Atomistic Kinetic Monte Carlo Simulations of Polycrystalline Copper Electrodeposition
Treeratanaphitak, Tanyakarn; Abukhdeir, Nasser Mohieddin
2014-01-01
A high-fidelity kinetic Monte Carlo (KMC) simulation method (T. Treeratanaphitak, M. Pritzker, N. M. Abukhdeir, Electrochim. Acta 121 (2014) 407--414) using the semi-empirical multi-body embedded-atom method (EAM) potential has been extended to model polycrystalline metal electrodeposition. The presented KMC-EAM method enables true three-dimensional atomistic simulations of electrodeposition over experimentally relevant timescales. Simulations using KMC-EAM are performed over a range of overpotentials to predict the effect on deposit texture evolution. Results show strong agreement with past experimental results both with respect to deposition rates on various copper surfaces and roughness-time power law behaviour. It is found that roughness scales with time $\\propto t^\\beta$ where $\\beta=0.62 \\pm 0.12$, which is in good agreement with past experimental results. Furthermore, the simulations provide insights into sub-surface deposit morphologies which are not directly accessible from experimental measurements.
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...
Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys
International Nuclear Information System (INIS)
Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed
Energy Technology Data Exchange (ETDEWEB)
Martin-Bragado, Ignacio [Synopsys Inc. 700 E. Middlefield Road, 94043 Mountain View, CA (United States)], E-mail: nacho@synopsys.com; Zographos, Nikolas [Synopsys Switzerland LLC, Affolternstrasse 52, 8050 Zurich (Switzerland); Jaraiz, Martin [Dept. Electronica. ETSIT. Universidad de Valladolid, Valladolid (Spain)
2008-12-05
According to the ITRS, the development of predictive TCAD models and simulators is one of the keystone for future CMOS technologies. The kinetic Monte Carlo (kMC) technique is particularly well placed between the poles of physical ab initio but very slow simulations, and more empirical, fast simulations by partial differential equations. Nevertheless, in other to fulfill the necessities of the semiconductor industry, faster kMC simulations would be desirable. This work shows techniques to increase the simulation speed of kMC simulations an average of 2 x while still maintaining accuracy. These techniques modify the original kMC method by using different jump distances and performing two jumps at once during the same simulation cycle. We also show the problems and limitations of these strategies, how to detect them, and how to overcome them, if possible. Finally, a comprehensive set of simulations - including amorphization, recrystallization, extended defect ripening, diffusion and activation/deactivation of several dopants used in CMOS technologies - with and without speed up techniques are compared to experimental SIMS to elucidate how reliable these techniques are.
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Castin, N., E-mail: ncastin@sckcen.be [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium); Pascuet, M.I., E-mail: pascuet@cnea.gov.ar [Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires (Argentina); Malerba, L. [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium)
2012-10-15
The formation of Cu-rich precipitates under irradiation is a major cause for changes in the mechanical response to load of reactor pressure vessel steels. In previous works, it has been shown that the mechanism under which precipitation occurs is governed by diffusion of vacancy-copper (VCu) complexes, also in the absence of irradiation. Coarse-grained computer models (such as object kinetic Monte Carlo) aimed at simulating irradiation processes in model alloys or steels should therefore explicitly include the mobility of Cu precipitates, as a consequence of vacancy hops at their surface. For this purpose, in this work we calculate diffusion coefficients and lifetimes for a large variety of VCu complexes. We use an innovative atomistic model, where vacancy migration energies are calculated with little approximations, taking into account all effects of static relaxation and long-range chemical interaction as predicted by an interatomic potential. Our results show that, contrary to what intuition might suggest, saturation in vacancies tend to slow down the transport of Cu atoms.
Atomistic Monte Carlo simulation of lipid membranes
DEFF Research Database (Denmark)
Wüstner, Daniel; Sklenar, Heinz
2014-01-01
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......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...
International Nuclear Information System (INIS)
We apply a novel atomistic kinetic Monte Carlo model, which includes local chemistry and relaxation effects when assessing the migration energy barriers of point defects, to the study of the microchemical evolution driven by vacancy diffusion in FeCu and FeCuNi alloys. These alloys are of importance for nuclear applications because Cu precipitation, enhanced by the presence of Ni, is one of the main causes of hardening and embrittlement in reactor pressure vessel steels used in existing nuclear power plants. Local chemistry and relaxation effects are introduced using artificial intelligence techniques, namely a conveniently trained artificial neural network, to calculate the migration energy barriers of vacancies as functions of the local atomic configuration. We prove, through a number of results, that the use of the neural network is fully equivalent to calculating the migration energy barriers on-the-fly, using computationally expensive methods such as nudged elastic bands with an interatomic potential. The use of the neural network makes the computational cost affordable, so that simulations of the same type as those hitherto carried out using heuristic formulas for the assessment of the energy barriers can now be performed, at the same computational cost, using more rigorously calculated barriers. This method opens the way to properly treating more complex problems, such as the case of self-interstitial cluster formation, in an atomistic kinetic Monte Carlo framework.
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
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We briefly present our atomistic kinetic Monte Carlo approach to model the diffusion of point-defects in Fe-based alloys, and therefore to simulate diffusion induced mass transport and subsequent nano-structural and microchemical changes. This methodology has been hitherto successfully applied to the simulation of thermal annealing experiments. We here present our achievements in the generalization of this method to the simulation of neutron irradiation damage. (authors)
Diffusion of hydrogen within idealised grains of bcc-Fe: A kinetic Monte Carlo study
Du, Yaojun A.; Rogal, Jutta; Drautz, Ralf
2012-01-01
Structural defects in materials such as vacancies, grain boundaries, and dislocations may trap hydrogen and a local accumulation of hydrogen at these defects can lead to the degradation of the materials properties. An important aspect in obtaining insight into hydrogen induced embrittlement on the atomistic level is to understand the diffusion of hydrogen in these materials. In our study we employ kinetic Monte Carlo (kMC) simulations to investigate hydrogen diffusion in bcc iron within diffe...
Kinetic Monte Carlo simulation of dislocation dynamics
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A kinetic Monte Carlo simulation of dislocation motion is introduced. The dislocations are assumed to be composed of pure edge and screw segments confined to a fixed lattice. The stress and temperature dependence of the dislocation velocity is studied, and finite-size effects are discussed. It is argued that surfaces and boundaries may play a significant role in the velocity of dislocations. The simulated dislocations are shown to display kinetic roughening according to the exponents predicted by the Kardar-Parisi-Zhang equation. copyright 1999 The American Physical Society
SPQR: a Monte Carlo reactor kinetics code
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The SPQR Monte Carlo code has been developed to analyze fast reactor core accident problems where conventional methods are considered inadequate. The code is based on the adiabatic approximation of the quasi-static method. This initial version contains no automatic material motion or feedback. An existing Monte Carlo code is used to calculate the shape functions and the integral quantities needed in the kinetics module. Several sample problems have been devised and analyzed. Due to the large statistical uncertainty associated with the calculation of reactivity in accident simulations, the results, especially at later times, differ greatly from deterministic methods. It was also found that in large uncoupled systems, the Monte Carlo method has difficulty in handling asymmetric perturbations
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.
Object Kinetic Monte Carlo calculations of electron and He irradiation of nickel
International Nuclear Information System (INIS)
We present results of an Object Kinetic Monte Carlo model (OKMC) of nucleation of He-vacancy complexes under irradiation of nickel. This OKMC model has been constructed using the existing atomistic information on migration energies and binding energies of vacancies, self-interstitials and He-vacancy interactions, as well as He migration from embedded atom interatomic potentials. We use this model to first study the different annealing stages of electron irradiated Ni and the influence of impurities in the recovery of damage during isochronal annealing. Then, He desorption from implanted Ni is studied for different doses and compared to existing experimental measurements.
Graphite melting: atomistic kinetics bridges theory and experiment
Orekhov, Nikita; Stegailov, Vladimir
2015-06-01
Unique thermophysical properties of graphite result in its important role in science and engineering. However, the experimental data on graphite melting temperature (Tm) still remain controversial despite the long history of investigation. The experimental results of several works cover the wide span from 3800 to 5000 K that is an essentially larger uncertainty than the errors of individual experiments. In this work we deploy the molecular dynamics (MD) method and study the kinetics of graphite melting, concerning the aspects of defect formation, single graphene layer melting and the rates of spontaneous liquid nuclei formation. Our MD calculations show an unexpectedly weak kinetics of the melting front propagation in graphite that is several orders slower than that in metals. We demonstrate that at sufficiently high heating rates (higher than 105 - 106 K/s) the temperatures 500-1000 K above the graphite melting temperature can be reached before the crystal decay. It allows us to explain long-standing problem of the discrepancy in the experimental data making a hypothesis that there is a strong dependence between experimentally measured graphite melting temperatures and corresponding rates of heating.
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.)
