeng, Serge [Laboratoire de Sciences des Materiaux, Departement de Physique, Universite de Yaounde i, BP 812 Yaounde (Cameroon); Greneche, Jean-Marc [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France)

    2012-11-15

    We present a numerical study of the magnetic structure of nanostructured iron fluoride, using the Monte Carlo Metropolis simulated annealing technique and a classical Heisenberg Hamiltonian with superexchange angle dependent interactions. The parameters are adjusted on experimental results, and the atomic structure and topology taken from a previous atomistic model of grain boundaries in the same system. We find perfect antiferromagnetic crystalline grains and a disordered magnetic configuration (speromagnetic) at the grain boundary, in agreement with experimental features. Both the lowest magnetic energy and the rate of magnetic frustration are found to be dependent on the relative disorientation of crystalline grains, i.e. on the cationic topology. We conclude on possible extensions of the model.

  19. New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

    Science.gov (United States)

    Saether, E.; Yamakov, V.; Glaessgen, E.

    2008-01-01

    A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

  20. An atomistic model for cross-linked HNBR elastomers used in seals

    Science.gov (United States)

    Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

    2015-03-01

    Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

  1. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the pos......In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us...... that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  2. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

    Science.gov (United States)

    Pande, Vijay S; Baker, Ian; Chapman, Jarrod; Elmer, Sidney P; Khaliq, Siraj; Larson, Stefan M; Rhee, Young Min; Shirts, Michael R; Snow, Christopher D; Sorin, Eric J; Zagrovic, Bojan

    2003-01-01

    Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.

  3. Quantum Thermodynamics: Non-equilibrium 3D Description of an Unbounded System at an Atomistic Level

    Directory of Open Access Journals (Sweden)

    Vittorio Verda

    2010-03-01

    Full Text Available Quantum thermodynamics (QT provides a general framework for the description of non-equilibrium phenomena at any level, particularly the atomistic one. This theory and its dynamical postulate are used here to extend the work reported in previous papers of modeling the storage of hydrogen in an isolated system, by extending the modeling to 3D. The system is prepared in a state with the hydrogen molecules initially far from stable equilibrium after which the system is allowed to relax (evolve to a state of stable equilibrium. The so-called energy eigenvalue problem, which entails a many-body problem that for dilute and moderately dense gases can be solved using virial expansion theory, is used to determine the energy eigenvalues and eigenstates of the system. This information is then used in the nonlinear Beretta equation of motion of QT to determine the evolution of the thermodynamic state of the system as well as the spatial distributions of the hydrogen molecules in time. The results of our simulations provide a quantification of the entropy generated due to irreversibilities at an atomistic level and show in detail the trajectory of the state of the system as the hydrogen molecules, which are initially arranged to be far from the carbon nanotube, spread out in the system and eventually become more concentrated near the carbon atoms which make up the nanotube.

  4. Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation.

    Science.gov (United States)

    Zahariev, Tsvetan K; Slavchov, Radomir I; Tadjer, Alia V; Ivanova, Anela N

    2014-04-15

    Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems.

  5. Fracture toughness from atomistic simulations: Brittleness induced by emission of sessile dislocations

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1998-08-04

    Using atomistic simulations of crack response for intermetallic materials the author shows that when the emitted dislocations are sessile and stay in the immediate vicinity of the crack tip the emitted dislocations can actually lead to brittle failure. She present the results of an atomistic simulation study of the simultaneous dislocation emission and crack propagation process in this class of materials. She used a molecular statics technique with embedded atom (EAM) potentials developed for NiAl. The crystal structure of NiAl is the CsCl type (B2) with a lattice parameter of 0.287 nm, which is reproduced by the potential together with the cohesive energy and elastic constants. The compound stays ordered up to the melting point, indicating a strong tendency towards chemical ordering with a relatively high energy of the antiphase boundary (APB). As a result of this relatively large energy the dislocations of 1/2<111> type Burgers vectors imply a high energy and the deformation process occurs via the larger <100> type dislocations.

  6. Atomistic studies of dislocations in {alpha}-iron using bond-order potential

    Energy Technology Data Exchange (ETDEWEB)

    Mrovec, Matous; Elsaesser, Christian; Gumbsch, Peter [Fraunhofer-Institut fuer Werkstoffmechanik IWM, Freiburg (Germany); IZBS, Universitaet Karlsruhe, Karlsruhe (Germany)

    2010-07-01

    Macroscopic plastic behavior is closely linked to properties of dislocations at the nanometer scale. Direct experimental observations of the dislocation core region and of its changes during dislocation motion are unfortunately impossible and better understanding of these phenomena can be obtained only with the help of atomistic simulations. Recent atomistic studies of dislocations in iron have provided however very different outcomes, both in terms of atomic structures and energetics. The most likely reason of these large differences is a lack of reliable interatomic potentials, which would be able to describe adequately the atomic bonding and magnetic interactions in iron. In the present work we present studies of dislocations in {alpha}-iron using a bond-order potential, which is based on a tight-binding bond representation. The model is able to capture the directional character of bonds present in transition metals and includes a description of magnetic effects within the Stoner model of itinerant magnetism. We compare results of our simulations with available first-principles predictions as well as with predictions of other empirical interatomic potentials and discuss underlying causes of the differences.

  7. Monte Carlo approach to turbulence

    Energy Technology Data Exchange (ETDEWEB)

    Dueben, P.; Homeier, D.; Muenster, G. [Muenster Univ. (Germany). Inst. fuer Theoretische Physik; Jansen, K. [DESY, Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Mesterhazy, D. [Humboldt Univ., Berlin (Germany). Inst. fuer Physik

    2009-11-15

    The behavior of the one-dimensional random-force-driven Burgers equation is investigated in the path integral formalism on a discrete space-time lattice. We show that by means of Monte Carlo methods one may evaluate observables, such as structure functions, as ensemble averages over different field realizations. The regularization of shock solutions to the zero-viscosity limit (Hopf-equation) eventually leads to constraints on lattice parameters required for the stability of the simulations. Insight into the formation of localized structures (shocks) and their dynamics is obtained. (orig.)

  8. Monte Carlo techniques in radiation therapy

    CERN Document Server

    Verhaegen, Frank

    2013-01-01

    Modern cancer treatment relies on Monte Carlo simulations to help radiotherapists and clinical physicists better understand and compute radiation dose from imaging devices as well as exploit four-dimensional imaging data. With Monte Carlo-based treatment planning tools now available from commercial vendors, a complete transition to Monte Carlo-based dose calculation methods in radiotherapy could likely take place in the next decade. Monte Carlo Techniques in Radiation Therapy explores the use of Monte Carlo methods for modeling various features of internal and external radiation sources, including light ion beams. The book-the first of its kind-addresses applications of the Monte Carlo particle transport simulation technique in radiation therapy, mainly focusing on external beam radiotherapy and brachytherapy. It presents the mathematical and technical aspects of the methods in particle transport simulations. The book also discusses the modeling of medical linacs and other irradiation devices; issues specific...

  9. Monte Carlo Simulation of Linear Polymer Thermal Depolymerization under Isothermal and Dynamic Modes

    Directory of Open Access Journals (Sweden)

    Elena V. Bystritskaya

    2011-01-01

    Full Text Available Kinetics of linear polymer thermal depolymerization under isothermal and dynamic TGA modes was simulated by the Monte Carlo method. The simulation was carried out on model arrays having the same initial degree of polymerization =100 and different width (polydispersity index, PDI=/=1∼3 at three constant temperatures and five heating rates. Kinetics of the process in both modes is described by the Avrami equation, the exponent in which decreasing as the distribution width increases. Treatment of the model kinetic curves of degradation using the nonlinear regression method by the Avrami equation, under both isothermal and dynamic modes, gives correct activation energy and pre-exponential factor values independently of the initial PDI. Data obtained in the dynamic mode were also treated by two isoconversion methods, widely applied to kinetic analysis of TGA curves (Flynn-Wall-Ozawa method and Kissinger-Akahira-Sunose (KAS method.

  10. Folding Kinetics of Riboswitch Transcriptional Terminators

    Science.gov (United States)

    Sauerwine, Benjamin; Widom, Michael

    2009-03-01

    Riboswitches control the expression of genes in bacteria by halting gene transcription or allowing it to proceed based on the presence of ligands in solution. A key feature of every riboswitch is a transcriptional terminator in which the messenger RNA folds into a secondary structure with the stem-loop structure of a hairpin. Through kinetic Monte Carlo simulation we show that terminators have been naturally selected to fold with high reliability on the time-scale of gene transcription. This efficient folding behavior is preserved among two classes of riboswitch and among two species of bacteria.

  11. Meaningful timescales from Monte Carlo simulations of particle systems with hard-core interactions

    Science.gov (United States)

    Costa, Liborio I.

    2016-12-01

    A new Markov Chain Monte Carlo method for simulating the dynamics of particle systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is associated with minima in the energy landscape, in the proposed method, the state of the system is associated with the set of paths traveled by the atoms and the transition probabilities for an atom to be displaced are proportional to the corresponding velocities. In this way, the number of possible state-to-state transitions is reduced to a discrete set, and a direct link between the Monte Carlo time step and true physical time is naturally established. The resulting rejection-free algorithm is validated against event-driven molecular dynamics: the equilibrium and non-equilibrium dynamics of hard disks converge to the exact results with decreasing displacement size.

  12. Mean field simulation for Monte Carlo integration

    CERN Document Server

    Del Moral, Pierre

    2013-01-01

    In the last three decades, there has been a dramatic increase in the use of interacting particle methods as a powerful tool in real-world applications of Monte Carlo simulation in computational physics, population biology, computer sciences, and statistical machine learning. Ideally suited to parallel and distributed computation, these advanced particle algorithms include nonlinear interacting jump diffusions; quantum, diffusion, and resampled Monte Carlo methods; Feynman-Kac particle models; genetic and evolutionary algorithms; sequential Monte Carlo methods; adaptive and interacting Marko

  13. Approaching Chemical Accuracy with Quantum Monte Carlo

    OpenAIRE

    Petruzielo, Frank R.; Toulouse, Julien; Umrigar, C. J.

    2012-01-01

    International audience; A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreem...

  14. 1-D EQUILIBRIUM DISCRETE DIFFUSION MONTE CARLO

    Energy Technology Data Exchange (ETDEWEB)

    T. EVANS; ET AL

    2000-08-01

    We present a new hybrid Monte Carlo method for 1-D equilibrium diffusion problems in which the radiation field coexists with matter in local thermodynamic equilibrium. This method, the Equilibrium Discrete Diffusion Monte Carlo (EqDDMC) method, combines Monte Carlo particles with spatially discrete diffusion solutions. We verify the EqDDMC method with computational results from three slab problems. The EqDDMC method represents an incremental step toward applying this hybrid methodology to non-equilibrium diffusion, where it could be simultaneously coupled to Monte Carlo transport.

  15. Monte Carlo Treatment Planning for Advanced Radiotherapy

    DEFF Research Database (Denmark)

    Cronholm, Rickard

    and validation of a Monte Carlo model of a medical linear accelerator (i), converting a CT scan of a patient to a Monte Carlo compliant phantom (ii) and translating the treatment plan parameters (including beam energy, angles of incidence, collimator settings etc) to a Monte Carlo input file (iii). A protocol...... previous algorithms since it uses delineations of structures in order to include and/or exclude certain media in various anatomical regions. This method has the potential to reduce anatomically irrelevant media assignment. In house MATLAB scripts translating the treatment plan parameters to Monte Carlo...

  16. Quantum Monte Carlo Studies of Relativistic Effects in Light Nuclei

    CERN Document Server

    Forest, J L; Arriaga, A

    1999-01-01

    Relativistic Hamiltonians are defined as the sum of relativistic one-body kinetic energy, two- and three-body potentials and their boost corrections. In this work we use the variational Monte Carlo method to study two kinds of relativistic effects in the binding energy of 3H and 4He. The first is due to the nonlocalities in the relativistic kinetic energy and relativistic one-pion exchange potential (OPEP), and the second is from boost interaction. The OPEP contribution is reduced by about 15% by the relativistic nonlocality, which may also have significant effects on pion exchange currents. However, almost all of this reduction is canceled by changes in the kinetic energy and other interaction terms, and the total effect of the nonlocalities on the binding energy is very small. The boost interactions, on the other hand, give repulsive contributions of 0.4 (1.9) MeV in 3H (4He) and account for 37% of the phenomenological part of the three-nucleon interaction needed in the nonrelativistic Hamiltonians.

  17. Quantum Monte Carlo studies of relativistic effects in light nuclei

    Science.gov (United States)

    Forest, J. L.; Pandharipande, V. R.; Arriaga, A.

    1999-07-01

    Relativistic Hamiltonians are defined as the sum of relativistic one-body kinetic energy, two- and three-body potentials, and their boost corrections. In this work we use the variational Monte Carlo method to study two kinds of relativistic effects in 3H and 4He, using relativistic Hamiltonians. The first is due to the nonlocalities in the relativistic kinetic energy and relativistic one-pion exchange potential (OPEP), and the second is from boost interaction. The OPEP contribution is reduced by ~15% by the relativistic nonlocality, which may also have significant effects on pion exchange currents. However, almost all of this reduction is canceled by changes in the kinetic energy and other interaction terms, and the total effect of the nonlocalities on the binding energy is very small. The boost interactions, on the other hand, give repulsive contributions of ~0.4 (1.9) MeV in 3H (4He) and account for ~37% of the phenomenological part of the three-nucleon interaction needed in the nonrelativistic Hamiltonians. The wave functions of nuclei are not significantly changed by these effects.