Pogodin, Sergey; López, Núria
2014-01-01
The theoretical study of catalysis would substantialy benefit from the use of atomistic simulations that can provide information beyond mean-field approaches. To date, the nanoscale understanding of surface reactions has been only qualitatively achieved by means of kinetic Monte Carlo coupled to density functional theory, KMC-DFT. Here, we examine a widely employed model for oxygen interaction with the RuO2(110) surface, a highly anisotropic system. Our analysis reveals several covert problem...
International Nuclear Information System (INIS)
This work will show how the kinetic Monte Carlo (KMC) technique is able to successfully model the defects and diffusion of dopants in Si-based materials for advanced microelectronic devices, especially for non-equilibrium conditions. Charge states of point defects and paired dopants are also simulated, including the dependency of the diffusivities on the Fermi level and charged particle drift coming from the electric field. The KMC method is used to simulate the diffusion of the point defects, and formation and dissolution of extended defects, whereas a quasi-atomistic approach is used to take into account the carrier densities. The simulated mechanisms include the kick-out diffusion mechanism, extended defect formation and the activation/deactivation of dopants through the formation of impurity clusters. Damage accumulation and amorphization are also taken into account. Solid phase epitaxy regrowth is included, and also the dopants redistribution during recrystallization of the amorphized regions. Regarding the charged defects, the model considers the dependencies of charge reactions, electric bias, pairing and break-up reactions according to the local Fermi level. Some aspects of the basic physical mechanisms have also been taken into consideration: how to smooth out the atomistic dopant point charge distribution, avoiding very abrupt and unphysical charge profiles and how to implement the drift of charged particles into the existing electric field. The work will also discuss the efficiency, accuracy and relevance of the method, together with its implementation in a technology computer aided design process simulator
Controlling the long-range corrections in atomistic Monte Carlo simulations of two-phase systems.
Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice; Tildesley, Dominic J
2015-10-13
The long-range correction to the surface tension can amount to up to 55% of the calculated value of the surface tension for cutoffs in the range of 2.1-6.4 σ. The calculation of the long-range corrections to the surface tension and to the configurational energy in two-phase systems remains an active area of research. In this work, we compare the long-range corrections methods proposed by Guo and Lu ( J. Chem. Phys. 1997 , 106 , 3688 - 3695 ) and Janeček ( J. Phys. Chem. B 2006 , 110 , 6264 - 6269 ) for the calculation of the surface tension and of the coexisting densities in Monte Carlo simulations of the truncated Lennard-Jones potential and the truncated and shifted Lennard-Jones potential models. These methods require an estimate of the long-range correction at each step in the Monte Carlo simulation. We apply the full version of the Guo and Lu method, which involves the calculation of a double integral that contains a series of density differences, and we compare these results with the simplified version of the method which is routinely used in two-phase simulations. We conclude that the cutoff dependencies of the surface tension and coexisting densities are identical for the full versions of Guo and Lu and Janeček methods. We show that it is possible to avoid applying the long-range correction at every step by using the truncated Lennard-Jones potential with a cutoff rc ≥ 5 σ. The long-range correction can then be applied at the end of the simulation. The limiting factor in the accurate calculation of this final correction is an accurate estimate of the coexisting densities. Link-cell simulations performed using a cutoff rc = 5.5 σ require twice as much computing time as those with a more typical cutoff of rc = 3.0 σ. The application of the Janeček correction increases the running time of the simulation by less than 10%, and it can be profitably applied with the shorter cutoff. PMID:26574249
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.
Self-learning kinetic Monte Carlo simulations of Al diffusion in Mg
Nandipati, Giridhar; Govind, Niranjan; Andersen, Amity; Rohatgi, Aashish
2016-04-01
Vacancy-mediated diffusion of an Al atom in the pure Mg matrix is studied using the atomistic, on-lattice self-learning kinetic Monte Carlo (SLKMC) method. Activation barriers for vacancy-Mg and vacancy-Al atom exchange processes are calculated on the fly using the climbing image nudged-elastic-band method and binary Mg-Al modified embedded-atom method interatomic potential. Diffusivities of an Al atom obtained from SLKMC simulations show the same behavior as observed in experimental and theoretical studies available in the literature; that is, an Al atom diffuses faster within the basal plane than along the c-axis. Although the effective activation barriers for an Al atom diffusion from SLKMC simulations are close to experimental and theoretical values, the effective prefactors are lower than those obtained from experiments. We present all the possible vacancy-Mg and vacancy-Al atom exchange processes and their activation barriers identified in SLKMC simulations. A simple mapping scheme to map an HCP lattice onto a simple cubic lattice is described, which enables simulation of the HCP lattice using the on-lattice framework. We also present the pattern recognition scheme which is used in SLKMC simulations to identify the local Al atom configuration around a vacancy.
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.
Self-learning kinetic Monte Carlo simulations of Al diffusion in Mg
International Nuclear Information System (INIS)
Vacancy-mediated diffusion of an Al atom in the pure Mg matrix is studied using the atomistic, on-lattice self-learning kinetic Monte Carlo (SLKMC) method. Activation barriers for vacancy-Mg and vacancy-Al atom exchange processes are calculated on the fly using the climbing image nudged-elastic-band method and binary Mg–Al modified embedded-atom method interatomic potential. Diffusivities of an Al atom obtained from SLKMC simulations show the same behavior as observed in experimental and theoretical studies available in the literature; that is, an Al atom diffuses faster within the basal plane than along the c-axis. Although the effective activation barriers for an Al atom diffusion from SLKMC simulations are close to experimental and theoretical values, the effective prefactors are lower than those obtained from experiments. We present all the possible vacancy-Mg and vacancy-Al atom exchange processes and their activation barriers identified in SLKMC simulations. A simple mapping scheme to map an HCP lattice onto a simple cubic lattice is described, which enables simulation of the HCP lattice using the on-lattice framework. We also present the pattern recognition scheme which is used in SLKMC simulations to identify the local Al atom configuration around a vacancy. (paper)
Atomic kinetic Monte Carlo modeling of multi-component Fe dilute alloys under irradiation
International Nuclear Information System (INIS)
The ageing of pressure vessel steels under radiation has been correlated with the formation of more or less dilute solute clusters which are investigated in this work using a multi-scale approach based on ab initio and atomistic kinetic Monte Carlo (AKMC) simulations. The microstructure evolution of Fe alloys is modeled by AKMC on a lattice, using pair interactions adjusted on DFT (Density Functional Theory) calculations. Several substitutional elements (Cu, Ni, Mn, Si, P) and foreign interstitials (C, N) are taken into account to describe the alloy. The point defect created by the irradiation, i.e. the vacancies and self interstitials have a tendency to form clusters. The evolution of these clusters is governed by the migration energy of the individual point defects which is very heavy in terms of computing time due to the large number of AKMC steps required. The structure of all the possible objects that can form is complex and some optimized and accelerated methods will be presented. The results obtained are in agreement with the experimental trends and indicate that the formation of solute clusters takes place via segregation mechanisms on the point defect clusters
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We report a Monte Carlo simulation study of the molten Fe-C-S system with the aim of developing a theoretical understanding of the influence of sulphur during decarburization reactions in Fe-C alloys. Focussing specifically on the role played by free surfaces, computer simulations were based on the hexagonal atomistic model of Fe-C-S system using isotropic atomic interaction parameters; free surfaces were characterized by a missing layer of atoms. Three geometrical configurations, namely a liquid bath, a prismatic block and a spherical droplet, were investigated. Simulations were carried out as a function of melt carbon and sulphur concentration, temperatures and surface/volume ratios of the simulation cell. Sulphur atoms were found to preferentially concentrate in the top few layers, with the second layer showing the highest amounts of sulphur; very little sulphur was observed in the bulk liquid. This trend was observed in all three simulation configurations over a wide carbon/sulphur concentration range and temperatures. Significant levels of iron were observed in the top surface layer. The influence of free surfaces on atomic concentration profiles was found to be a strong function of the surface/volume ratio. The surface segregation of S was more pronounced for small exposed surfaces and was much smaller for liquids with large exposed surfaces. The presence of surface-active sulphur resulted in a major re-distribution of carbon. Carbon tended to concentrate deeper in the bulk, with the surface region being severely depleted of carbon. In addition to several new findings and a better understanding of liquid surfaces, these simulations have helped overcome major limitations of Sain and Belton's model. Key experimental results on decarburization have been explained within the framework of our simulations. These simulation results have significant implications for surface decarburization reactions and carbon-boil phenomena in smelting technologies.
Kinetic Monte Carlo with fields: diffusion in heterogeneous systems
Caro, Jose Alfredo
2011-03-01
It is commonly perceived that to achieve breakthrough scientific discoveries in the 21st century an integration of world leading experimental capabilities with theory, computational modeling and high performance computer simulations is necessary. Lying between the atomic and the macro scales, the meso scale is crucial for advancing materials research. Deterministic methods result computationally too heavy to cover length and time scales relevant for this scale. Therefore, stochastic approaches are one of the options of choice. In this talk I will describe recent progress in efficient parallelization schemes for Metropolis and kinetic Monte Carlo [1-2], and the combination of these ideas into a new hybrid Molecular Dynamics-kinetic Monte Carlo algorithm developed to study the basic mechanisms taking place in diffusion in concentrated alloys under the action of chemical and stress fields, incorporating in this way the actual driving force emerging from chemical potential gradients. Applications are shown on precipitation and segregation in nanostructured materials. Work in collaboration with E. Martinez, LANL, and with B. Sadigh, P. Erhart and A. Stukowsky, LLNL. Supported by the Center for Materials at Irradiation and Mechanical Extremes, an Energy Frontier Research Center funded by the U.S. Department of Energy (Award # 2008LANL1026) at Los Alamos National Laboratory
Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study
International Nuclear Information System (INIS)
Graphical abstract: Stochastic theory of interfacial enzyme kinetics is formulated. Numerical results of macroscopic phenomenon of lag-burst kinetics is obtained by using a kinetic Monte Carlo approach to single enzyme activity. Highlights: ► An enzyme is attached with the fluid state phospholipid molecules on the Langmuir monolayer. ► Through the diffusion, the enzyme molecule reaches the gel–fluid interface. ► After hydrolysing a phospholipid molecule it predominantly leaves the surface in the lag phase. ► The enzyme is strictly attached to the surface with scooting mode of motion and the burst phase appears. - Abstract: In the spirit of Gillespie’s stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.
International Nuclear Information System (INIS)
This study explores for the first time the possibility of using an evolutionary algorithm (EA) for the determination of atomistic rates for use in kinetic Monte Carlo (KMC) simulations of anisotropic etching of silicon for the manufacture of microelectromechanical systems (MEMS). Traditionally, KMC rates are determined based on (i) computationally expensive density functional theory (DFT) calculations or, when possible, (ii) a combination of physical insight and a labor-intensive, manual procedure where, e.g., experimental and simulated surface morphologies are visually matched for a collection of surface orientations. Compared to these approaches, the evolutionary KMC method proposed in this study provides a more flexible, autonomous procedure to describe correctly a wide variety of etching conditions. We focus on the use of a functional representation of the atomistic rates, referred to as the removal probability function (RPF). This simplifies the EA search space to just a few parameters and reduces the number of required experimental data points to just a few etch rates. By proposing two alternative RPFs with four and six parameters, respectively, we show that the ability to explain the orientation dependence of the etch rate for a wide variety of etchants increases with the number of parameters and conclude that the six-parameter RPF provides sufficiently good simulations for a wide range of etching conditions, including KOH, KOH+IPA, TMAH and TMAH+Triton at different concentrations and temperatures. By uncovering the relationships between the parameters and the concentration of the etchant, it is possible to extend the simulations to nonmeasured etching conditions. Although the use of an RPF effectively restricts the search to a subspace of the atomistic rates, the present results suggest that physically meaningful KMC rates can probably be determined in the near future by direct comparison of macroscopic experiments and simulations through the use of
Xing, Y.; Gosálvez, M. A.; Sato, K.; Tian, M.; Yi, H.
2012-08-01
This study explores for the first time the possibility of using an evolutionary algorithm (EA) for the determination of atomistic rates for use in kinetic Monte Carlo (KMC) simulations of anisotropic etching of silicon for the manufacture of microelectromechanical systems (MEMS). Traditionally, KMC rates are determined based on (i) computationally expensive density functional theory (DFT) calculations or, when possible, (ii) a combination of physical insight and a labor-intensive, manual procedure where, e.g., experimental and simulated surface morphologies are visually matched for a collection of surface orientations. Compared to these approaches, the evolutionary KMC method proposed in this study provides a more flexible, autonomous procedure to describe correctly a wide variety of etching conditions. We focus on the use of a functional representation of the atomistic rates, referred to as the removal probability function (RPF). This simplifies the EA search space to just a few parameters and reduces the number of required experimental data points to just a few etch rates. By proposing two alternative RPFs with four and six parameters, respectively, we show that the ability to explain the orientation dependence of the etch rate for a wide variety of etchants increases with the number of parameters and conclude that the six-parameter RPF provides sufficiently good simulations for a wide range of etching conditions, including KOH, KOH+IPA, TMAH and TMAH+Triton at different concentrations and temperatures. By uncovering the relationships between the parameters and the concentration of the etchant, it is possible to extend the simulations to nonmeasured etching conditions. Although the use of an RPF effectively restricts the search to a subspace of the atomistic rates, the present results suggest that physically meaningful KMC rates can probably be determined in the near future by direct comparison of macroscopic experiments and simulations through the use of
Kinetic Monte Carlo modelling of neutron irradiation damage in iron
Energy Technology Data Exchange (ETDEWEB)
Gamez, L. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Departamento de Fisica Aplicada, ETSII, UPM, Madrid (Spain)], E-mail: linarejos.gamez@upm.es; Martinez, E. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Lawrence Livermore National Laboratory, LLNL, CA 94550 (United States); Perlado, J.M.; Cepas, P. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Caturla, M.J. [Departamento de Fisica Aplicada, Universidad de Alicante, Alicante (Spain); Victoria, M. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Marian, J. [Lawrence Livermore National Laboratory, LLNL, CA 94550 (United States); Arevalo, C. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Hernandez, M.; Gomez, D. [CIEMAT, Madrid (Spain)
2007-10-15
Ferritic steels (FeCr based alloys) are key materials needed to fulfill the requirements expected in future nuclear fusion facilities, both for magnetic and inertial confinement, and advanced fission reactors (GIV) and transmutation systems. Research in such field is actually a critical aspect in the European research program and abroad. Experimental and multiscale simulation methodologies are going hand by hand in increasing the knowledge of materials performance. At DENIM, it is progressing in some specific part of the well-linked simulation methodology both for defects energetics and diffusion, and for dislocation dynamics. In this study, results obtained from kinetic Monte Carlo simulations of neutron irradiated Fe under different conditions are presented, using modified ad hoc parameters. A significant agreement with experimental measurements has been found for some of the parameterization and mechanisms considered. The results of these simulations are discussed and compared with previous calculations.
Lanczos and Recursion Techniques for Multiscale Kinetic Monte Carlo Simulations
Energy Technology Data Exchange (ETDEWEB)
Rudd, R E; Mason, D R; Sutton, A P
2006-03-13
We review an approach to the simulation of the class of microstructural and morphological evolution involving both relatively short-ranged chemical and interfacial interactions and long-ranged elastic interactions. The calculation of the anharmonic elastic energy is facilitated with Lanczos recursion. The elastic energy changes affect the rate of vacancy hopping, and hence the rate of microstructural evolution due to vacancy mediated diffusion. The elastically informed hopping rates are used to construct the event catalog for kinetic Monte Carlo simulation. The simulation is accelerated using a second order residence time algorithm. The effect of elasticity on the microstructural development has been assessed. This article is related to a talk given in honor of David Pettifor at the DGP60 Workshop in Oxford.
Large-scale epitaxial growth kinetics of graphene: A kinetic Monte Carlo study
International Nuclear Information System (INIS)
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 C1-attachment for concave growth-front segments and C5-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
Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study
Energy Technology Data Exchange (ETDEWEB)
Das, Biswajit [S.N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Gangopadhyay, Gautam, E-mail: gautam@bose.res.in [S.N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India)
2012-01-17
Graphical abstract: Stochastic theory of interfacial enzyme kinetics is formulated. Numerical results of macroscopic phenomenon of lag-burst kinetics is obtained by using a kinetic Monte Carlo approach to single enzyme activity. Highlights: Black-Right-Pointing-Pointer An enzyme is attached with the fluid state phospholipid molecules on the Langmuir monolayer. Black-Right-Pointing-Pointer Through the diffusion, the enzyme molecule reaches the gel-fluid interface. Black-Right-Pointing-Pointer After hydrolysing a phospholipid molecule it predominantly leaves the surface in the lag phase. Black-Right-Pointing-Pointer The enzyme is strictly attached to the surface with scooting mode of motion and the burst phase appears. - Abstract: In the spirit of Gillespie's stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.
Monte Carlo simulation on kinetics of batch and semi-batch free radical polymerization
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.
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.
Kinetic Monte Carlo Simulation of Oxygen Diffusion in Ytterbium Disilicate
Good, Brian S.