  18. Error in Monte Carlo, quasi-error in Quasi-Monte Carlo

    OpenAIRE

    Kleiss, R. H. P.; Lazopoulos, A.

    2006-01-01

    While the Quasi-Monte Carlo method of numerical integration achieves smaller integration error than standard Monte Carlo, its use in particle physics phenomenology has been hindered by the abscence of a reliable way to estimate that error. The standard Monte Carlo error estimator relies on the assumption that the points are generated independently of each other and, therefore, fails to account for the error improvement advertised by the Quasi-Monte Carlo method. We advocate the construction o...

  19. Coupled Simulations of Mechanical Deformation and Microstructural Evolution Using Polycrystal Plasticity and Monte Carlo Potts Models

    Energy Technology Data Exchange (ETDEWEB)

    Battaile, C.C.; Buchheit, T.E.; Holm, E.A.; Neilsen, M.K.; Wellman, G.W.

    1999-01-12

    The microstructural evolution of heavily deformed polycrystalline Cu is simulated by coupling a constitutive model for polycrystal plasticity with the Monte Carlo Potts model for grain growth. The effects of deformation on boundary topology and grain growth kinetics are presented. Heavy deformation leads to dramatic strain-induced boundary migration and subsequent grain fragmentation. Grain growth is accelerated in heavily deformed microstructures. The implications of these results for the thermomechanical fatigue failure of eutectic solder joints are discussed.

  20. Efficient implementation of the Hellmann-Feynman theorem in a diffusion Monte Carlo calculation.

    Science.gov (United States)

    Vitiello, S A

    2011-02-07

    Kinetic and potential energies of systems of (4)He atoms in the solid phase are computed at T = 0. Results at two densities of the liquid phase are presented as well. Calculations are performed by the multiweight extension to the diffusion Monte Carlo method that allows the application of the Hellmann-Feynman theorem in a robust and efficient way. This is a general method that can be applied in other situations of interest as well.

  1. Atomistic simulation of the premelting of iron and aluminum : Implications for high-pressure melting-curve measurements

    NARCIS (Netherlands)

    Starikov, Sergey V.; Stegailov, Vladimir V.

    2009-01-01

    Using atomistic simulations we show the importance of the surface premelting phenomenon for the melting-curve measurements at high pressures. The model under consideration mimics the experimental conditions deployed for melting studies with diamond-anvil cells. The iron is considered in this work be

  2. A hybrid atomistic electrodynamics-quantum mechanical approach for simulating surface-enhanced Raman scattering.

    Science.gov (United States)

    Payton, John L; Morton, Seth M; Moore, Justin E; Jensen, Lasse

    2014-01-21

    Surface-enhanced Raman scattering (SERS) is a technique that has broad implications for biological and chemical sensing applications by providing the ability to simultaneously detect and identify a single molecule. The Raman scattering of molecules adsorbed on metal nanoparticles can be enhanced by many orders of magnitude. These enhancements stem from a twofold mechanism: an electromagnetic mechanism (EM), which is due to the enhanced local field near the metal surface, and a chemical mechanism (CM), which is due to the adsorbate specific interactions between the metal surface and the molecules. The local field near the metal surface can be significantly enhanced due to the plasmon excitation, and therefore chemists generally accept that the EM provides the majority of the enhancements. While classical electrodynamics simulations can accurately simulate the local electric field around metal nanoparticles, they offer few insights into the spectral changes that occur in SERS. First-principles simulations can directly predict the Raman spectrum but are limited to small metal clusters and therefore are often used for understanding the CM. Thus, there is a need for developing new methods that bridge the electrodynamics simulations of the metal nanoparticle and the first-principles simulations of the molecule to facilitate direct simulations of SERS spectra. In this Account, we discuss our recent work on developing a hybrid atomistic electrodynamics-quantum mechanical approach to simulate SERS. This hybrid method is called the discrete interaction model/quantum mechanics (DIM/QM) method and consists of an atomistic electrodynamics model of the metal nanoparticle and a time-dependent density functional theory (TDDFT) description of the molecule. In contrast to most previous work, the DIM/QM method enables us to retain a detailed atomistic structure of the nanoparticle and provides a natural bridge between the electronic structure methods and the macroscopic

  3. Predictive atomistic simulations of electronic properties of realistic nanoscale devices: A multiscale modeling approach

    Science.gov (United States)

    Vedula, Ravi Pramod Kumar

    Scaling of CMOS towards its ultimate limits, where quantum effects and atomistic variability due to fabrication, along with recent emphasis on heterogeneous integration of non-digital devices for increasing the functional diversification presents us with fundamentally new challenges. A comprehensive understanding of design and operation of these nanoscale transistors, and other electronic devices like RF-MEMS, requires an insight into their electronic and mechanical properties that are strongly influenced by underlying atomic structure. Hence, continuum descriptions of materials and use of empirical models at these scales become questionable. This increase in complexity of electronic devices necessitates an understanding at a more fundamental level to accurately predict the performance and reliability of these devices. The objective of this thesis is to outline the application of multiscale predictive modeling methods, ranging from atoms to devices, for addressing these challenges. This capability is demonstrated using two examples: characterization of (i) dielectric charging in RF-MEMS, and (ii) transport properties of Ge-nanofins. For characterizing the dielectric charging phenomenon, a continuum dielectric charging model, augmented by first principles informed trap distributions, is used to predict current transient measurements across a broad range of voltages and temperatures. These simulations demonstrate using ab initio informed model not only reduces the empiricism (number of adjustable parameters) in the model but also leads to a more accurate model over a broad range of operating conditions, and enable the precise determination of additional material parameters. These atomistic calculations also provide detailed information about the nature of charge traps and their trapping mechanisms that are not accessible experimentally; such information could prove invaluable in defect engineering. The second problem addresses the effect of the in-homogeneous strain

  4. Non-Isothermal Kinetics.

    Science.gov (United States)

    Brown, M. E.; Phillpotts, C. A. R.

    1978-01-01

    Discusses the principle of nonisothermal kinetics and some of the factors involved in such reactions, especially when considering the reliability of the kinetic parameters, compared to those of isothermal conditions. (GA)

  5. Atomistic simulation of charge effects: From tunable thin film growth to isolation of surface states with spin-orbit coupling

    Science.gov (United States)

    Ming, Wenmei

    This dissertation revitalizes the importance of surface charge effects in semiconductor nanostructures, in particular in the context of thin film growth and exotic electronic structures under delicate spin-orbit coupling. A combination of simulation techniques, including density functional theory calculation, kinetic Monte Carlo method, nonequilibrium Green's function method, and tight binding method, were employed to reveal the underlying physical mechanisms of four topics: (1) Effects of Li doping on H-diffusion in MgH 2 for hydrogen storage. It addresses both the effect of Fermi level tuning by charged dopant and the effect of dopant-defect interaction, and the latter was largely neglected in previous works; (2) Tuning nucleation density of the metal island with charge doping of the graphene substrate. It is the first time that the surface charge doping effect is proposed and studied as an effective approach to tune the kinetics of island nucleation at the early stage of thin film growth; (3) Complete isolation of Rashba surface states on the saturated semiconductor surface. It shows that the naturally saturated semiconductor surface of InSe(0001) with Au single layer film provides a mechanism for the formation of Rashba states with large spin splitting; it opens up an innovative route to obtaining ideal Rashba states without the overwhelming bulk spin-degenerate carriers in spin-dependent transport; (4) Formation of large band gap quantum spin Hall state on Si surface. This study reveals the importance of atomic orbital composition in the formation of a topological insulator, and shows promisingly the possible integration of topological insulator technology into Si-based modern electronic devices.

  6. An introduction to Monte Carlo methods

    NARCIS (Netherlands)

    Walter, J. -C.; Barkema, G. T.

    2015-01-01

    Monte Carlo simulations are methods for simulating statistical systems. The aim is to generate a representative ensemble of configurations to access thermodynamical quantities without the need to solve the system analytically or to perform an exact enumeration. The main principles of Monte Carlo sim

  7. Methods of nonlinear kinetics

    OpenAIRE

    Gorban, A. N.; Karlin, I.V.

    2003-01-01

    Nonlinear kinetic equations are reviewed for a wide audience of specialists and postgraduate students in physics, mathematical physics, material science, chemical engineering and interdisciplinary research. Contents: The Boltzmann equation, Phenomenology and Quasi-chemical representation of the Boltzmann equation, Kinetic models, Discrete velocity models, Direct simulation, Lattice Gas and Lattice Boltzmann models, Minimal Boltzmann models for flows at low Knudsen number, Other kinetic equati...

  8. The Specific Bias in Dynamic Monte Carlo Simulations of Nuclear Reactor

    Science.gov (United States)

    Yamamoto, Toshihisa; Endo, Hiroshi; Ishizu, Tomoko; Tatewaki, Isao

    2014-06-01

    During the development of Monte-Carlo-based dynamic code system, we have encountered two major Monte-Carlo-specific problems. One is the break down due to "false super-criticality" which is caused by an accidentally large eigenvalue due to statistical error in spite of the fact that the reactor is actually not. The other problem, which is the main topic in this paper, is that the statistical error in power level using the reactivity calculated with Monte Carlo code is not symmetric about its mean but always positively biased. This signifies that the bias is accumulated as the calculation proceeds and consequently results in over-estimation of the final power level. It should be noted that the bias will not eliminated by refining time step as long as the variance is not zero. A preliminary investigation on this matter using the one-group-precursor point kinetic equations was made and it was concluded that the bias in power level is approximately proportional to the product of variance in Monte Carlo calculation and elapsed time. This conclusion was verified with some numerical experiments. This outcome is important in quantifying the required precision of the Monte-Carlo-based reactivity calculations.

  9. Challenges of Monte Carlo Transport

    Energy Technology Data Exchange (ETDEWEB)

    Long, Alex Roberts [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-06-10

    These are slides from a presentation for Parallel Summer School at Los Alamos National Laboratory. Solving discretized partial differential equations (PDEs) of interest can require a large number of computations. We can identify concurrency to allow parallel solution of discrete PDEs. Simulated particles histories can be used to solve the Boltzmann transport equation. Particle histories are independent in neutral particle transport, making them amenable to parallel computation. Physical parameters and method type determine the data dependencies of particle histories. Data requirements shape parallel algorithms for Monte Carlo. Then, Parallel Computational Physics and Parallel Monte Carlo are discussed and, finally, the results are given. The mesh passing method greatly simplifies the IMC implementation and allows simple load-balancing. Using MPI windows and passive, one-sided RMA further simplifies the implementation by removing target synchronization. The author is very interested in implementations of PGAS that may allow further optimization for one-sided, read-only memory access (e.g. Open SHMEM). The MPICH_RMA_OVER_DMAPP option and library is required to make one-sided messaging scale on Trinitite - Moonlight scales poorly. Interconnect specific libraries or functions are likely necessary to ensure performance. BRANSON has been used to directly compare the current standard method to a proposed method on idealized problems. The mesh passing algorithm performs well on problems that are designed to show the scalability of the particle passing method. BRANSON can now run load-imbalanced, dynamic problems. Potential avenues of improvement in the mesh passing algorithm will be implemented and explored. A suite of test problems that stress DD methods will elucidate a possible path forward for production codes.

  10. Mechanism of the Cassie-Wenzel transition via the atomistic and continuum string methods

    Energy Technology Data Exchange (ETDEWEB)

    Giacomello, Alberto, E-mail: alberto.giacomello@uniroma1.it; Casciola, Carlo Massimo [Dipartimento di Ingegneria Meccanica e Aerospaziale, Università di Roma “La Sapienza,” 00184 Rome (Italy); Meloni, Simone, E-mail: simone.meloni@epfl.ch [Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland); Müller, Marcus [Institut für Theoretische Physik, Georg-August-Universität Göttingen, 37077 Göttingen (Germany)

    2015-03-14

    The string method is a general and flexible strategy to compute the most probable transition path for an activated process (rare event). We apply here the atomistic string method in the density field to the Cassie-Wenzel transition, a central problem in the field of superhydrophobicity. We discuss in detail the mechanism of wetting of a submerged hydrophobic cavity of nanometer size and its dependence on the geometry of the cavity. Furthermore, we analyze the algorithmic analogies between the continuum “interface” string method and CREaM [Giacomello et al., Phys. Rev. Lett. 109, 226102 (2012)], a method inspired by the string that allows for a faster and simpler computation of the mechanism and of the free-energy profiles of the wetting process.

  11. Atomistic Investigation of Cu-Induced Misfolding in the Onset of Parkinson's Disease

    Science.gov (United States)

    Rose, Francis; Hodak, Miroslav; Bernholc, Jerry

    2009-03-01

    A nucleation mechanism for the misfolding of α-synuclein, the protein implicated in Parkinson's Disease (PD), is investigated using computer simulations. Through a combination of ab initio and classical simulation techniques, the conformational evolution of copper-ion-initiated misfolding of α-synuclein is determined. Based on these investigations and available experimental evidence, an atomistic model detailing the nucleation-initiated pathogenesis of PD is proposed. Once misfolded, the proteins can assemble into fibrils, the primary structural components of the deleterious PD plaques. Our model identifies a process of structural modifications to an initially unfolded α-synuclein that results in a partially folded intermediate with a well defined nucleation site as a precursor to the fully misfolded protein. The identified pathway can enable studies of reversal mechanisms and inhibitory agents, potentially leading to the development of effective therapies.

  12. Atomistic study of energy funneling in the light-harvesting complex of green sulfur bacteria

    CERN Document Server

    Huh, Joonsuk; Brookes, Jennifer C; Valleau, Stéphanie; Fujita, Takatoshi; Aspuru-Guzik, Alán

    2013-01-01

    Phototrophic organisms such as plants, photosynthetic bacteria and algae use microscopic complexes of pigment molecules to absorb sunlight. Within the light-harvesting complexes, which frequently have multiple functional and structural subunits, the energy is transferred in the form of molecular excitations with very high efficiency. Green sulfur bacteria are considered to be amongst the most efficient light-harvesting organisms. Despite multiple experimental and theoretical studies of these bacteria the physical origin of the efficient and robust energy transfer in their light-harvesting complexes is not well understood. To study excitation dynamics at the systems level we introduce an atomistic model that mimic a complete light-harvesting apparatus of green sulfur bacteria. The model contains about 4000 pigment molecules and comprises a double wall roll for the chlorosome, a baseplate and six Fenna-Matthews-Olson trimer complexes. We show that the fast relaxation within functional subunits combined with the...

  13. Atomistic Simulations of Functional Au-144(SR)(60) Gold Nanoparticles in Aqueous Environment

    DEFF Research Database (Denmark)

    Heikkila, E.; Gurtovenko, A. A.; Martinez-Seara, H.

    2012-01-01

    Charged monolayer-protected gold nanoparticles (AuNPs) have been studied in aqueous solution by performing atomistic molecular dynamics simulations at physiological temperature (310 K). Particular attention has been paid to electrostatic properties that modulate the formation of a complex comprised...... of the nanoparticle together with surrounding ions and water. We focus on Au-144 nanoparticles that comprise a nearly spherical Au core (diameter similar to 2 nm), a passivating Au-S interface, and functionalized alkanethiol chains. Cationic and anionic AuNPs have been modeled with amine and carboxyl terminal groups...... potential displays a minimum for AuNP- at 1.9 nm from the center of the nanoparticle, marking a preferable location for Na+, while the AuNP+ potential (affecting the distribution of Cl-) rises almost monotonically with a local maximum. Comparison to Debye-Huckel theory shows very good agreement for radial...

  14. Structures, nanomechanics, and disintegration of single-walled GaN nanotubes: atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Jeong Won; Hwang, Ho Jung; Song, Ki Oh; Choi, Won Young; Byun, Ki Ryang [Chung-Ang University, Seoul (Korea, Republic of); Kwon, Oh Keun [Semyung University, Jecheon (Korea, Republic of); Lee, Jun Ha [Sangmyung University, Chonan (Korea, Republic of); Kim, Won Woo [Juseong College, Cheongwon (Korea, Republic of)

    2003-09-15

    We have investigated the structural, mechanical, and thermal properties of single-walled GaN nanotubes by using atomistic simulations and a Tersoff-type potential. The Tersoff potential for GaN effectively describes the properties of GaN nanotubes. The nanomechanics of GaN nanotubes under tensile and compressive loadings have also been investigated, and Young's modulus has been calculated. The caloric curves of single-walled GaN nanotubes can be divided into three regions corresponding to nanotubes, the disintegrating range, and vapor. Since the stability or the stiffness of a tube decreases with increasing curving sheet-to-tube strain energy, the disintegration temperatures of GaN nanotubes are closely related to the curving sheet-to-tube strain energy.

  15. A Spectral Multiscale Method for Wave Propagation Analysis: Atomistic-Continuum Coupled Simulation

    CERN Document Server

    Patra, Amit K; Ganguli, Ranjan

    2014-01-01

    In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a ...

  16. Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code

    Energy Technology Data Exchange (ETDEWEB)

    Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

    1980-04-01

    This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.

  17. Mapping between atomistic simulations and Eshelby inclusions in the shear deformation of an amorphous silicon model

    Science.gov (United States)

    Albaret, T.; Tanguy, A.; Boioli, F.; Rodney, D.

    2016-05-01

    In this paper we perform quasistatic shear simulations of model amorphous silicon bulk samples with Stillinger-Weber-type potentials. Local plastic rearrangements identified based on local energy variations are fitted through their displacement fields on collections of Eshelby spherical inclusions, allowing determination of their transformation strain tensors. The latter are then used to quantitatively reproduce atomistic stress-strain curves, in terms of both shear and pressure components. We demonstrate that our methodology is able to capture the plastic behavior predicted by different Stillinger-Weber potentials, in particular, their different shear tension coupling. These calculations justify the decomposition of plasticity into shear transformations used so far in mesoscale models and provide atomic-scale parameters that can be used to limit the empiricism needed in such models up to now.

  18. Thermochemistry of organic reactions in microporous oxides by atomistic simulations: benchmarking against periodic B3LYP.

    Science.gov (United States)

    Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole

    2010-07-15

    The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol.

  19. Atomistic simulations of surface coverage effects in anisotropic wet chemical etching of crystalline silicon

    Energy Technology Data Exchange (ETDEWEB)

    Gosalvez, M.A.; Foster, A.S.; Nieminen, R.M

    2002-12-30

    Atomistic simulations of anisotropic wet chemical etching of crystalline silicon have been performed in order to determine the dependence of the etch rates of different crystallographic orientations on surface coverage and clustering of OH radicals. We show that the etch rate is a non-monotonic function of OH coverage and that there always exists a coverage value at which the etch rate reaches a maximum. The dependence of the anisotropy of the etching process on coverage, including the dependence of the fastest-etched plane orientation, is implicitly contained in the model and predictions of convex corner under-etching structures are made. We show that the whole etching process is controlled by only a few surface configurations involving a particular type of next-nearest neighbours. The relative value of the removal probabilities of these confitions determines the balance in the occurrence of step propagation and etch pitting for all surface orientations.

  20. Atomistic-Continuum Hybrid Simulation of Heat Transfer between Argon Flow and Copper Plates

    CERN Document Server

    Mao, Yijin; Chen, C L

    2016-01-01

    A simulation work aiming to study heat transfer coefficient between argon fluid flow and copper plate is carried out based on atomistic-continuum hybrid method. Navier-Stokes equations for continuum domain are solved through the Pressure Implicit with Splitting of Operators (PISO) algorithm, and the atom evolution in molecular domain is solved through the Verlet algorithm. The solver is validated by solving Couette flow and heat conduction problems. With both momentum and energy coupling method applied, simulations on convection of argon flows between two parallel plates are performed. The top plate is kept as a constant velocity and has higher temperature, while the lower one, which is modeled with FCC copper lattices, is also fixed but has lower temperature. It is found that, heat transfer between argon fluid flow and copper plate in this situation is much higher than that at macroscopic when the flow is fully developed.

  1. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    Science.gov (United States)

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; Stocks, G. Malcolm; Landau, David P.

    2017-01-01

    Using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. By calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. Comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnons leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.

  2. Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows

    CERN Document Server

    Fyta, Maria; Kaxiras, Efthimios; Succi, Sauro

    2007-01-01

    We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and mesoscopic scales and is capable of describing self-consistent hydrodynamic effects on molecular motion at a computational cost which scales linearly with both solute size and solvent volume. For an application of our multiscale method, we consider the much studied problem of biopolymer translocation through nanopores: we find that the method reproduces with remarkable accuracy the statistical scaling behavior of the translocation process and provides valuable insight into the cooperative aspects of biopolymer and hydrodynamic motion.

  3. Identifying early stage precipitation in large-scale atomistic simulations of superalloys

    Science.gov (United States)

    Schmidt, Eric; Bristowe, Paul D.

    2017-04-01

    A method for identifying and classifying ordered phases in large chemically and thermally disordered atomistic models is presented. The method uses Steinhardt parameters to represent local atomic configurations and develops probability density functions to classify individual atoms using naïve Bayes. The method is applied to large molecular dynamics simulations of supersaturated Ni-20 at% Al solid solutions in order to identify the formation of embryonic γ‧-Ni3Al. The composition and temperatures are chosen to promote precipitation, which is observed in the form of ordering and is found to occur more likely in regions with above average Al concentration producing ‘clusters’ of increasing size. The results are interpreted in terms of a precipitation mechanism in which the solid solution is unstable with respect to ordering and potentially followed by either spinodal decomposition or nucleation and growth.

  4. Atomistic study of deposition process of Al thin film on Cu substrate

    Energy Technology Data Exchange (ETDEWEB)

    Cao Yongzhi, E-mail: yzcaohit@gmail.com [Center for Precision Engineering, Harbin Institute of Technology, Harbin (China); Zhang Junjie; Sun Tao; Yan Yongda; Yu Fuli [Center for Precision Engineering, Harbin Institute of Technology, Harbin (China)

    2010-08-01

    In this paper we report molecular dynamics based atomistic simulations of deposition process of Al atoms onto Cu substrate and following nanoindentation process on that nanostructured material. Effects of incident energy on the morphology of deposited thin film and mechanical property of this nanostructured material are emphasized. The results reveal that the morphology of growing film is layer-by-layer-like at incident energy of 0.1-10 eV. The epitaxy mode of film growth is observed at incident energy below 1 eV, but film-mixing mode commences when incident energy increase to 10 eV accompanying with increased disorder of film structure, which improves quality of deposited thin film. Following indentation studies indicate deposited thin films pose lower stiffness than single crystal Al due to considerable amount of defects existed in them, but Cu substrate is strengthened by the interface generated from lattice mismatch between deposited Al thin film and Cu substrate.

  5. Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia.

    Directory of Open Access Journals (Sweden)

    Ramon Reigada

    Full Text Available The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic and carbon tetrachloride (non-anesthetic. Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.

  6. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    Science.gov (United States)

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Summary Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  7. NATO Advanced Study Institute on Surface Diffusion : Atomistic and Collective Processes

    CERN Document Server

    1997-01-01

    The interest in the problem of surface diffusion has been steadily growing over the last fifteen years. This is clearly evident from the increase in the number of papers dealing with the problem, the development of new experimental techniques, and the specialized sessions focusing on diffusion in national and international meetings. Part of the driving force behind this increasing activity is our recently acquired ability to observe and possibly control atomic scale phenomena. It is now possible to look selectively at individual atomistic processes and to determine their relative importance during growth and reactions at surfaces. The number of researchers interested in this problem also has been growing steadily which generates the need for a good reference source to farniliarize newcomers to the problem. While the recent emphasis is on the role of diffusion during growth, there is also continuing progress on the more traditional aspects of the problem describing mass transport in an ensemble of particles. S...

  8. Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface

    Science.gov (United States)

    He, Xibing; Guvench, Olgun; MacKerell, Alexander D.; Klein, Michael L.

    2010-01-01

    Molecular Dynamics simulations with the CHARMM atomistic force field have been used to study monolayers of a series of linear alkylbenzene sulfonates (LAS) at the water/air interface. Both the numbers of carbon atoms in the LAS alkyl tail (1 to 11), and the position of attachment of the benzene ring on the alkyl chain have been varied. Totally 36 LAS homologues and isomers have been investigated. The surface tensions of the systems and the average tilt angles of the LAS molecules are found to be related to both the length and the degree of branching of the alkyl tails, whereas the solubility and mobility are mostly determined by the tail length. PMID:20614916

  9. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    Science.gov (United States)

    Seppä, Jeremias; Reischl, Bernhard; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Raiteri, Paolo; Rohl, Andrew L.; Nordlund, Kai; Lassila, Antti

    2017-03-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation.

  10. Subtle Monte Carlo Updates in Dense Molecular Systems.

    Science.gov (United States)

    Bottaro, Sandro; Boomsma, Wouter; E Johansson, Kristoffer; Andreetta, Christian; Hamelryck, Thomas; Ferkinghoff-Borg, Jesper

    2012-02-14

    Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.

  11. Lattice gauge theories and Monte Carlo simulations

    CERN Document Server

    Rebbi, Claudio

    1983-01-01

    This volume is the most up-to-date review on Lattice Gauge Theories and Monte Carlo Simulations. It consists of two parts. Part one is an introductory lecture on the lattice gauge theories in general, Monte Carlo techniques and on the results to date. Part two consists of important original papers in this field. These selected reprints involve the following: Lattice Gauge Theories, General Formalism and Expansion Techniques, Monte Carlo Simulations. Phase Structures, Observables in Pure Gauge Theories, Systems with Bosonic Matter Fields, Simulation of Systems with Fermions.