2015-01-01
Silicon-based ceramic components for next-generation jet turbine engines offer potential weight savings, as well as higher operating temperatures, both of which lead to increased efficiency and lower fuel costs. Silicon carbide (SiC), in particular, offers low density, good strength at high temperatures, and good oxidation resistance in dry air. However, reaction of SiC with high-temperature water vapor, as found in the hot section of jet turbine engines in operation, can cause rapid surface recession, which limits the lifetime of such components. Environmental Barrier Coatings (EBCs) are therefore needed if long component lifetime is to be achieved. Rare earth silicates such as Yb2Si2O7 and Yb2SiO5 have been proposed for such applications; in an effort to better understand diffusion in such materials, we have performed kinetic Monte Carlo (kMC) simulations of oxygen diffusion in Ytterbium disilicate, Yb2- Si2O7. The diffusive process is assumed to take place via the thermally activated hopping of oxygen atoms among oxygen vacancy sites or among interstitial sites. Migration barrier energies are computed using density functional theory (DFT).
Kinetic Monte Carlo Simulation of Oxygen Diffusion in Ytterbium Disilicate
Good, Brian S.
2015-01-01
Ytterbium disilicate is of interest as a potential environmental barrier coating for aerospace applications, notably for use in next generation jet turbine engines. In such applications, the transport of oxygen and water vapor through these coatings to the ceramic substrate is undesirable if high temperature oxidation is to be avoided. In an effort to understand the diffusion process in these materials, we have performed kinetic Monte Carlo simulations of vacancy-mediated and interstitial oxygen diffusion in Ytterbium disilicate. Oxygen vacancy and interstitial site energies, vacancy and interstitial formation energies, and migration barrier energies were computed using Density Functional Theory. We have found that, in the case of vacancy-mediated diffusion, many potential diffusion paths involve large barrier energies, but some paths have barrier energies smaller than one electron volt. However, computed vacancy formation energies suggest that the intrinsic vacancy concentration is small. In the case of interstitial diffusion, migration barrier energies are typically around one electron volt, but the interstitial defect formation energies are positive, with the result that the disilicate is unlikely to exhibit experience significant oxygen permeability except at very high temperature.
Method of tallying adjoint fluence and calculating kinetics parameters in Monte Carlo codes
International Nuclear Information System (INIS)
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 βeff 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. (authors)
Energy Technology Data Exchange (ETDEWEB)
De Backer, A., E-mail: andree.debacker@ccfe.ac.uk [UMET, UMR 8207, Université Lille 1, Villeneuve d’Ascq (France); CCFE, Culham Centre for Fusion Energy, Abingdon, Oxon (United Kingdom); Adjanor, G.; Domain, C.; Lescoat, M.L. [EDF R& D, MMC Centre des Renardières, Moret-sur-Loing (France); Jublot-Leclerc, S.; Fortuna, F.; Gentils, A. [CSNSM, Univ Paris-Sud, CNRS/IN2P3, Orsay (France); Ortiz, C.J. [CIEMAT, Laboratorio Nacional de Fusión por Confinamiento Magnético, Madrid (Spain); Souidi, A. [Université Dr. Tahar Moulay de Saida, Saida (Algeria); Becquart, C.S. [UMET, UMR 8207, Université Lille 1, Villeneuve d’Ascq (France)
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 × 10{sup 19} He/m{sup 2}) 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.
Pogodin, Sergey; López, Núria
2014-07-01
The theoretical study of catalysis would substantialy benefit from the use of atomistic simulations that can provide information beyond mean-field approaches. To date, the nanoscale understanding of surface reactions has been only qualitatively achieved by means of kinetic Monte Carlo coupled to density functional theory, KMC-DFT. Here, we examine a widely employed model for oxygen interaction with the RuO2(110) surface, a highly anisotropic system. Our analysis reveals several covert problems that render as questionable the model's predictions. We suggest an advanced approach that considers all the relevant elementary steps and configurations while smoothing the intrinsic errors in the DFT description of oxygen. Under these conditions, KMC provides quantitative agreement to temperature-programmed desorption experiments. These results illustrate how KMC-based simulations can be pushed forward so that they evolve toward being the standard methodology to study complex chemistry at the nanoscale. PMID:25061545
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.
Kinetic Monte Carlo Studies of Hydrogen Abstraction from Graphite
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...
Energy Technology Data Exchange (ETDEWEB)
Messina, Luca, E-mail: messina@kth.se [KTH Royal Institute of Technology, Reactor Physics, 106 91 Stockholm (Sweden); Malerba, Lorenzo [Structural Materials Group, Institute of Nuclear Materials Science, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Olsson, Pär [KTH Royal Institute of Technology, Reactor Physics, 106 91 Stockholm (Sweden)
2015-06-01
Manganese and nickel solute atoms in irradiated ferritic steels play a major role in the nanostructural evolution of reactor pressure vessels (RPV), as they are responsible for the formation of embrittling nanofeatures even in the absence of copper. The stability and mobility of small vacancy–solute clusters is here studied with an atomistic kinetic Monte Carlo approach based on ab initio calculations, in order to investigate the influence of Mn and Ni on the early life of small radiation-induced vacancy clusters, and to provide the necessary parameters for advanced object kinetic Monte Carlo simulations of the RPV long-term nanostructural evolution. Migration barriers are obtained by direct ab initio calculations or through a binding energy model based on ab initio data. Our results show a clear immobilizing and stabilizing effect on vacancy clusters as the solute content is increased, whereas the only evident difference between the two solute species is a somewhat longer elongation of the cluster mean free path in the presence of a few Mn atoms.
Interacting multiagent systems kinetic equations and Monte Carlo methods
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...
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 by...
International Nuclear Information System (INIS)
Full text of publication follows. We propose a novel approach for simulating, with atomistic kinetic Monte Carlo (KMC), the segregation or depletion of solute atoms at interfaces, via transport by vacancies. Differently from classical lattice KMC, no assumption is made regarding the crystallographic structure. The model can thus potentially be applied to any type of interfaces, e.g. grain boundaries. Fully off-lattice KMC models were already proposed in the literature, but are rather demanding in CPU time, mainly because of the necessity to perform static relaxation several times at every step of the simulation, and to calculate migration energies between different metastable states. In our LA-KMC model, we aim at performing static relaxation only once per step at the most, and define possible transitions to other metastable states following a generic predefined procedure. The corresponding migration energies can then be calculated using artificial neural networks, trained to predict them as a function of a full description of the local atomic environment, in term of both the exact location in space of atoms and in term of their chemical nature. Our model is thus a compromise between fully off-lattice and fully on-lattice models: (a) The description of the system is not bound to strict assumptions, but is readapted automatically performing the minimum required amount of static relaxation; (b) The procedure to define transition events is not guaranteed to find all important transitions, and is thereby potentially disregarding some mechanisms of system evolution. This shortcoming is in fact classical to non-fully off-lattice models, but is in our case limited thanks to the application of relaxation at every step; (c) Computing time is largely reduced thanks to the use of neural network to calculate the migration energies. In this presentation, we show the premises of this novel approach, in the case of grain-boundaries for bcc Fe-Cr alloys. (authors)
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
Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study
Das, Biswajit; Gangopadhyay, Gautam
2012-01-01
In the spirit of Gillespie's stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.
Monte Carlo implementation of a guiding-center Fokker-Planck kinetic equation
International Nuclear Information System (INIS)
A Monte Carlo method for the collisional guiding-center Fokker-Planck kinetic equation is derived in the five-dimensional guiding-center phase space, where the effects of magnetic drifts due to the background magnetic field nonuniformity are included. It is shown that, in the limit of a homogeneous magnetic field, our guiding-center Monte Carlo collision operator reduces to the guiding-center Monte Carlo Coulomb operator previously derived by Xu and Rosenbluth [Phys. Fluids B 3, 627 (1991)]. Applications of the present work will focus on the collisional transport of energetic ions in complex nonuniform magnetized plasmas in the large mean-free-path (collisionless) limit, where magnetic drifts must be retained
Stochastic method for accommodation of equilibrating basins in kinetic Monte Carlo simulations
Van Siclen, Clinton DeW.
2008-01-01
A computationally simple way to accommodate 'basins' of trapping sites in standard kinetic Monte Carlo simulations is presented. By assuming the system is effectively equilibrated in the basin, the residence time (time spent in the basin before escape) and the probabilities for transition to states outside the basin may be calculated. This is demonstrated for point defect diffusion over a periodic grid of sites containing a complex basin.
Monte Carlo simulation of hot-carrier phenomena in open quantum devices: A kinetic approach
Rossi, Fausto; Proietti Zaccaria, Remo; Iotti, Rita Claudia
2004-01-01
An alternative simulation strategy for the study of nonequilibrium carrier dynamics in quantum devices with open boundaries is presented. In particular, we propose replacing the usual modeling of open quantum systems based on phenomenological injection/loss rates with a kinetic description of the system-reservoir thermalization process. More specifically, in this simulation scheme the partial carrier thermalization induced by the device spatial boundaries is treated within the standard Monte ...
KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations
Leetmaa, Mikael; Skorodumova, Natalia V.
2014-01-01
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 i...