  12. Fast quantum Monte Carlo on a GPU

    CERN Document Server

    Lutsyshyn, Y

    2013-01-01

    We present a scheme for the parallelization of quantum Monte Carlo on graphical processing units, focusing on bosonic systems and variational Monte Carlo. We use asynchronous execution schemes with shared memory persistence, and obtain an excellent acceleration. Comparing with single core execution, GPU-accelerated code runs over x100 faster. The CUDA code is provided along with the package that is necessary to execute variational Monte Carlo for a system representing liquid helium-4. The program was benchmarked on several models of Nvidia GPU, including Fermi GTX560 and M2090, and the latest Kepler architecture K20 GPU. Kepler-specific optimization is discussed.

  13. Monte carlo simulation for soot dynamics

    KAUST Repository

    Zhou, Kun

    2012-01-01

    A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.

  14. Monte Carlo approaches to light nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Carlson, J.

    1990-01-01

    Significant progress has been made recently in the application of Monte Carlo methods to the study of light nuclei. We review new Green's function Monte Carlo results for the alpha particle, Variational Monte Carlo studies of {sup 16}O, and methods for low-energy scattering and transitions. Through these calculations, a coherent picture of the structure and electromagnetic properties of light nuclei has arisen. In particular, we examine the effect of the three-nucleon interaction and the importance of exchange currents in a variety of experimentally measured properties, including form factors and capture cross sections. 29 refs., 7 figs.

  15. 11th International Conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing

    CERN Document Server

    Nuyens, Dirk

    2016-01-01

    This book presents the refereed proceedings of the Eleventh International Conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing that was held at the University of Leuven (Belgium) in April 2014. These biennial conferences are major events for Monte Carlo and quasi-Monte Carlo researchers. The proceedings include articles based on invited lectures as well as carefully selected contributed papers on all theoretical aspects and applications of Monte Carlo and quasi-Monte Carlo methods. Offering information on the latest developments in these very active areas, this book is an excellent reference resource for theoreticians and practitioners interested in solving high-dimensional computational problems, arising, in particular, in finance, statistics and computer graphics.

  16. Systematic hierarchical coarse-graining with the inverse Monte Carlo method

    Energy Technology Data Exchange (ETDEWEB)

    Lyubartsev, Alexander P., E-mail: alexander.lyubartsev@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Naômé, Aymeric, E-mail: aymeric.naome@unamur.be [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Vercauteren, Daniel P., E-mail: daniel.vercauteren@unamur.be [UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Laaksonen, Aatto, E-mail: aatto@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Science for Life Laboratory, 17121 Solna (Sweden)

    2015-12-28

    We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730–3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.

  17. Systematic hierarchical coarse-graining with the inverse Monte Carlo method

    Science.gov (United States)

    Lyubartsev, Alexander P.; Naômé, Aymeric; Vercauteren, Daniel P.; Laaksonen, Aatto

    2015-12-01

    We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730-3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.

  18. Monte Carlo simulations for plasma physics

    Energy Technology Data Exchange (ETDEWEB)

    Okamoto, M.; Murakami, S.; Nakajima, N.; Wang, W.X. [National Inst. for Fusion Science, Toki, Gifu (Japan)

    2000-07-01

    Plasma behaviours are very complicated and the analyses are generally difficult. However, when the collisional processes play an important role in the plasma behaviour, the Monte Carlo method is often employed as a useful tool. For examples, in neutral particle injection heating (NBI heating), electron or ion cyclotron heating, and alpha heating, Coulomb collisions slow down high energetic particles and pitch angle scatter them. These processes are often studied by the Monte Carlo technique and good agreements can be obtained with the experimental results. Recently, Monte Carlo Method has been developed to study fast particle transports associated with heating and generating the radial electric field. Further it is applied to investigating the neoclassical transport in the plasma with steep gradients of density and temperatures which is beyong the conventional neoclassical theory. In this report, we briefly summarize the researches done by the present authors utilizing the Monte Carlo method. (author)

  19. Monte Vista NWR Water Use Report- 1964

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes water use at Monte Vista NWR for 1964. The document includes summaries of 1964 water use, 1965 water program recommendations, and proposed...

  20. Improved Monte Carlo Renormalization Group Method

    Science.gov (United States)

    Gupta, R.; Wilson, K. G.; Umrigar, C.

    1985-01-01

    An extensive program to analyze critical systems using an Improved Monte Carlo Renormalization Group Method (IMCRG) being undertaken at LANL and Cornell is described. Here we first briefly review the method and then list some of the topics being investigated.

  1. Simulation and the Monte Carlo method

    CERN Document Server

    Rubinstein, Reuven Y

    2016-01-01

    Simulation and the Monte Carlo Method, Third Edition reflects the latest developments in the field and presents a fully updated and comprehensive account of the major topics that have emerged in Monte Carlo simulation since the publication of the classic First Edition over more than a quarter of a century ago. While maintaining its accessible and intuitive approach, this revised edition features a wealth of up-to-date information that facilitates a deeper understanding of problem solving across a wide array of subject areas, such as engineering, statistics, computer science, mathematics, and the physical and life sciences. The book begins with a modernized introduction that addresses the basic concepts of probability, Markov processes, and convex optimization. Subsequent chapters discuss the dramatic changes that have occurred in the field of the Monte Carlo method, with coverage of many modern topics including: Markov Chain Monte Carlo, variance reduction techniques such as the transform likelihood ratio...

  2. Avariide kiuste Monte Carlosse / Aare Arula

    Index Scriptorium Estoniae

    Arula, Aare

    2007-01-01

    Vt. ka Tehnika dlja Vsehh nr. 3, lk. 26-27. 26. jaanuaril 1937 Tallinnast Monte Carlo tähesõidule startinud Karl Siitanit ja tema meeskonda ootasid ees seiklused, mis oleksid neile peaaegu elu maksnud

  3. Smart detectors for Monte Carlo radiative transfer

    CERN Document Server

    Baes, Maarten

    2008-01-01

    Many optimization techniques have been invented to reduce the noise that is inherent in Monte Carlo radiative transfer simulations. As the typical detectors used in Monte Carlo simulations do not take into account all the information contained in the impacting photon packages, there is still room to optimize this detection process and the corresponding estimate of the surface brightness distributions. We want to investigate how all the information contained in the distribution of impacting photon packages can be optimally used to decrease the noise in the surface brightness distributions and hence to increase the efficiency of Monte Carlo radiative transfer simulations. We demonstrate that the estimate of the surface brightness distribution in a Monte Carlo radiative transfer simulation is similar to the estimate of the density distribution in an SPH simulation. Based on this similarity, a recipe is constructed for smart detectors that take full advantage of the exact location of the impact of the photon pack...

  4. Monte Carlo methods for particle transport

    CERN Document Server

    Haghighat, Alireza

    2015-01-01

    The Monte Carlo method has become the de facto standard in radiation transport. Although powerful, if not understood and used appropriately, the method can give misleading results. Monte Carlo Methods for Particle Transport teaches appropriate use of the Monte Carlo method, explaining the method's fundamental concepts as well as its limitations. Concise yet comprehensive, this well-organized text: * Introduces the particle importance equation and its use for variance reduction * Describes general and particle-transport-specific variance reduction techniques * Presents particle transport eigenvalue issues and methodologies to address these issues * Explores advanced formulations based on the author's research activities * Discusses parallel processing concepts and factors affecting parallel performance Featuring illustrative examples, mathematical derivations, computer algorithms, and homework problems, Monte Carlo Methods for Particle Transport provides nuclear engineers and scientists with a practical guide ...

  5. Quantum Monte Carlo Calculations of Light Nuclei

    CERN Document Server

    Pieper, Steven C

    2007-01-01

    During the last 15 years, there has been much progress in defining the nuclear Hamiltonian and applying quantum Monte Carlo methods to the calculation of light nuclei. I describe both aspects of this work and some recent results.

  6. Aasta film - joonisfilm "Mont Blanc" / Verni Leivak

    Index Scriptorium Estoniae

    Leivak, Verni, 1966-

    2002-01-01

    Eesti Filmiajakirjanike Ühing andis aasta 2001 parima filmi tiitli Priit Tenderi joonisfilmile "Mont Blanc" : Eesti Joonisfilm 2001.Ka filmikriitikute eelistused kinodes ja televisioonis 2001. aastal näidatud filmide osas

  7. Pheasant hunting on the Monte Vista NWR

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This letter to the Alamosa/Monte Vista NWR Refuge Manager discusses the need to alter management of pheasants in the area to halt the continued decline in population...

  8. Kinetics of methane fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Y. R.; Hashimoto, A. G.

    1978-01-01

    The kinetics on methane fermentation are described using published data for livestock residue, sewage sludge, and municipal refuse. Methods are presented to determine the kinetic constants and the finally attainable methane production using steady-state methane production data. The effects of temperature, loading rate, and influent substrate concentration on methane fermentation kinetics are discussed. These relationships were used to predict the rate of methane production of a pilot-scale fermentor with excellent results.

  9. Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

    CERN Document Server

    Beauchamp, Kyle A; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

    2015-01-01

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using t...

  10. Continuum Plate Theory and Atomistic Modeling to Find the Flexural Rigidity of a Graphene Sheet Interacting with a Substrate

    Directory of Open Access Journals (Sweden)

    M. W. Roberts

    2010-01-01

    Full Text Available Using a combination of continuum modeling, atomistic simulations, and numerical optimization, we estimate the flexural rigidity of a graphene sheet. We consider a rectangular sheet that is initially parallel to a rigid substrate. The sheet interacts with the substrate by van der Waals forces and deflects in response to loading on a pair of opposite edges. To estimate the flexural rigidity, we model the graphene sheet as a continuum and numerically solve an appropriate differential equation for the transverse deflection. This solution depends on the flexural rigidity. We then use an optimization procedure to find the value of the flexural rigidity that minimizes the difference between the numerical solutions and the deflections predicted by atomistic simulations. This procedure predicts a flexural rigidity of 0.26 nN nm=1.62 eV.

  11. Monte Carlo Hamiltonian:Inverse Potential

    Institute of Scientific and Technical Information of China (English)

    LUO Xiang-Qian; CHENG Xiao-Ni; Helmut KR(O)GER

    2004-01-01

    The Monte Carlo Hamiltonian method developed recently allows to investigate the ground state and low-lying excited states of a quantum system,using Monte Carlo(MC)algorithm with importance sampling.However,conventional MC algorithm has some difficulties when applied to inverse potentials.We propose to use effective potential and extrapolation method to solve the problem.We present examples from the hydrogen system.

  12. The Feynman Path Goes Monte Carlo

    OpenAIRE

    Sauer, Tilman

    2001-01-01

    Path integral Monte Carlo (PIMC) simulations have become an important tool for the investigation of the statistical mechanics of quantum systems. I discuss some of the history of applying the Monte Carlo method to non-relativistic quantum systems in path-integral representation. The principle feasibility of the method was well established by the early eighties, a number of algorithmic improvements have been introduced in the last two decades.

  13. Monte Carlo Algorithms for Linear Problems

    OpenAIRE

    DIMOV, Ivan

    2000-01-01

    MSC Subject Classification: 65C05, 65U05. Monte Carlo methods are a powerful tool in many fields of mathematics, physics and engineering. It is known, that these methods give statistical estimates for the functional of the solution by performing random sampling of a certain chance variable whose mathematical expectation is the desired functional. Monte Carlo methods are methods for solving problems using random variables. In the book [16] edited by Yu. A. Shreider one can find the followin...

  14. Principles of chemical kinetics

    CERN Document Server

    House, James E

    2007-01-01

    James House's revised Principles of Chemical Kinetics provides a clear and logical description of chemical kinetics in a manner unlike any other book of its kind. Clearly written with detailed derivations, the text allows students to move rapidly from theoretical concepts of rates of reaction to concrete applications. Unlike other texts, House presents a balanced treatment of kinetic reactions in gas, solution, and solid states. The entire text has been revised and includes many new sections and an additional chapter on applications of kinetics. The topics covered include quantitative rela

  15. Introduction to chemical kinetics

    CERN Document Server

    Soustelle, Michel

    2013-01-01

    This book is a progressive presentation of kinetics of the chemical reactions. It provides complete coverage of the domain of chemical kinetics, which is necessary for the various future users in the fields of Chemistry, Physical Chemistry, Materials Science, Chemical Engineering, Macromolecular Chemistry and Combustion. It will help them to understand the most sophisticated knowledge of their future job area. Over 15 chapters, this book present the fundamentals of chemical kinetics, its relations with reaction mechanisms and kinetic properties. Two chapters are then devoted to experimental re

  16. Error in Monte Carlo, quasi-error in Quasi-Monte Carlo

    CERN Document Server

    Kleiss, R H

    2006-01-01

    While the Quasi-Monte Carlo method of numerical integration achieves smaller integration error than standard Monte Carlo, its use in particle physics phenomenology has been hindered by the abscence of a reliable way to estimate that error. The standard Monte Carlo error estimator relies on the assumption that the points are generated independently of each other and, therefore, fails to account for the error improvement advertised by the Quasi-Monte Carlo method. We advocate the construction of an estimator of stochastic nature, based on the ensemble of pointsets with a particular discrepancy value. We investigate the consequences of this choice and give some first empirical results on the suggested estimators.