Atomistic simulations of plasma-wall interactions in fusion reactors
International Nuclear Information System (INIS)
Atomistic computer simulations, especially molecular dynamics, but also kinetic Monte Carlo simulations and electronic structure calculations, have proven to be a valuable tool for studying radiation effects in fusion reactor materials. In this paper, I will first review a few cases where these methods have given additional insights into the interaction between a fusion plasma and the first wall of a reactor. Then I will, in the spirit of the workshop theme of 'new directions in plasma-wall interactions' discuss some possible future avenues of research
Directory of Open Access Journals (Sweden)
Michael Müller
2011-01-01
Full Text Available The ordering kinetics in free and supported L10 nanoparticles was studied by means of lattice-based kinetic Monte-Carlo simulations. Starting from a fully disordered particle of Wulff shape, the simulations show that the nucleation of ordered domains is starting quickly on various (100 facets but is retarded in the particle volume due to the lack of vacancies compared with a thin film geometry. If a substrate is present, we do not find significant differences in the ordering behavior. This holds true, even if we impose a massively increased thermodynamic driving force for interface segregation, because the nucleation of ordered domains on free facets is significantly faster than the bulk diffusion of the segregating species to the interface. In cases where wetting of the substrate or surface facetting occurs, we find that diffusional atomic motion on the surface goes along with an enhanced long-range order.
Estimation of Adjoint-Weighted Kinetics Parameters in Monte Carlo Wieland Calculations
International Nuclear Information System (INIS)
The effective delayed neutron fraction, βeff, and the prompt neutron generation time, Λ, in the point kinetics equation are weighted by the adjoint flux to improve the accuracy of the reactivity estimate. Recently the Monte Carlo (MC) kinetics parameter estimation methods by using the self-consistent adjoint flux calculated in the MC forward simulations have been developed and successfully applied for the research reactor analyses. However these adjoint estimation methods based on the cycle-by-cycle genealogical table require a huge memory size to store the pedigree hierarchy. In this paper, we present a new adjoint estimation in which the pedigree of a single history is utilized by applying the MC Wielandt method. The effectiveness of the new method is demonstrated in the kinetics parameter estimations for infinite homogeneous two-group problems and the Godiva critical facility
Estimation of Adjoint-Weighted Kinetics Parameters in Monte Carlo Wieland Calculations
Energy Technology Data Exchange (ETDEWEB)
Choi, Sung Hoon; Shim, Hyung Jin [Seoul National Univ., Seoul (Korea, Republic of)
2013-07-01
The effective delayed neutron fraction, β{sub eff}, and the prompt neutron generation time, Λ, in the point kinetics equation are weighted by the adjoint flux to improve the accuracy of the reactivity estimate. Recently the Monte Carlo (MC) kinetics parameter estimation methods by using the self-consistent adjoint flux calculated in the MC forward simulations have been developed and successfully applied for the research reactor analyses. However these adjoint estimation methods based on the cycle-by-cycle genealogical table require a huge memory size to store the pedigree hierarchy. In this paper, we present a new adjoint estimation in which the pedigree of a single history is utilized by applying the MC Wielandt method. The effectiveness of the new method is demonstrated in the kinetics parameter estimations for infinite homogeneous two-group problems and the Godiva critical facility.
International Nuclear Information System (INIS)
The effective delayed neutron fraction, βeff, and the prompt neutron generation time, Λ, in the point kinetics equation are weighted by the adjoint flux to improve the accuracy of the reactivity estimate. Recently the Monte Carlo (MC) kinetics parameter estimation methods by using the adjoint flux calculated in the MC forward simulations have been developed and successfully applied for reactor analyses. However these adjoint estimation methods based on the cycle-by-cycle genealogical table require a huge memory size to store the pedigree hierarchy. In this paper, we present a new adjoint estimation method in which the pedigree of a single history is utilized by applying the MC Wielandt method. The algorithm of the new method is derived and its effectiveness is demonstrated in the kinetics parameter estimations for infinite homogeneous two-group problems and critical facilities. (author)
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...
Kunz, Lothar; Kuhn, Frank M.; Deutschmann, Olaf
2015-07-01
So far most kinetic Monte Carlo (kMC) simulations of heterogeneously catalyzed gas phase reactions were limited to flat crystal surfaces. The newly developed program MoCKA (Monte Carlo Karlsruhe) combines graph-theoretical and lattice-based principles to be able to efficiently handle multiple lattices with a large number of sites, which account for different facets of the catalytic nanoparticle and the support material, and pursues a general approach, which is not restricted to a specific surface or reaction. The implementation uses the efficient variable step size method and applies a fast update algorithm for its process list. It is shown that the analysis of communication between facets and of (reverse) spillover effects is possible by rewinding the kMC simulation. Hence, this approach offers a wide range of new applications for kMC simulations in heterogeneous catalysis.
Multi-level Monte Carlo for stochastically modeled chemical kinetic systems
Anderson, David F
2011-01-01
A chemical reaction network involves multiple reactions and species. The simplest stochastic models of such networks treat the system as a continuous time Markov chain with the state being the number of molecules of each species and with reactions modeled as possible transitions of the chain. While there are methods that generate exact sample paths of the Markov chain, their computational cost scales linearly with the number of reaction events. Therefore, such methods become computationally intense for even moderately sized systems. This drawback is greatly exacerbated when such simulations are performed in conjunction with Monte Carlo techniques, as is the norm, which require the generation of many paths. We show how to extend a recently proposed multi-level Monte Carlo approach to this stochastic chemical kinetic setting, lowering the computational complexity needed to compute expected values of functions of the state of the system to a specified accuracy. The extension is non-trivial and a novel coupling o...
Kinetic Monte Carlo and Cellular Particle Dynamics Simulations of Multicellular Systems
Flenner, Elijah; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan
2011-01-01
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. Computer simulations based on Metropolis Monte Carlo (MMC) algorithms were successful in explaining and predicting the resulting stationary structures (corresponding to the lowest adhesion energy state). Here we introduce two alternatives to the MMC approach for modeling cellular motion and self-assembly: (1) a kinetic Monte Carlo (KMC), and (2) a cellular particle dynamics (CPD) method. Unlike MMC, both KMC and CPD methods are capable of simulating the dynamics of the cellular system in real time. In the KMC approach a transition rate is associated with possible rearrangements of the cellular system, and the corresponding time evolution is expressed in terms of these rates. In the CPD approach cells are modeled as interacting cellular ...
Parallelization of kinetic Monte Carlo algorithm to simulate AL3Sc precipitation
Moura, Alfredo de; Esteves, António
2015-01-01
The present paper reports the precipitation process of Al3Sc structures in an aluminum scandium alloy, which has been simulated with a synchronous parallel kinetic Monte Carlo (spkMC) algorithm. The spkMC implementation is based on the vacancy diffusion mechanism. To filter the raw data generated by the spkMC simulations, the density-based clustering with noise (DBSCAN) method has been employed. spkMC and DBSCAN algorithms were implemented in the C language and using MPI library. The simulati...
Moura, Alfredo de; Esteves, António
2013-01-01
The present paper reports the precipitation process of Al3Sc structures in an aluminum scandium alloy, which has been simulated with a kinetic Monte Carlo (kMC) method. The kMC implementation is based on the vacancy diffusion mechanism. To filter the raw data generated by the kMC simulation, the density-based clustering with noise (DBSCAN) method was employed. kMC and DBSCAN algorithms were implemented in the C language. The undertaken simulations were conducted in the SeARCH cluster at the U...
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.
Kinetic Monte Carlo simulation of formation of microstructures in liquid droplets
Energy Technology Data Exchange (ETDEWEB)
Block, M [Institut fuer Theoretische Physik, Technische Universitaet Berlin, D-10623 Berlin (Germany); Kunert, R [Institut fuer Theoretische Physik, Technische Universitaet Berlin, D-10623 Berlin (Germany); Schoell, E [Institut fuer Theoretische Physik, Technische Universitaet Berlin, D-10623 Berlin (Germany); Boeck, T [Institut fuer Kristallzuechtung Berlin, D-12489 Berlin (Germany); Teubner, Th [Institut fuer Kristallzuechtung Berlin, D-12489 Berlin (Germany)
2004-11-01
We study the deposition of indium droplets on a glass surface and the subsequent formation of silicon microcrystals inside these droplets. Kinetic Monte Carlo methods are used to analyse the influence of growth temperature, flux of incoming particles, surface coverage, and in particular an energy parameter simulating the surface tension, upon the morphology of growth. According to the experimental conditions of crystallization, a temperature gradient and diffusion in spherical droplets are included. The simulations explain the formation of silicon crystal structures in good agreement with the experiment. The dependence of their shape and the conditions of formation on the growth parameters are investigated in detail.
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.
Ligand-receptor binding kinetics in surface plasmon resonance cells: A Monte Carlo analysis
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...
Kinetic Monte Carlo simulation of surface segregation in Pd–Cu alloys
International Nuclear Information System (INIS)
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
Kinetic Monte Carlo Simulation of Oxygen and Cation Diffusion in Yttria-Stabilized Zirconia
Good, Brian
2011-01-01
Yttria-stabilized zirconia (YSZ) is of interest to the aerospace community, notably for its application as a thermal barrier coating for turbine engine components. In such an application, diffusion of both oxygen ions and cations is of concern. Oxygen diffusion can lead to deterioration of a coated part, and often necessitates an environmental barrier coating. Cation diffusion in YSZ is much slower than oxygen diffusion. However, such diffusion is a mechanism by which creep takes place, potentially affecting the mechanical integrity and phase stability of the coating. In other applications, the high oxygen diffusivity of YSZ is useful, and makes the material of interest for use as a solid-state electrolyte in fuel cells. The kinetic Monte Carlo (kMC) method offers a number of advantages compared with the more widely known molecular dynamics simulation method. In particular, kMC is much more efficient for the study of processes, such as diffusion, that involve infrequent events. We describe the results of kinetic Monte Carlo computer simulations of oxygen and cation diffusion in YSZ. Using diffusive energy barriers from ab initio calculations and from the literature, we present results on the temperature dependence of oxygen and cation diffusivity, and on the dependence of the diffusivities on yttria concentration and oxygen sublattice vacancy concentration. We also present results of the effect on diffusivity of oxygen vacancies in the vicinity of the barrier cations that determine the oxygen diffusion energy barriers.
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.
A global reaction route mapping-based kinetic Monte Carlo algorithm
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.
Menzel, Stephan; Kaupmann, Philip; Waser, Rainer
2015-07-01
We report on a 2D kinetic Monte Carlo model that describes the resistive switching in electrochemical metallization cells. To simulate the switching process, we consider several different processes on the atomic scale: electron-transfer reactions at the boundaries, ion migration, adsorption/desorption from/to interfaces, surface diffusion and nucleation. These processes result in a growth/dissolution of a metallic filament within an insulating matrix. In addition, the model includes electron tunneling between the growing filament and the counter electrode, which allows for simulating multilevel switching. It is shown that the simulation model can reproduce the reported switching kinetics, switching variability and multilevel capabilities of ECM devices. As a major result, the influence of mechanical stress working on the host matrix due to the filamentary growth is investigated. It is demonstrated that the size and shape of the filament depend on the Young's modulus of the insulating matrix. For high values a wire-like structure evolves, whereas the shape is dendritic if the Young's modulus is negligible.We report on a 2D kinetic Monte Carlo model that describes the resistive switching in electrochemical metallization cells. To simulate the switching process, we consider several different processes on the atomic scale: electron-transfer reactions at the boundaries, ion migration, adsorption/desorption from/to interfaces, surface diffusion and nucleation. These processes result in a growth/dissolution of a metallic filament within an insulating matrix. In addition, the model includes electron tunneling between the growing filament and the counter electrode, which allows for simulating multilevel switching. It is shown that the simulation model can reproduce the reported switching kinetics, switching variability and multilevel capabilities of ECM devices. As a major result, the influence of mechanical stress working on the host matrix due to the filamentary growth is
International Nuclear Information System (INIS)
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
Kinetic Monte Carlo simulation of film morphologies at the initial stages
Institute of Scientific and Technical Information of China (English)
无
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.
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.
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.
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.
A three-dimensional self-learning kinetic Monte Carlo model: application to Ag(111)
International Nuclear Information System (INIS)
The reliability of kinetic Monte Carlo (KMC) simulations depends on accurate transition rates. The self-learning KMC method (Trushin et al 2005 Phys. Rev. B 72 115401) combines the accuracy of rates calculated from a realistic potential with the efficiency of a rate catalog, using a pattern recognition scheme. This work expands the original two-dimensional method to three dimensions. The concomitant huge increase in the number of rate calculations on the fly needed can be avoided by setting up an initial database, containing exact activation energies calculated for processes gathered from a simpler KMC model. To provide two representative examples, the model is applied to the diffusion of Ag monolayer islands on Ag(111), and the homoepitaxial growth of Ag on Ag(111) at low temperatures.
Extended pattern recognition scheme for self-learning kinetic Monte Carlo simulations
International Nuclear Information System (INIS)
We report the development of a pattern recognition scheme that takes into account both fcc and hcp adsorption sites in performing self-learning kinetic Monte Carlo (SLKMC-II) simulations on the fcc(111) surface. In this scheme, the local environment of every under-coordinated atom in an island is uniquely identified by grouping fcc sites, hcp sites and top-layer substrate atoms around it into hexagonal rings. As the simulation progresses, all possible processes, including those such as shearing, reptation and concerted gliding, which may involve fcc-fcc, hcp-hcp and fcc-hcp moves are automatically found, and their energetics calculated on the fly. In this article we present the results of applying this new pattern recognition scheme to the self-diffusion of 9-atom islands (M9) on M(111), where M = Cu, Ag or Ni.
International Nuclear Information System (INIS)
A novel kinetic Monte Carlo simulator 'ARC' was developed to investigate hydrogen diffusion process in metals and alloys. The results of the hydrogen diffusion coefficients in palladium, silver, and Pd1-xAgx (x ≤ 0.5) are in excellent agreement with experimental results. Two different diffusion sites, Pd-rich diffusion site and Ag-rich diffusion site, are found to be necessary to explain diffusion behaviors of hydrogen in palladium-silver alloys. Detailed analysis clarified that hydrogen atoms preferentially diffuse through the palladium-rich region of palladium-silver alloys at low silver concentrations, and that the hydrogen diffusion process at low silver contents is dominated by the jumps in palladium-rich regions. The migration barrier of hydrogen from Pd-rich diffusion site to Ag-rich diffusion site is estimated to be between 0.40 and 0.45 eV
Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations
International Nuclear Information System (INIS)
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
Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations
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
Simulating structural transitions with kinetic Monte Carlo: The case of epitaxial graphene on SiC
Deretzis, I.; La Magna, A.
2016-03-01
We have developed a kinetic Monte Carlo numerical scheme, specifically suited to simulate structural transitions in crystalline materials, and implemented it for the case of epitaxial graphene on SiC. In this process, surface Si atoms selectively sublimate, while the residual C atoms rearrange from a position occupied in the SiC hexagonal lattice to the graphene honeycomb structure, modifying their hybridization (from s p3 to s p2 ) and bond partners (from Si-C to C-C). The model is based on the assumption that the Monte Carlo particles follow the evolution of their reference crystal until they experience a thermally activated reversible transition to another crystal structure. We demonstrate that, in a formulation based on three parallel lattices, the method is able to recover the complex evolution steps of epitaxial graphene on SiC. Moreover, the simulation results are in noteworthy agreement with the overall experimental scenario, both when varying the structural properties of the material (e.g., the initial surface configuration or polarity) as well as the process conditions (e.g., the temperature and pressure).
Emo, Jonathan; Pareige, Cristelle; Saillet, Sébastien; Domain, Christophe; Pareige, Philippe
2014-08-01
This paper presents the first simulations of the kinetics of spinodal decomposition and G-phase precipitation occurring in ferrite of duplex stainless steels. The kinetics was simulated using a simple but effective atomic kinetic Monte Carlo model in a ternary alloy. The simulations reproduced the α/α‧ spinodal structure with precipitates at the α/α‧ interface. The comparison of simulated results with experiments shows that the simulations quantitatively reproduce the kinetics of phase transformation and the synergy observed experimentally between the spinodal decomposition and G-phase precipitation. By following the vacancy pathway, we show that the coarsening of G-phase precipitates proceeds via diffusion along the α/α‧ interfaces. The simulations made it possible to explain the origin of the kinetic synergy between spinodal decomposition and G-phase precipitation.
Mobility of large clusters on a semiconductor surface: Kinetic Monte Carlo simulation results
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 < α < -0.75. The value of α is found to be independent of cluster sizes and temperature values (170-220 K) considered in this study. As the diffusion along the perimeter of the cluster becomes prohibitive, the exponent approaches a value of -0.5. The diffusion coefficient is found to change by one order of magnitude as a function of cluster size.
Markov chain Monte Carlo based analysis of post-translationally modified VDAC1 gating kinetics
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Shivendra eTewari
2015-01-01
Full Text Available 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 VDAC1 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 suggests 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.
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.
Michael Müller; Karsten Albe
2011-01-01
The ordering kinetics in free and supported L10 nanoparticles was studied by means of lattice-based kinetic Monte-Carlo simulations. Starting from a fully disordered particle of Wulff shape, the simulations show that the nucleation of ordered domains is starting quickly on various (100) facets but is retarded in the particle volume due to the lack of vacancies compared with a thin film geometry. If a substrate is present, we do not find significant differences in the ordering behavior. This h...