  17. A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems

    Energy Technology Data Exchange (ETDEWEB)

    Farrell, Kathryn, E-mail: kfarrell@ices.utexas.edu; Oden, J. Tinsley, E-mail: oden@ices.utexas.edu; Faghihi, Danial, E-mail: danial@ices.utexas.edu

    2015-08-15

    A general adaptive modeling algorithm for selection and validation of coarse-grained models of atomistic systems is presented. A Bayesian framework is developed to address uncertainties in parameters, data, and model selection. Algorithms for computing output sensitivities to parameter variances, model evidence and posterior model plausibilities for given data, and for computing what are referred to as Occam Categories in reference to a rough measure of model simplicity, make up components of the overall approach. Computational results are provided for representative applications.

  18. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    Directory of Open Access Journals (Sweden)

    Radhakrishna Bettadapura

    2015-10-01

    Full Text Available There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data, and 3D reconstructed cryo-electron microscopy (3D EM maps (albeit at coarser resolution of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2 fit (Polar Fast Fourier Fitting for the best possible structural alignment of atomistic structures with 3D EM. While PF(2 fit enables only a rigid, six dimensional (6D alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

  19. Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

    Science.gov (United States)

    Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.

    2011-01-01

    Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

  20. Atomistic study of hydrogen embrittlement of grain boundaries in nickel: I. Fracture

    Science.gov (United States)

    Tehranchi, A.; Curtin, W. A.

    Hydrogen ingress into a metal is a persistent source of embrittlement. Fracture surfaces are often intergranular, suggesting favorable cleave crack growth along grain boundaries (GBs) as one driver for embrittlement. Here, atomistic simulations are used to investigate the effects of segregated hydrogen on the behavior of cracks along various symmetric tilt grain boundaries in fcc Nickel. An atomistic potential for Ni-H is first recalibrated against new quantum level computations of the energy of H in specific sites within the NiΣ5(120)⟨100⟩ GB. The binding energy of H atoms to various atomic sites in the NiΣ3(111) (twin), NiΣ5(120)⟨100⟩, NiΣ99(557)⟨110⟩, and NiΣ9(221)⟨110⟩ GBs, and to various surfaces created by separating these GBs into two possible fracture surfaces, are computed and used to determine equilibrium H concentrations at bulk H concentrations typical of embrittlement in Ni. Mode I fracture behavior is then studied, examining the influence of H in altering the competition between dislocation emission (crack blunting; "ductile" behavior) and cleavage fracture ("brittle" behavior) for intergranular cracks. Simulation results are compared with theoretical predictions (Griffith theory for cleavage; Rice theory for emission) using the computed surface energies. The deformation behavior at the GBs is, however, generally complex and not as simple as cleavage or emission at a sharp crack tip, which is not unexpected due to the complexity of the GB structures. In cases predicted to emit dislocations from the crack tip, the presence of H atoms reduces the critical load for emission of the dislocations and no cleavage is found. In the cases predicted to cleave, the presence of H atoms reduces the cleavage stress intensity and makes cleavage easier, including NiΣ9(221)⟨110⟩ which emits dislocations in the absence of H. Aside from the one unusual NiΣ9(221)⟨110⟩ case, no tendency is found for H to cause a ductile

  1. Atomistic modeling of nanowires, small-scale fatigue damage in cast magnesium, and materials for MEMS

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Martin L. [Univ. of Colorado, Boulder, CO (United States); Talmage, Mellisa J. [Univ. of Colorado, Boulder, CO (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); West, Neil [Univ. of Colorado, Boulder, CO (United States); Gullett, Philip Michael [Mississippi State Univ., Mississippi State, MS (United States); Miller, David C. [Univ. of Colorado, Boulder, CO (United States); Spark, Kevin [Univ. of Colorado, Boulder, CO (United States); Diao, Jiankuai [Univ. of Colorado, Boulder, CO (United States); Horstemeyer, Mark F. [Mississippi State Univ., Mississippi State, MS (United States); Zimmerman, Jonathan A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gall, K. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2006-10-01

    Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project

  2. Atomistic simulation of the structure and elastic properties of gold nanowires

    Science.gov (United States)

    Diao, Jiankuai; Gall, Ken; Dunn, Martin L.

    2004-09-01

    We performed atomistic simulations to study the effect of free surfaces on the structure and elastic properties of gold nanowires aligned in the and crystallographic directions. Computationally, we formed a nanowire by assembling gold atoms into a long wire with free sides by putting them in their bulk fcc lattice positions. We then performed a static relaxation on the assemblage. The tensile surface stresses on the sides of the wire cause the wire to contract along the length with respect to the original fcc lattice, and we characterize this deformation in terms of an equilibrium strain versus the cross-sectional area. While the surface stress causes wires of both orientations and all sizes to increasingly contract with decreasing cross-sectional area, when the cross-sectional area of a nanowire is less than 1.83 nm×1.83 nm, the wire undergoes a phase transformation from fcc to bct, and the equilibrium strain increases by an order of magnitude. We then applied a uniform uniaxial strain incrementally to 1.2% to the relaxed nanowires in a molecular statics framework. From the simulation results we computed the effective axial Young's modulus and Poisson's ratios of the nanowire as a function of cross-sectional area. We used two approaches to compute the effective elastic moduli, one based on a definition in terms of the strain derivative of the total energy and another in terms of the virial stress often used in atomistic simulations. Both give quantitatively similar results, showing an increase in Young's modulus with a decrease of cross-sectional area in the nanowires that do not undergo a phase transformation. Those that undergo a phase transformation experience an increase of about a factor of three of Young's modulus. The Poisson's ratio of the wires that do not undergo a phase transformation show little change with the cross-sectional area. Those wires that undergo a phase transformation experience an increase of about 10% in Poisson's ratio. The wires show

  3. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

    Science.gov (United States)

    Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

    2016-08-25

    The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

  4. Kinetic model of II-VI(001) semiconductor surfaces : Growth rates in atomic layer epitaxy

    NARCIS (Netherlands)

    Volkmann, T; Ahr, M; Biehl, M

    2004-01-01

    We present a zinc-blende lattice gas model of II-VI(001) surfaces, which is investigated by means of kinetic Monte Carlo simulations. Anisotropic effective interactions between surface metal atoms allow for the description of, e.g., the sublimation of CdTe(001), including the reconstruction of Cd-te

  5. Monte Carlo EM加速算法%Acceleration of Monte Carlo EM Algorithm

    Institute of Scientific and Technical Information of China (English)

    罗季

    2008-01-01

    EM算法是近年来常用的求后验众数的估计的一种数据增广算法,但由于求出其E步中积分的显示表达式有时很困难,甚至不可能,限制了其应用的广泛性.而Monte Carlo EM算法很好地解决了这个问题,将EM算法中E步的积分用Monte Carlo模拟来有效实现,使其适用性大大增强.但无论是EM算法,还是Monte Carlo EM算法,其收敛速度都是线性的,被缺损信息的倒数所控制,当缺损数据的比例很高时,收敛速度就非常缓慢.而Newton-Raphson算法在后验众数的附近具有二次收敛速率.本文提出Monte Carlo EM加速算法,将Monte Carlo EM算法与Newton-Raphson算法结合,既使得EM算法中的E步用Monte Carlo模拟得以实现,又证明了该算法在后验众数附近具有二次收敛速度.从而使其保留了Monte Carlo EM算法的优点,并改进了Monte Carlo EM算法的收敛速度.本文通过数值例子,将Monte Carlo EM加速算法的结果与EM算法、Monte Carlo EM算法的结果进行比较,进一步说明了Monte Carlo EM加速算法的优良性.

  6. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    Science.gov (United States)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  7. An Atomistic View of the Incipient Growth of Zinc Oxide Nanolayers

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Manh Hung; Tian, Liang; Chaker, Ahmad; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon D.; Ciatto, Gianluca

    2016-09-07

    The growth of zinc oxide thin films by atomic layer deposition is believed to proceed through an embryonic step in which three-dimensional nanoislands form and then coalesce to trigger a layer-by-layer growth mode. This transient initial state is characterized by a poorly ordered atomic structure, which may be inaccessible by X-ray diffraction techniques. In this work, we apply X-ray absorption spectroscopy in situ to address the local structure of Zn after each atomic layer deposition cycle, using a custom-built reactor mounted at a synchrotron beamline, and we shed light on the atomistic mechanisms taking place during the first stages of the growth. We find that such mechanisms are surprisingly different for zinc oxide growth on amorphous (silica) and crystalline (sapphire) substrate. Ab initio simulations and quantitative data analysis allow the formulation of a comprehensive growth model, based on the different effects of surface atoms and grain boundaries in the nanoscale islands, and the consequent induced local disorder. From a comparison of these specttoscopy results with those from X-ray diffraction reported recently, we observe that the final structure of the zinc oxide nanolayers depends strongly on the mechanisms taking place during the initial stages of growth. The approach followed here for the case of zinc oxide will be of general interest for characterizing and optimizing the growth and properties of more complex nanostructures.

  8. Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

    KAUST Repository

    Hong, Bingbing

    2013-10-02

    We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH 2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henrys constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henrys constant. Dependence of the calculated Henrys constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. © 2013 Taylor & Francis.

  9. Features of structure and phase transitions in pure uranium and U-Mo alloys: atomistic simulation

    Science.gov (United States)

    Kolotova, L. N.; Kuksin, A. Yu; Smirnova, D. E.; Starikov, S. V.; Tseplyaev, V. I.

    2016-11-01

    We study structural properties of cubic and tetragonal phases of U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. For pure uranium and U-Mo alloys at low temperatures we observe body-centered tetragonal (bct) structure, which is similar to the metastable γ°-phase found in the experiments. At higher temperatures bct structure transforms to a quasi body-centered cubic (q-bcc) phase that exhibits cubic symmetry just on the scale of several interatomic spacings or when averaged over time. Instantaneous pair distribution function (PDF) differs from PDF for the time-averaged atomic coordinates corresponding to the bcc lattice. The local positions of uranium atoms in q-bcc lattice correspond to the bct structure, which is energetically favourable due to formation of short U-U bonds. Transition from bct to q-bcc could be considered as ferro-to paraelastic transition of order-disorder type. The temperature of transition depends on Mo concentration. For pure uranium it is equal to about 700 K, which is well below than the upper boundary of the stability region of the α-U phase. Due to this reason, bct phase is observed only in uranium alloys containing metals with low solubility in α-U.

  10. Atomistic Analysis of Room Temperature Quantum Coherence in Two-Dimensional CdSe Nanostructures.

    Science.gov (United States)

    Pal, Sougata; Nijjar, Parmeet; Frauenheim, Thomas; Prezhdo, Oleg V

    2017-03-02

    Recent experiments on CdSe nanoplatelets synthesized with precisely controlled thickness that eliminates ensemble disorder have allowed accurate measurement of quantum coherence at room temperature. Matching exactly the CdSe cores of the experimentally studied particles and considering several defects, we establish the atomistic origins of the loss of coherence between heavy and light hole excitations in two-dimensional CdSe and CdSe/CdZnS core/shell structures. The coherence times obtained using molecular dynamics based on tight-binding density functional theory are in excellent agreement with the measured values. We show that a long coherence time is a consequence of both small fluctuations in the energy gap between the excited state pair, which is much less than thermal energy, and a slow decay of correlation between the energies of the two states. Anionic defects at the core/shell interface have little effect on the coherence lifetime, while cationic defects strongly perturb the electronic structure, destroying the experimentally observed coherence. By coupling to the same phonon modes, the heavy and light holes synchronize their energy fluctuations, facilitating long-lived coherence. We further demonstrate that the electronic excitations are localized close to the surface of these narrow nanoscale systems, and therefore, they couple most strongly to surface acoustic phonons. The established features of electron-phonon coupling and the influence of defects, surfaces, and core/shell interfaces provide important insights into quantum coherence in nanoscale materials in general.

  11. Role of atomistic structure in the stochastic nature of conductivity in substoichiometric tantalum pentoxide

    Science.gov (United States)

    Bondi, Robert J.; Fox, Brian P.; Marinella, Matthew J.

    2016-03-01

    First-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influence on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.

  12. Molecular Simulations of Cyclic Loading Behavior of Carbon Nanotubes Using the Atomistic Finite Element Method

    Directory of Open Access Journals (Sweden)

    Jianfeng Wang

    2009-01-01

    Full Text Available The potential applications of carbon nanotubes (CNT in many engineered bionanomaterials and electromechanical devices have imposed an urgent need on the understanding of the fatigue behavior and mechanism of CNT under cyclic loading conditions. To date, however, very little work has been done in this field. This paper presents the results of a theoretical study on the behavior of CNT subject to cyclic tensile and compressive loads using quasi-static molecular simulations. The Atomistic Finite Element Method (AFEM has been applied in the study. It is shown that CNT exhibited extreme cyclic loading resistance with yielding strain and strength becoming constant within limited number of loading cycles. Viscoelastic behavior including nonlinear elasticity, hysteresis, preconditioning (stress softening, and large strain have been observed. Chiral symmetry was found to have appreciable effects on the cyclic loading behavior of CNT. Mechanisms of the observed behavior have been revealed by close examination of the intrinsic geometric and mechanical features of tube structure. It was shown that the accumulated residual defect-free morphological deformation was the primary mechanism responsible for the cyclic failure of CNT, while the bond rotating and stretching experienced during loading/unloading played a dominant role on the strength, strain and modulus behavior of CNT.