Monte Carlo kinetics simulations of ice-mantle formation on interstellar grains
Garrod, Robin
2015-08-01
The majority of interstellar dust-grain chemical kinetics models use rate equations, or alternative population-based simulation methods, to trace the time-dependent formation of grain-surface molecules and ice mantles. Such methods are efficient, but are incapable of considering explicitly the morphologies of the dust grains, the structure of the ices formed thereon, or the influence of local surface composition on the chemistry.A new Monte Carlo chemical kinetics model, MIMICK, is presented here, whose prototype results were published recently (Garrod 2013, ApJ, 778, 158). The model calculates the strengths and positions of the potential mimima on the surface, on the fly, according to the individual pair-wise (van der Waals) bonds between surface species, allowing the structure of the ice to build up naturally as surface diffusion and chemistry occur. The prototype model considered contributions to a surface particle's potential only from contiguous (or "bonded") neighbors; the full model considers contributions from surface constituents from short to long range. Simulations are conducted on a fully 3-D user-generated dust-grain with amorphous surface characteristics. The chemical network has also been extended from the simple water system previously published, and now includes 33 chemical species and 55 reactions. This allows the major interstellar ice components to be simulated, such as water, methane, ammonia and methanol, as well as a small selection of more complex molecules, including methyl formate (HCOOCH3).The new model results indicate that the porosity of interstellar ices are dependent on multiple variables, including gas density, the dust temperature, and the relative accretion rates of key gas-phase species. The results presented also have implications for the formation of complex organic molecules on dust-grain surfaces at very low temperatures.
International Nuclear Information System (INIS)
Highlights: • Among the kinetic parameters, the most important ones are βeff and Λ. • Several methods including the Rossi-α and Feynman-α techniques, slope fit and MCNPX code have been investigated. • The Monte Carlo MCNPX code was used to simulate a geometrical model of the TRIGA core. • The results of the methods have been validated. - Abstract: In this study, noise analysis techniques including Feynman-α (variance-to-mean) and Rossi-α (correlation) and dynamic method such as slope fit method have been used to calculate effective delayed neutron fraction (βeff) and neutron reproduction time (Λ) in Accelerator Driven Subcritical TRIGA reactor. The obtained results have been compared with MCNPX code results. The relative difference between MCNPX code with Feynman-α and Rossi-α techniques and slope fit method for βeff are approximately −5.4%, 1.2%, and −10.6%, −14.8%, respectively, and also for Λ is approximately 2.1%. According to results, the noise methods can been considered ideal for detection with high efficiency and zero dead time and in the slope fit method, the decay of the delayed neutrons has been neglected and only the prompt neutrons have been taken into account. In addition, quantities simulated in the current study are validated against both the reference data and the results of MCNPX code. Therefore, the purpose of this study is to simulate the commonly used experimental methods by MCNPX code and investigate the convergence as well as accuracy of the computational results for different analysis methods in calculation of the kinetic parameters in an Accelerator Driven Subcritical TRIGA reactor
Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems
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.
KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations
Leetmaa, Mikael
2014-01-01
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 pe...
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.
Energy Technology Data Exchange (ETDEWEB)
Krueger, Rachel A. [Department of Chemistry, California Institute of Technology, Pasadena, California 91125 (United States); Haibach, Frederick G. [Confluent Science, Wilbraham, Massachusetts 01095 (United States); Fry, Dana L.; Gomez, Maria A., E-mail: magomez@mtholyoke.edu [Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075 (United States)
2015-04-21
A centrality measure based on the time of first returns rather than the number of steps is developed and applied to finding proton traps and access points to proton highways in the doped perovskite oxides: AZr{sub 0.875}D{sub 0.125}O{sub 3}, where A is Ba or Sr and the dopant D is Y or Al. The high centrality region near the dopant is wider in the SrZrO{sub 3} systems than the BaZrO{sub 3} systems. In the aluminum-doped systems, a region of intermediate centrality (secondary region) is found in a plane away from the dopant. Kinetic Monte Carlo (kMC) trajectories show that this secondary region is an entry to fast conduction planes in the aluminum-doped systems in contrast to the highest centrality area near the dopant trap. The yttrium-doped systems do not show this secondary region because the fast conduction routes are in the same plane as the dopant and hence already in the high centrality trapped area. This centrality measure complements kMC by highlighting key areas in trajectories. The limiting activation barriers found via kMC are in very good agreement with experiments and related to the barriers to escape dopant traps.
A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins
International Nuclear Information System (INIS)
Many relevant biological processes take place on time scales not reachable by standard all-atom computer simulations. The translocation of antibiotics through non-specific bacterial porins is an example. Microscopic effects compete to determine penetration routes and, consequently, free energy barriers to be overcome. Since bacteria can develop resistance to treatment also by reducing their antibiotic permeability, to understand the microscopic aspects of antibiotic translocation is an important step to rationalize drug design. Here, to investigate the translocation we propose a complete numerical model that combines the diffusion-controlled rate theory and a kinetic Monte Carlo scheme based on both experimental data and microscopically well-founded all-atom simulations. Within our model, an antibiotic translocating through an hour-glass-shaped channel can be described as a molecule moving on a potential of mean force featuring several affinity sites and a high central barrier. The implications of our results for the characterization of antibiotic translocation at in vivo concentrations are discussed. The presence of an affinity site close to the mouth of the channel seems to favor the translocation of antibiotics, the affinity site acting as a particle reservoir. Possible connections between results and the appearance of mutations in clinical strains are also outlined. (paper)
Tavarone, Raffaele; Charbonneau, Patrick; Stark, Holger
2016-03-01
Recent experiments have demonstrated that in a dense monolayer of photo-switchable dye methyl-red molecules the relaxation of an initial birefringence follows a power-law decay, typical for glass-like dynamics. The slow relaxation can efficiently be controlled and accelerated by illuminating the monolayer with circularly polarized light, which induces trans-cis isomerization cycles. To elucidate the microscopic mechanism, we develop a two-dimensional molecular model in which the trans and cis isomers are represented by straight and bent needles, respectively. As in the experimental system, the needles are allowed to rotate and to form overlaps but they cannot translate. The out-of-equilibrium rotational dynamics of the needles is generated using kinetic Monte Carlo simulations. We demonstrate that, in a regime of high density and low temperature, the power-law relaxation can be traced to the formation of spatio-temporal correlations in the rotational dynamics, i.e., dynamic heterogeneity. We also show that the nearly isotropic cis isomers can prevent dynamic heterogeneity from forming in the monolayer and that the relaxation then becomes exponential.
First principles kinetic Monte Carlo study on the growth patterns of WSe2 monolayer
Nie, Yifan; Liang, Chaoping; Zhang, Kehao; Zhao, Rui; Eichfeld, Sarah M.; Cha, Pil-Ryung; Colombo, Luigi; Robinson, Joshua A.; Wallace, Robert M.; Cho, Kyeongjae
2016-06-01
The control of domain morphology and defect level of synthesized transition metal dichalcogenides (TMDs) is of crucial importance for their device applications. However, current TMDs synthesis by chemical vapor deposition and molecular beam epitaxy is in an early stage of development, where much of the understanding of the process-property relationships is highly empirical. In this work, we use a kinetic Monte Carlo coupled with first principles calculations to study one specific case of the deposition of monolayer WSe2 on graphene, which can be expanded to the entire TMD family. Monolayer WSe2 domains are investigated as a function of incident flux, temperature and precursor ratio. The quality of the grown WSe2 domains is analyzed by the stoichiometry and defect density. A phase diagram of domain morphology is developed in the space of flux and the precursor stoichiometry, in which the triangular compact, fractal and dendritic domains are identified. The phase diagram has inspired a new synthesis strategy for large TMD domains with improved quality.
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Mass and kinetic energy distribution of nuclear fragments after neutron induced fission of 235U have been studied using a Monte-Carlo simulation. Besides that the pronounced peak in the standard deviation of the kinetic energy σE(m) at the mass number around m = 110 was reproduced, a second peak was found at m = 126. These results are in good agreement with experimental data obtained by Belhafaf et. al. We have concluded that the obtained results are consequence of the characteristics of neutron evaporation for the fragments and sharp variation on primary mass yield curve. (authors)
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The mass and kinetic energy distribution of nuclear fragments after neutron-induced fission of 235U have been studied using a Monte-Carlo simulation. Besides reproducing the pronounced peak in the standard deviation of the kinetic energy σE(m) at the fragment mass number around m=109, our simulation also produces a second peak at about m=126. These results are in good agreement with experimental data obtained by Belhafaf et.al. We conclude that the obtained results are consequence of the characteristics of the fragments' neutron evaporation and of the sharp variation on the primary mass yield curve. (orig.)
International Nuclear Information System (INIS)
We have performed Kinetic Monte Carlo simulation work to study the effect of diffusion anisotropy, bonding anisotropy and edge diffusion on island formation at different temperatures during the sub-monolayer film growth in Molecular Beam Epitaxy. We use simple cubic solid on solid model and event based Bortz, Kalos and Labowitch (BKL) algorithm on the Kinetic Monte Carlo method to simulate the physical phenomena. We have found that the island morphology and growth exponent are found to be influenced by substrate anisotropy as well as edge diffusion, however they do not play a significant role in island elongation. The growth exponent and island size distribution are observed to be influenced by substrate anisotropy but are negligibly influenced by edge diffusion. We have found fractal islands when edge diffusion is excluded and compact islands when edge diffusion is included. (author)
Comprehensive modeling of solid phase epitaxial growth using Lattice Kinetic Monte Carlo
International Nuclear Information System (INIS)
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
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.