  13. Atomistic simulations of CO2 and N2 within cage-type silica zeolites.

    Science.gov (United States)

    Madison, Lindsey; Heitzer, Henry; Russell, Colin; Kohen, Daniela

    2011-03-01

    The behavior of CO(2) and N(2), both as single components and as binary mixtures, in two cage-type silica zeolites was studied using atomistic simulations. The zeolites considered, ITQ-3 and paradigm cage-type zeolite ZK4 (the all-silica analog of LTA), were chosen so that the principles illustrated can be generalized to other adsorbent/adsorbate systems with similar topology and types of interactions. N(2) was chosen both because of the potential uses of N(2)/CO(2) separations and because it differs from CO(2) most significantly in the magnitude of its Coulombic interactions with zeolites. Despite similarities between N(2) and CO(2) diffusion in other materials, we show here that the diffusion of CO(2) within cage-type zeolites is dominated by an energy barrier to diffusion located at the entrance to the narrow channels connecting larger cages. This barrier originates in Coulombic interactions between zeolites and CO(2)'s quadrupole and results in well-defined orientations for the diffusing molecules. Furthermore, CO(2)'s favorable electrostatic interactions with the zeolite framework result in preferential binding in the windows between cages. N(2)'s behavior, in contrast, is more consistent with that of molecules previously studied. Our analysis suggests that CO(2)'s behavior might be common for adsorbates with quadrupoles that interact strongly with a material that has narrow windows between cages.

  14. Atomistic insights into dislocation-based mechanisms of void growth and coalescence

    Science.gov (United States)

    Mi, Changwen; Buttry, Daniel A.; Sharma, Pradeep; Kouris, Demitris A.

    2011-09-01

    One of the low-temperature failure mechanisms in ductile metallic alloys is the growth of voids and their coalescence. In the present work we attempt to obtain atomistic insights into the mechanisms underpinning cavitation in a representative metal, namely Aluminum. Often the pre-existing voids in metallic alloys such as Al have complex shapes (e.g. corrosion pits) and the defromation/damage mechanisms exhibit a rich size-dependent behavior across various material length scales. We focus on these two issues in this paper through large-scale calculations on specimens of sizes ranging from 18 thousand to 1.08 million atoms. In addition to the elucidation of the dislocation propagation based void growth mechanism we highlight the observed length scale effect reflected in the effective stress-strain response, stress triaxiality and void fraction evolution. Furthermore, as expected, the conventionally used Gurson's model fails to capture the observed size-effects calling for a mechanistic modification that incorporates the mechanisms observed in our (and other researchers') simulation. Finally, in our multi-void simulations, we find that, the splitting of a big void into a distribution of small ones increases the load-carrying capacity of specimens. However, no obvious dependence of the void fraction evolution on void coalescence is observed.

  15. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Science.gov (United States)

    Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

    2016-08-01

    This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  16. Atomistic simulations of fracture in the B2 phase of the Nb-Ti-Al system

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Computer Simulation Lab.

    1998-06-30

    Atomistic simulations of the crack tip configuration in the B2 phase of Nb-rich alloys in the Nb-Ti-Al are presented. The alloy compositions studied are Nb-16Al-16Ti and Nb-16Al-33Ti. The simulations were carried out using molecular statics and empirical embedded atom method (EAM) potentials for the ternary system developed in previous work. The behavior of a semi-infinite crack was studied under mode I loading for different crack tip geometries. The crack was embedded in a simulation cell with periodic boundary conditions along the direction parallel to the crack front and fixed boundary conditions along the periphery of the simulation cell. The quasi-static simulations were carried out using a molecular statics relaxation technique to obtain the minimum energy configuration of the atoms starting from their initial elastic positions, under increasingly higher stress intensities. The competition between dislocation emission and cleavage was studied in these alloys as a function of Ti content. Cracks along {l_brace}110{r_brace}-type planes with crack fronts oriented along different directions were studied. The alloys showed increased ductility with increased Ti content. The simulations show more ductile behavior than other intermetallics, due to easier dislocation emission processes at the crack tip. (orig.) 30 refs.

  17. Atomistic structure of the coherent Ni/Ni[sub 3]Al interface

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. (Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering); Campos, M.F. de; Souze, R.M. de; Goldenstein, H. (Escola Politecnica USP, Sao Paulo (Brazil). Dept. de Metalurgia)

    1994-02-01

    Most Ni-based superalloys are strengthened by the presence of coherent precipitates of an ordered fcc bases phase, known as [gamma][prime]. This phase is basically Ni[sub 3]Al. The precipitates are coherent up to a certain size and they present a cubic shape with faces oriented in the (100) planes of both matrix and precipitate. The detailed atomistic structure of this interface has not been studied. Interest in the use of ordered intermetallic compounds as possible structural materials has resulted in a large amount of work in Ni[sub 3]Al and in particular, the development of interatomic potentials for the Ni-Al system using the embedded atom technique. These potentials have been employed in the simulation of a variety of defects in Ni[sub 3]Al, including dislocation cores, grain boundaries and free surfaces. However, there is no simulation of the Ni/Ni[sub 3]Al interface structure using the embedded atom method. The objective of the present work is to carry out such a simulation. Besides the practical importance of the interface in superalloys, it is the simplest type of interface that can be modeled and it is a good starting point for interface work using the embedded atom technique.

  18. Analytical potential for atomistic simulations of silicon, carbon, and silicon carbide

    Science.gov (United States)

    Erhart, Paul; Albe, Karsten

    2005-01-01

    We present an analytical bond-order potential for silicon, carbon, and silicon carbide that has been optimized by a systematic fitting scheme. The functional form is adopted from a preceding work [Phys. Rev. B 65, 195124 (2002)] and is built on three independently fitted potentials for SiSi , CC , and SiC interaction. For elemental silicon and carbon, the potential perfectly reproduces elastic properties and agrees very well with first-principles results for high-pressure phases. The formation enthalpies of point defects are reasonably reproduced. In the case of silicon stuctural features of the melt agree nicely with data taken from literature. For silicon carbide the dimer as well as the solid phases B1, B2, and B3 were considered. Again, elastic properties are very well reproduced including internal relaxations under shear. Comparison with first-principles data on point defect formation enthalpies shows fair agreement. The successful validation of the potentials for configurations ranging from the molecular to the bulk regime indicates the transferability of the potential model and makes it a good choice for atomistic simulations that sample a large configuration space.

  19. A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nomura, K; Seymour, R; Wang, W; Kalia, R; Nakano, A; Vashishta, P; Shimojo, F; Yang, L H

    2009-02-17

    A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based on hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).

  20. Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

    KAUST Repository

    French, William R.

    2013-01-01

    We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

  1. Tunnel-coupled quantum dots: Atomistic Theory of Quantum Dot Molecules and Arrays

    Science.gov (United States)

    Bryant, Garnett W.; Aizpurua, J.; Jaskolski, W.; Zielinski, Michal

    2003-03-01

    Quantum dots are studied as artificial atoms for building novel artificial solids, as nanodevices in nanoelectronics, and as bio/nanohybrids. We present an atomistic tight-binding theory of coupled CdS nanocrystals and vertically and laterally coupled InAs self-assembled dots. Electron states of coupled dots follow the analogy of coupled dots as artificial molecules. Symmetric/antisymmetric pairs are formed with strongest coupling between states with high density at interdot interfaces. Complex coupling of hole states, with significant departures from the artificial molecule analogy, occurs because the coupling is determined by the hole envelope function and the hole atomic state. Some hole states couple to form symmetric/antisymmetric pairs. Other hole states couple through additional intermediate states to form two strongly split symmetric states and an antisymmetric state insensitive to coupling. These coupling effects lead to level reordering, changes in state symmetry, conversion of dark states to bright states and vice versa, and tailored polarization dependence.

  2. Atomistic study of mixing at high Z / low Z interfaces at Warm Dense Matter Conditions

    Science.gov (United States)

    Haxhimali, Tomorr; Glosli, James; Rudd, Robert; Lawrence Livermore National Laboratory Team

    2016-10-01

    We use atomistic simulations to study different aspects of mixing occurring at an initially sharp interface of high Z and low Z plasmas in the Warm/Hot Dense Matter regime. We consider a system of Diamond (the low Z component) in contact with Ag (the high Z component), which undergoes rapid isochoric heating from room temperature up to 10 eV, rapidly changing the solids into warm dense matter at solid density. We simulate the motion of ions via the screened Coulomb potential. The electric field, the electron density and ionizations level are computed on the fly by solving Poisson equation. The spatially varying screening lengths computed from the electron cloud are included in this effective interaction; the electrons are not simulated explicitly. We compute the electric field generated at the Ag-C interface as well as the dynamics of the ions during the mixing process occurring at the plasma interface. Preliminary results indicate an anomalous transport of high Z ions (Ag) into the low Z component (C); a phenomenon that is partially related to the enhanced transport of ions due to the generated electric field. These results are in agreement with recent experimental observation on Au-diamond plasma interface. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.

  3. Prediction of TF target sites based on atomistic models of protein-DNA complexes

    Directory of Open Access Journals (Sweden)

    Collado-Vides Julio

    2008-10-01

    Full Text Available Abstract Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.

  4. Atomistic Insights Into the Oriented Attachment of Tunnel-Based Oxide Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Yifei; Wood, Stephen M; He, Kun; Yao, Wentao; Tompsett, David; Lu, Jun; Nie, Anmin; Islam, M. Saiful; Shahbazian-Yassar, Reza

    2016-01-01

    Controlled synthesis of nanomaterials is one of the grand challenges facing materials scientists. In particular, how tunnel-based nanomaterials aggregate during synthesis while maintaining their well-aligned tunneled structure is not fully understood. Here, we describe the atomistic mechanism of oriented attachment (OA) during solution synthesis of tunneled α-MnO2 nanowires based on a combination of in situ liquid cell transmission electron microscopy (TEM), aberration-corrected scanning TEM with subangstrom spatial resolution, and first-principles calculations. It is found that primary tunnels (1 × 1 and 2 × 2) attach along their common {110} lateral surfaces to form interfaces corresponding to 2 × 3 tunnels that facilitate their short-range ordering. The OA growth of α-MnO2 nanowires is driven by the stability gained from elimination of {110} surfaces and saturation of Mn atoms at {110}-edges. During this process, extra [MnOx] radicals in solution link the two adjacent {110} surfaces and bond with the unsaturated Mn atoms from both surface edges to produce stable nanowire interfaces. Our results provide insights into the controlled synthesis and design of nanomaterials in which tunneled structures can be tailored for use in catalysis, ion exchange, and energy storage applications.

  5. Atomistic study of energy funneling in the light-harvesting complex of green sulfur bacteria.

    Science.gov (United States)

    Huh, Joonsuk; Saikin, Semion K; Brookes, Jennifer C; Valleau, Stéphanie; Fujita, Takatoshi; Aspuru-Guzik, Alán

    2014-02-05

    Phototrophic organisms such as plants, photosynthetic bacteria, and algae use microscopic complexes of pigment molecules to absorb sunlight. Within the light-harvesting complexes, which frequently have several functional and structural subunits, the energy is transferred in the form of molecular excitations with very high efficiency. Green sulfur bacteria are considered to be among the most efficient light-harvesting organisms. Despite multiple experimental and theoretical studies of these bacteria, the physical origin of the efficient and robust energy transfer in their light-harvesting complexes is not well understood. To study excitation dynamics at the systems level, we introduce an atomistic model that mimics a complete light-harvesting apparatus of green sulfur bacteria. The model contains approximately 4000 pigment molecules and comprises a double wall roll for the chlorosome, a baseplate, and six Fenna-Matthews-Olson trimer complexes. We show that the fast relaxation within functional subunits combined with the transfer between collective excited states of pigments can result in robust energy funneling to the initial excitation conditions and temperature changes. Moreover, the same mechanism describes the coexistence of multiple time scales of excitation dynamics frequently observed in ultrafast optical experiments. While our findings support the hypothesis of supertransfer, the model reveals energy transport through multiple channels on different length scales.

  6. Development and assessment of atomistic models for predicting static friction coefficients

    Science.gov (United States)

    Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

    2016-08-01

    The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

  7. Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

    Science.gov (United States)

    Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

    2012-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

  8. Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

    Directory of Open Access Journals (Sweden)

    Helgi Adalsteinsson

    2008-01-01

    Full Text Available Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-level dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.

  9. Calculation of phonon dispersion in carbon nanotubes using a continuum-atomistic finite element approach

    Directory of Open Access Journals (Sweden)

    Michael J. Leamy

    2011-12-01

    Full Text Available Dispersion calculations are presented for cylindrical carbon nanotubes using a manifold-based continuum-atomistic finite element formulation combined with Bloch analysis. The formulated finite elements allow any (n,m chiral nanotube, or mixed tubes formed by periodically-repeating heterojunctions, to be examined quickly and accurately using only three input parameters (radius, chiral angle, and unit cell length and a trivial structured mesh, thus avoiding the tedious geometry generation and energy minimization tasks associated with ab initio and lattice dynamics-based techniques. A critical assessment of the technique is pursued to determine the validity range of the resulting dispersion calculations, and to identify any dispersion anomalies. Two small anomalies in the dispersion curves are documented, which can be easily identified and therefore rectified. They include difficulty in achieving a zero energy point for the acoustic twisting phonon, and a branch veering in nanotubes with nonzero chiral angle. The twisting mode quickly restores its correct group velocity as wavenumber increases, while the branch veering is associated with a rapid exchange of eigenvectors at the veering point, which also lessens its impact. By taking into account the two noted anomalies, accurate predictions of acoustic and low-frequency optical branches can be achieved out to the midpoint of the first Brillouin zone.

  10. Atomistic-Scale Simulations of Defect Formation in Graphene under Noble Gas Ion Irradiation.

    Science.gov (United States)

    Yoon, Kichul; Rahnamoun, Ali; Swett, Jacob L; Iberi, Vighter; Cullen, David A; Vlassiouk, Ivan V; Belianinov, Alex; Jesse, Stephen; Sang, Xiahan; Ovchinnikova, Olga S; Rondinone, Adam J; Unocic, Raymond R; van Duin, Adri C T

    2016-09-27

    Despite the frequent use of noble gas ion irradiation of graphene, the atomistic-scale details, including the effects of dose, energy, and ion bombardment species on defect formation, and the associated dynamic processes involved in the irradiations and subsequent relaxation have not yet been thoroughly studied. Here, we simulated the irradiation of graphene with noble gas ions and the subsequent effects of annealing. Lattice defects, including nanopores, were generated after the annealing of the irradiated graphene, which was the result of structural relaxation that allowed the vacancy-type defects to coalesce into a larger defect. Larger nanopores were generated by irradiation with a series of heavier noble gas ions, due to a larger collision cross section that led to more detrimental effects in the graphene, and by a higher ion dose that increased the chance of displacing the carbon atoms from graphene. Overall trends in the evolution of defects with respect to a dose, as well as the defect characteristics, were in good agreement with experimental results. Additionally, the statistics in the defect types generated by different irradiating ions suggested that the most frequently observed defect types were Stone-Thrower-Wales (STW) defects for He(+) irradiation and monovacancy (MV) defects for all other ion irradiations.

  11. Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex.

    Science.gov (United States)

    Shim, Sangwoo; Rebentrost, Patrick; Valleau, Stéphanie; Aspuru-Guzik, Alán

    2012-02-08

    A remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed long-lived quantum coherence in the electronic energy transfer process in biological photosynthetic systems. Although successful in many respects, several widely used descriptions only include an effective treatment of the protein-chromophore interactions. In this work, by combining an all-atom molecular dynamics simulation, time-dependent density functional theory, and open quantum system approaches, we successfully simulate the dynamics of the electronic energy transfer of the Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic beating of populations and quantum coherences is in good agreement with the experimental results and the hierarchy equation of motion approach. The experimental absorption, linear, and circular dichroism spectra and dephasing rates are recovered at two different temperatures. In addition, we provide an extension of our method to include zero-point fluctuations of the vibrational environment. This work thus presents, to our knowledge, one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description.

  12. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Directory of Open Access Journals (Sweden)

    Thomas M. Vlasic

    2016-08-01

    Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  13. Hierarchical Statistical 3D ' Atomistic' Simulation of Decanano MOSFETs: Drift-Diffusion, Hydrodynamic and Quantum Mechanical Approaches

    Science.gov (United States)

    Asenov, Asen; Brown, A. R.; Slavcheva, G.; Davies, J. H.

    2000-01-01

    When MOSFETs are scaled to deep submicron dimensions the discreteness and randomness of the dopant charges in the channel region introduces significant fluctuations in the device characteristics. This effect, predicted 20 year ago, has been confirmed experimentally and in simulation studies. The impact of the fluctuations on the functionality, yield, and reliability of the corresponding systems shifts the paradigm of the numerical device simulation. It becomes insufficient to simulate only one device representing one macroscopical design in a continuous charge approximation. An ensemble of macroscopically identical but microscopically different devices has to be characterized by simulation of statistically significant samples. The aims of the numerical simulations shift from predicting the characteristics of a single device with continuous doping towards estimating the mean values and the standard deviations of basic design parameters such as threshold voltage, subthreshold slope, transconductance, drive current, etc. for the whole ensemble of 'atomistically' different devices in the system. It has to be pointed out that even the mean values obtained from 'atomistic' simulations are not identical to the values obtained from continuous doping simulations. In this paper we present a hierarchical approach to the 'atomistic' simulation of aggressively scaled decanano MOSFETs. A full scale 3D drift-diffusion'atomostic' simulation approach is first described and used for verification of the more economical, but also more restricted, options. To reduce the processor time and memory requirements at high drain voltage we have developed a self-consistent option based on a thin slab solution of the current continuity equation only in the channel region. This is coupled to the Poisson's equation solution in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison with the full self-consistent solution. At low drain

  14. Monte Carlo模拟在聚合反应速率常数估算中的运用%Estimation of rate constants for polymerization based on Monte Carlo simulation

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 詹晓力; 阳永荣

    2006-01-01

    The application of Monte Carlo method in estimating rate constants for polymerization was described.A general program for Monte Carlo simulation was determined first according to the elementary reactions, after which the rate constants could be automatically adjusted and optimized through comparing of experimental and simulated data with an error expression that meeted a given minimum criterion.Such a process made the rate constants to be estimated without kinetic model in advance.The technique was applied to estimate the rate constants of the bulk polymerization of styrene catalyzed by the rare earth catalyst.The estimated results showed the Monte Carlo method was feasible and effective for estimating rate constants in polymerization engineering.

  15. Reactive molecular dynamics simulation and chemical kinetic modeling of pyrolysis and combustion of n-dodecane

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Quan-De [College of Chemistry, Sichuan University, Chengdu (China); Wang, Jing-Bo; Li, Juan-Qin; Tan, Ning-Xin; Li, Xiang-Yuan [College of Chemical Engineering, Sichuan University, Chengdu (China)

    2011-02-15

    The initiation mechanisms and kinetics of pyrolysis and combustion of n-dodecane are investigated by using the reactive molecular dynamics (ReaxFF MD) simulation and chemical kinetic modeling. From ReaxFF MD simulations, we find the initiation mechanisms of pyrolysis of n-dodecane are mainly through two pathways, (1) the cleavage of C-C bond to form smaller hydrocarbon radicals, and (2) the dehydrogenation reaction to form an H radical and the corresponding n-C{sub 12}H{sub 25} radical. Another pathway is the H-abstraction reactions by small radicals including H, CH{sub 3}, and C{sub 2}H{sub 5}, which are the products after the initiation reaction of n-dodecane pyrolysis. ReaxFF MD simulations lead to reasonable Arrhenius parameters compared with experimental results based on first-order kinetic analysis of n-dodecane pyrolysis. The density/pressure effects on the pyrolysis of n-dodecane are also analyzed. By appropriate mapping of the length and time from macroscopic kinetic modeling to ReaxFF MD, a simple comparison of the conversion of n-dodecane from ReaxFF MD simulations and that from kinetic modeling is performed. In addition, the oxidation of n-dodecane is studied by ReaxFF MD simulations. We find that formaldehyde molecule is an important intermediate in the oxidation of n-dodecane, which has been confirmed by kinetic modeling, and ReaxFF leads to reasonable reaction pathways for the oxidation of n-dodecane. These results indicate that ReaxFF MD simulations can give an atomistic description of the initiation mechanism and product distributions of pyrolysis and combustion for hydrocarbon fuels, and can be further used to provide molecular based robust kinetic reaction mechanism for chemical kinetic modeling of hydrocarbon fuels. (author)

  16. 1D to 3D diffusion-reaction kinetics of defects in crystals

    DEFF Research Database (Denmark)

    Trinkaus, H.; Heinisch, H.L.; Barashev, A.V.

    2002-01-01

    Microstructural features evolving in crystalline solids from diffusion-reaction kinetics of mobile components depend crucially on the dimension of the underlying diffusion process which is commonly assumed to be three-dimensional (3D). In metals, irradiation-induced displacement cascades produce ...... and 3D limiting cases. The analytical result is fully confirmed by kinetic Monte Carlo simulations.......Microstructural features evolving in crystalline solids from diffusion-reaction kinetics of mobile components depend crucially on the dimension of the underlying diffusion process which is commonly assumed to be three-dimensional (3D). In metals, irradiation-induced displacement cascades produce...

  17. A particle-in-cell plus Monte Carlo study of plasma-induced damage of normal incidence collector optics used in extreme ultraviolet lithography

    NARCIS (Netherlands)

    Wieggers, R. C.; W. J. Goedheer,; M.R. Akdim,; F. Bijkerk,; Zegeling, P. A.

    2008-01-01

    We present a kinetic simulation of the plasma formed by photoionization in the intense flux of an extreme ultraviolet lithography (EUVL) light source. The model is based on the particle-in-cell plus Monte Carlo approach. The photoelectric effect and ionization by electron collisions are included. Th

  18. Approaching Chemical Accuracy with Quantum Monte Carlo

    CERN Document Server

    Petruzielo, F R; Umrigar, C J

    2012-01-01

    A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space.

  19. Monte Carlo Simulation of Propylene Polymerization ( I ) Effects of Impurity on Propylene Polymerization%丙烯聚合的Monte Carlo模拟(Ⅰ)活性杂质对丙烯聚合的影响

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 曹志凯; 苏耀堂

    2006-01-01

    A comprehensive mechanism for propylene polymerization was proposed by considering the effects of main impurities in the material on propylene polymerization. According to the proposed mechanism, Monte Carlo simulation was employed to investigate the polymerization kinetics in order to determine the effects of the main impurities on the polymerization. Significant influences of the main impurities on the rate, number-average degree and controlling capability of hydrogen of the polymerization were analyzed.

  20. Kinetic Pathways of the DNA Melting Transition

    CERN Document Server

    Santos, Aaron

    2012-01-01

    We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the critical droplet profile, the initial growth modes, and the exponent characterizing the divergence of the susceptibility near the spinodal. In the PDB model, we use a mean field analysis to calculate susceptibility exponent. We compare these theoretical results with Monte Carlo and Brownian dynamic simulations on the PS and PDB models, respectively. We find that by increasing the range of interaction, the system can be brought close to a pseudospinodal, and that in this region the nucleating droplet is diffuse in contrast to the compact droplets predicted by classical nucleation theory.

  1. Irreversible processes kinetic theory

    CERN Document Server

    Brush, Stephen G

    2013-01-01

    Kinetic Theory, Volume 2: Irreversible Processes deals with the kinetic theory of gases and the irreversible processes they undergo. It includes the two papers by James Clerk Maxwell and Ludwig Boltzmann in which the basic equations for transport processes in gases are formulated, together with the first derivation of Boltzmann's ""H-theorem"" and a discussion of this theorem, along with the problem of irreversibility.Comprised of 10 chapters, this volume begins with an introduction to the fundamental nature of heat and of gases, along with Boltzmann's work on the kinetic theory of gases and s

  2. Quantum Monte Carlo with Variable Spins

    CERN Document Server

    Melton, Cody A; Mitas, Lubos

    2016-01-01

    We investigate the inclusion of variable spins in electronic structure quantum Monte Carlo, with a focus on diffusion Monte Carlo with Hamiltonians that include spin-orbit interactions. Following our previous introduction of fixed-phase spin-orbit diffusion Monte Carlo (FPSODMC), we thoroughly discuss the details of the method and elaborate upon its technicalities. We present a proof for an upper-bound property for complex nonlocal operators, which allows for the implementation of T-moves to ensure the variational property. We discuss the time step biases associated with our particular choice of spin representation. Applications of the method are also presented for atomic and molecular systems. We calculate the binding energies and geometry of the PbH and Sn$_2$ molecules, as well as the electron affinities of the 6$p$ row elements in close agreement with experiments.

  3. Quantum speedup of Monte Carlo methods.

    Science.gov (United States)

    Montanaro, Ashley

    2015-09-08

    Monte Carlo methods use random sampling to estimate numerical quantities which are hard to compute deterministically. One important example is the use in statistical physics of rapidly mixing Markov chains to approximately compute partition functions. In this work, we describe a quantum algorithm which can accelerate Monte Carlo methods in a very general setting. The algorithm estimates the expected output value of an arbitrary randomized or quantum subroutine with bounded variance, achieving a near-quadratic speedup over the best possible classical algorithm. Combining the algorithm with the use of quantum walks gives a quantum speedup of the fastest known classical algorithms with rigorous performance bounds for computing partition functions, which use multiple-stage Markov chain Monte Carlo techniques. The quantum algorithm can also be used to estimate the total variation distance between probability distributions efficiently.

  4. Adiabatic optimization versus diffusion Monte Carlo methods

    Science.gov (United States)

    Jarret, Michael; Jordan, Stephen P.; Lackey, Brad

    2016-10-01

    Most experimental and theoretical studies of adiabatic optimization use stoquastic Hamiltonians, whose ground states are expressible using only real nonnegative amplitudes. This raises a question as to whether classical Monte Carlo methods can simulate stoquastic adiabatic algorithms with polynomial overhead. Here we analyze diffusion Monte Carlo algorithms. We argue that, based on differences between L1 and L2 normalized states, these algorithms suffer from certain obstructions preventing them from efficiently simulating stoquastic adiabatic evolution in generality. In practice however, we obtain good performance by introducing a method that we call Substochastic Monte Carlo. In fact, our simulations are good classical optimization algorithms in their own right, competitive with the best previously known heuristic solvers for MAX-k -SAT at k =2 ,3 ,4 .

  5. Random Numbers and Monte Carlo Methods

    Science.gov (United States)

    Scherer, Philipp O. J.

    Many-body problems often involve the calculation of integrals of very high dimension which cannot be treated by standard methods. For the calculation of thermodynamic averages Monte Carlo methods are very useful which sample the integration volume at randomly chosen points. After summarizing some basic statistics, we discuss algorithms for the generation of pseudo-random numbers with given probability distribution which are essential for all Monte Carlo methods. We show how the efficiency of Monte Carlo integration can be improved by sampling preferentially the important configurations. Finally the famous Metropolis algorithm is applied to classical many-particle systems. Computer experiments visualize the central limit theorem and apply the Metropolis method to the traveling salesman problem.

  6. CosmoPMC: Cosmology Population Monte Carlo

    CERN Document Server

    Kilbinger, Martin; Cappe, Olivier; Cardoso, Jean-Francois; Fort, Gersende; Prunet, Simon; Robert, Christian P; Wraith, Darren

    2011-01-01

    We present the public release of the Bayesian sampling algorithm for cosmology, CosmoPMC (Cosmology Population Monte Carlo). CosmoPMC explores the parameter space of various cosmological probes, and also provides a robust estimate of the Bayesian evidence. CosmoPMC is based on an adaptive importance sampling method called Population Monte Carlo (PMC). Various cosmology likelihood modules are implemented, and new modules can be added easily. The importance-sampling algorithm is written in C, and fully parallelised using the Message Passing Interface (MPI). Due to very little overhead, the wall-clock time required for sampling scales approximately with the number of CPUs. The CosmoPMC package contains post-processing and plotting programs, and in addition a Monte-Carlo Markov chain (MCMC) algorithm. The sampling engine is implemented in the library pmclib, and can be used independently. The software is available for download at http://www.cosmopmc.info.

  7. Shell model the Monte Carlo way

    Energy Technology Data Exchange (ETDEWEB)

    Ormand, W.E.

    1995-03-01

    The formalism for the auxiliary-field Monte Carlo approach to the nuclear shell model is presented. The method is based on a linearization of the two-body part of the Hamiltonian in an imaginary-time propagator using the Hubbard-Stratonovich transformation. The foundation of the method, as applied to the nuclear many-body problem, is discussed. Topics presented in detail include: (1) the density-density formulation of the method, (2) computation of the overlaps, (3) the sign of the Monte Carlo weight function, (4) techniques for performing Monte Carlo sampling, and (5) the reconstruction of response functions from an imaginary-time auto-correlation function using MaxEnt techniques. Results obtained using schematic interactions, which have no sign problem, are presented to demonstrate the feasibility of the method, while an extrapolation method for realistic Hamiltonians is presented. In addition, applications at finite temperature are outlined.

  8. Monte Carlo strategies in scientific computing

    CERN Document Server

    Liu, Jun S

    2008-01-01

    This paperback edition is a reprint of the 2001 Springer edition This book provides a self-contained and up-to-date treatment of the Monte Carlo method and develops a common framework under which various Monte Carlo techniques can be "standardized" and compared Given the interdisciplinary nature of the topics and a moderate prerequisite for the reader, this book should be of interest to a broad audience of quantitative researchers such as computational biologists, computer scientists, econometricians, engineers, probabilists, and statisticians It can also be used as the textbook for a graduate-level course on Monte Carlo methods Many problems discussed in the alter chapters can be potential thesis topics for masters’ or PhD students in statistics or computer science departments Jun Liu is Professor of Statistics at Harvard University, with a courtesy Professor appointment at Harvard Biostatistics Department Professor Liu was the recipient of the 2002 COPSS Presidents' Award, the most prestigious one for sta...

  9. Monte Carlo simulation of neutron scattering instruments

    Energy Technology Data Exchange (ETDEWEB)

    Seeger, P.A.

    1995-12-31

    A library of Monte Carlo subroutines has been developed for the purpose of design of neutron scattering instruments. Using small-angle scattering as an example, the philosophy and structure of the library are described and the programs are used to compare instruments at continuous wave (CW) and long-pulse spallation source (LPSS) neutron facilities. The Monte Carlo results give a count-rate gain of a factor between 2 and 4 using time-of-flight analysis. This is comparable to scaling arguments based on the ratio of wavelength bandwidth to resolution width.

  10. Monte carlo simulations of organic photovoltaics.

    Science.gov (United States)

    Groves, Chris; Greenham, Neil C

    2014-01-01

    Monte Carlo simulations are a valuable tool to model the generation, separation, and collection of charges in organic photovoltaics where charges move by hopping in a complex nanostructure and Coulomb interactions between charge carriers are important. We review the Monte Carlo techniques that have been applied to this problem, and describe the results of simulations of the various recombination processes that limit device performance. We show how these processes are influenced by the local physical and energetic structure of the material, providing information that is useful for design of efficient photovoltaic systems.

  11. Monte Carlo dose distributions for radiosurgery

    Energy Technology Data Exchange (ETDEWEB)

    Perucha, M.; Leal, A.; Rincon, M.; Carrasco, E. [Sevilla Univ. (Spain). Dept. Fisiologia Medica y Biofisica; Sanchez-Doblado, F. [Sevilla Univ. (Spain). Dept. Fisiologia Medica y Biofisica]|[Hospital Univ. Virgen Macarena, Sevilla (Spain). Servicio de Oncologia Radioterapica; Nunez, L. [Clinica Puerta de Hierro, Madrid (Spain). Servicio de Radiofisica; Arrans, R.; Sanchez-Calzado, J.A.; Errazquin, L. [Hospital Univ. Virgen Macarena, Sevilla (Spain). Servicio de Oncologia Radioterapica; Sanchez-Nieto, B. [Royal Marsden NHS Trust (United Kingdom). Joint Dept. of Physics]|[Inst. of Cancer Research, Sutton, Surrey (United Kingdom)

    2001-07-01

    The precision of Radiosurgery Treatment planning systems is limited by the approximations of their algorithms and by their dosimetrical input data. This fact is especially important in small fields. However, the Monte Carlo methods is an accurate alternative as it considers every aspect of particle transport. In this work an acoustic neurinoma is studied by comparing the dose distribution of both a planning system and Monte Carlo. Relative shifts have been measured and furthermore, Dose-Volume Histograms have been calculated for target and adjacent organs at risk. (orig.)

  12. The Rational Hybrid Monte Carlo Algorithm

    CERN Document Server

    Clark, M A

    2006-01-01

    The past few years have seen considerable progress in algorithmic development for the generation of gauge fields including the effects of dynamical fermions. The Rational Hybrid Monte Carlo (RHMC) algorithm, where Hybrid Monte Carlo is performed using a rational approximation in place the usual inverse quark matrix kernel is one of these developments. This algorithm has been found to be extremely beneficial in many areas of lattice QCD (chiral fermions, finite temperature, Wilson fermions etc.). We review the algorithm and some of these benefits, and we compare against other recent algorithm developements. We conclude with an update of the Berlin wall plot comparing costs of all popular fermion formulations.

  13. The Rational Hybrid Monte Carlo algorithm

    Science.gov (United States)

    Clark, Michael

    2006-12-01

    The past few years have seen considerable progress in algorithmic development for the generation of gauge fields including the effects of dynamical fermions. The Rational Hybrid Monte Carlo (RHMC) algorithm, where Hybrid Monte Carlo is performed using a rational approximation in place the usual inverse quark matrix kernel is one of these developments. This algorithm has been found to be extremely beneficial in many areas of lattice QCD (chiral fermions, finite temperature, Wilson fermions etc.). We review the algorithm and some of these benefits, and we compare against other recent algorithm developements. We conclude with an update of the Berlin wall plot comparing costs of all popular fermion formulations.

  14. Monte Carlo Hamiltonian:Linear Potentials

    Institute of Scientific and Technical Information of China (English)

    LUOXiang-Qian; HelmutKROEGER; 等

    2002-01-01

    We further study the validity of the Monte Carlo Hamiltonian method .The advantage of the method,in comparison with the standard Monte Carlo Lagrangian approach,is its capability to study the excited states.We consider two quantum mechanical models:a symmetric one V(x)=/x/2;and an asymmetric one V(x)==∞,for x<0 and V(x)=2,for x≥0.The results for the spectrum,wave functions and thermodynamical observables are in agreement with the analytical or Runge-Kutta calculations.

  15. Parallel Markov chain Monte Carlo simulations.

    Science.gov (United States)

    Ren, Ruichao; Orkoulas, G

    2007-06-07

    With strict detailed balance, parallel Monte Carlo simulation through domain decomposition cannot be validated with conventional Markov chain theory, which describes an intrinsically serial stochastic process. In this work, the parallel version of Markov chain theory and its role in accelerating Monte Carlo simulations via cluster computing is explored. It is shown that sequential updating is the key to improving efficiency in parallel simulations through domain decomposition. A parallel scheme is proposed to reduce interprocessor communication or synchronization, which slows down parallel simulation with increasing number of processors. Parallel simulation results for the two-dimensional lattice gas model show substantial reduction of simulation time for systems of moderate and large size.

  16. Dynamic Monte Carlo simulation of chain growth polymerization and its concentration effect

    Institute of Scientific and Technical Information of China (English)

    LüWenqi

    2005-01-01

    [1]He, J., Zhang, H., Chen, J. et al., Monte Carlo simulation of kinetics and chain length distributions in living free-radical polymerization, Macromolecules, 1997, 30: 8010-8018.[2]Li, L., He, J., Yang, Y., Monte Carlo simulation on living radical polymerization with RAFT process, Chem. J. Chinese Univ. (in Chinese), 2000, 21(7): 1146-1148.[3]Ling, J., Shen, Z., Chen W., Algorithm and application of Monte Carlo simulation for multi-dispersive copolymerization system, Science in China, Series B, 2002, 45(3): 243-250.[4]Butte, A., Storti, G., Morbidelli, M., Evaluation of the chain length distribution in free-radical polymerization, 1. Bulk polymerization, Macromol. Theory Simul., 2002, 11: 22-36.[5]Smith, G. B., Russell, G. T., Heuts, J. P. A., Termination in dilute-solution free-radical polymerization: A composite model, Macromol. Theory Simul., 2003, 12: 299-314.[6]Zetterlund, P. B., Yamazoe, H., Yamada, B., Free radical bulk po- lymerization of styrene: Simulation of molecular weight distribu- tions to high conversion using experimentally obtained rate coef- ficients, Macromol. Theory Simul., 2003, 12: 379-385.[7]Binder, K., Paul, W., Monte Carlo simulations of polymer dy- namics: Recent advances, J. Polym. Sci., Polym. Phys. Ed., 1997, 35(1): 1-31.[8]Rouault, Y., Milchev, A., Monte Carlo study of living polymers with the bond-fluctuation method, Phys. Rev. E, 1995, 51(6): 5905-5910.[9]Jo, W. H., Lee, J. W., Lee, M. S. et al., Effect of interchange reactions on the molecular weight distribution of poly(ethylene terephthalate): A Monte Carlo simulation, J. Polym. Sci., Polym. Phys. Ed., 1996, 34: 725-729.[10]Jang, S. S., Ha, W. S., Jo, W. H. et al., Monte Carlo simulation of copolymerization by ester interchange reaction in miscible polyester blends, J. Polym. Sci., Polym. Phys. Ed., 1998, 36: 1637-1645.[11]Lee, Y. U., Jang, S. S., Jo, W. H., Off-lattice Monte Carlo simulation of hyperbranched polymers, 1. Polycondensation of AB2 type monomers, Macromol. Theory

  17. Fast sequential Monte Carlo methods for counting and optimization

    CERN Document Server

    Rubinstein, Reuven Y; Vaisman, Radislav

    2013-01-01

    A comprehensive account of the theory and application of Monte Carlo methods Based on years of research in efficient Monte Carlo methods for estimation of rare-event probabilities, counting problems, and combinatorial optimization, Fast Sequential Monte Carlo Methods for Counting and Optimization is a complete illustration of fast sequential Monte Carlo techniques. The book provides an accessible overview of current work in the field of Monte Carlo methods, specifically sequential Monte Carlo techniques, for solving abstract counting and optimization problems. Written by authorities in the

  18. Kinetic equations: computation

    CERN Document Server

    Pareschi, Lorenzo

    2013-01-01

    Kinetic equations bridge the gap between a microscopic description and a macroscopic description of the physical reality. Due to the high dimensionality the construction of numerical methods represents a challenge and requires a careful balance between accuracy and computational complexity.

  19. Thermal kinetic inductance detector

    Energy Technology Data Exchange (ETDEWEB)

    Cecil, Thomas; Gades, Lisa; Miceli, Antonio; Quaranta, Orlando

    2016-12-20

    A microcalorimeter for radiation detection that uses superconducting kinetic inductance resonators as the thermometers. The detector is frequency-multiplexed which enables detector systems with a large number of pixels.

  20. Chemical Kinetics Database

    Science.gov (United States)

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.