Modeling the atomistic growth behavior of gold nanoparticles in solution
Turner, C. Heath; Lei, Yu; Bao, Yuping
2016-04-01
The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.
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.
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
International Nuclear Information System (INIS)
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
Surface patterning by ion bombardment: predictions of large-scale atomistic simulations
International Nuclear Information System (INIS)
Despite of intense studies in recent years, atomistic understanding of surface evolution during ion irradiation is still under discussion. Continuum models, like the Bradley and Harper theory, cannot explain microscopic processes during ion irradiation. So far, atomistic simulations could not describe pattern dynamics on spatiotemporal scales of experiments. We present a novel program package that unifies the simulation of collision cascades with kinetic Monte-Carlo simulations. The 3D atom relocations were calculated in the Binary Collision Approximation (BCA), whereas the thermally activated relaxation of energetically unstable atomic configurations as well as diffusive processes were simulated by a very efficient bit-coded kinetic 3D Monte Carlo code. Our studies show that: (i) bulk defects continuously created within the collision cascade are responsible for local surface topography fluctuations and induce surface mass currents. These currents smooth the surface from normal incidence up to θ=40 , whereas at θ>40 ripple patterns appear; (ii) sputtering is not the dominant driving force for the ripple formation at non-grazing incidence angles. Surface patterning is caused by processes like bulk and surface defect migration, recombination, bulk and surface diffusion and ion induced diffusion.
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We present two major optimizations for the kinetic Activation-Relaxation Technique (k-ART), an off-lattice self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search THAT has been successfully applied to study a number of semiconducting and metallic systems. K-ART is parallelized in a non-trivial way: A master process uses several worker processes to perform independent event searches for possible events, while all bookkeeping and the actual simulation is performed by the master process. Depending on the complexity of the system studied, the parallelization scales well for tens to more than one hundred processes. For dealing with large systems, we present a near order 1 implementation. Techniques such as Verlet lists, cell decomposition and partial force calculations are implemented, and the CPU time per time step scales sublinearly with the number of particles, providing an efficient use of computational resources.
In-silico analysis on biofabricating vascular networks using kinetic Monte Carlo simulations
International Nuclear Information System (INIS)
We present a computational modeling approach to study the fusion of multicellular aggregate systems in a novel scaffold-less biofabrication process, known as ‘bioprinting’. In this novel technology, live multicellular aggregates are used as fundamental building blocks to make tissues or organs (collectively known as the bio-constructs,) via the layer-by-layer deposition technique or other methods; the printed bio-constructs embedded in maturogens, consisting of nutrient-rich bio-compatible hydrogels, are then placed in bioreactors to undergo the cellular aggregate fusion process to form the desired functional bio-structures. Our approach reported here is an agent-based modeling method, which uses the kinetic Monte Carlo (KMC) algorithm to evolve the cellular system on a lattice. In this method, the cells and the hydrogel media, in which cells are embedded, are coarse-grained to material’s points on a three-dimensional (3D) lattice, where the cell–cell and cell–medium interactions are quantified by adhesion and cohesion energies. In a multicellular aggregate system with a fixed number of cells and fixed amount of hydrogel media, where the effect of cell differentiation, proliferation and death are tactically neglected, the interaction energy is primarily dictated by the interfacial energy between cell and cell as well as between cell and medium particles on the lattice, respectively, based on the differential adhesion hypothesis. By using the transition state theory to track the time evolution of the multicellular system while minimizing the interfacial energy, KMC is shown to be an efficient time-dependent simulation tool to study the evolution of the multicellular aggregate system. In this study, numerical experiments are presented to simulate fusion and cell sorting during the biofabrication process of vascular networks, in which the bio-constructs are fabricated via engineering designs. The results predict the feasibility of fabricating the vascular
Runov, A. M.; Kasilov, S. V.; Helander, P.
2015-11-01
A kinetic Monte Carlo model suited for self-consistent transport studies is proposed and tested. The Monte Carlo collision operator is based on a widely used model of Coulomb scattering by a drifting Maxwellian and a new algorithm enforcing the momentum and energy conservation laws. The difference to other approaches consists in a specific procedure of calculating the background Maxwellian parameters, which does not require ensemble averaging and, therefore, allows for the use of single-particle algorithms. This possibility is useful in transport balance (steady state) problems with a phenomenological diffusive ansatz for the turbulent transport, because it allows a direct use of variance reduction methods well suited for single particle algorithms. In addition, a method for the self-consistent calculation of the electric field is discussed. Results of testing of the new collision operator using a set of 1D examples, and preliminary results of 2D modelling in realistic tokamak geometry, are presented.
Numerical tools for atomistic simulations.
Energy Technology Data Exchange (ETDEWEB)
Fang, H. (Mississippi State University); Gullett, Philip Michael; Slepoy, Alexander (Sandia National Laboratories, Albuquerque, NM); Horstemeyer, Mark F. (Mississippi State University); Baskes, Michael I. (Los Alamos National Laboratory, Los Alamos, NM); Wagner, Gregory John; Li, Mo (Materials Science and Engineering, Atlanta, GA)
2004-01-01
The final report for a Laboratory Directed Research and Development project entitled 'Parallel Atomistic Computing for Failure Analysis of Micromachines' is presented. In this project, atomistic algorithms for parallel computers were developed to assist in quantification of microstructure-property relations related to weapon micro-components. With these and other serial computing tools, we are performing atomistic simulations of various sizes, geometries, materials, and boundary conditions. These tools provide the capability to handle the different size-scale effects required to predict failure. Nonlocal continuum models have been proposed to address this problem; however, they are phenomenological in nature and are difficult to validate for micro-scale components. Our goal is to separately quantify damage nucleation, growth, and coalescence mechanisms to provide a basis for macro-scale continuum models that will be used for micromachine design. Because micro-component experiments are difficult, a systematic computational study that employs Monte Carlo methods, molecular statics, and molecular dynamics (EAM and MEAM) simulations to compute continuum quantities will provide mechanism-property relations associated with the following parameters: specimen size, number of grains, crystal orientation, strain rates, temperature, defect nearest neighbor distance, void/crack size, chemical state, and stress state. This study will quantify sizescale effects from nanometers to microns in terms of damage progression and thus potentially allow for optimized micro-machine designs that are more reliable and have higher fidelity in terms of strength. In order to accomplish this task, several atomistic methods needed to be developed and evaluated to cover the range of defects, strain rates, temperatures, and sizes that a material may see in micro-machines. Therefore we are providing a complete set of tools for large scale atomistic simulations that include pre
International Nuclear Information System (INIS)
Within the last decade molecular dynamics simulations of displacement cascades have revealed that glissile clusters of self-interstitial crowdions are formed directly in cascades. Also, under various conditions, a crowdion cluster can change its Burgers vector and glide along a different close-packed direction. In order to incorporate the migration properties of crowdion clusters into analytical rate theory models, it is necessary to describe the reaction kinetics of defects that migrate one-dimensionally with occasional changes in their Burgers vector. To meet this requirement, atomic-scale kinetic Monte Carlo (KMC) simulations have been used to study the defect reaction kinetics of one-dimensionally migrating crowdion clusters as a function of the frequency of direction changes, specifically to determine the sink strengths for such one-dimensionally migrating defects. The KMC experiments are used to guide the development of analytical expressions for use in reaction rate theories and especially to test their validity. Excellent agreement is found between the results of KMC experiments and the analytical expressions derived for the transition from one-dimensional to three-dimensional reaction kinetics. Furthermore, KMC simulations have been performed to investigate the significant role of crowdion clusters in the formation and stability of void lattices. The necessity for both one-dimensional migration and Burgers vectors changes for achieving a stable void lattice is demonstrated.
KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations
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
Mermigkis, Panagiotis G; Tsalikis, Dimitrios G; Mavrantzas, Vlasis G
2015-10-28
A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, D(eff), of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, D(eff) is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for D(eff) as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on D(eff) (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and
International Nuclear Information System (INIS)
A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, Deff, of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, Deff is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for Deff as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on Deff (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them
DEFF Research Database (Denmark)
Heinisch, H.L.; Trinkaus, H.; Singh, Bachu Narain
2007-01-01
The reaction kinetics of the various species of mobile defects in irradiated materials are crucially dependent on the dimensionality of their migration. Sink strengths for one-dimensionally (1D) gliding interstitial loops undergoing occasional direction changes have been described analytically and...... 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 to the...
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.
International Nuclear Information System (INIS)
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
Veenendaal, van E.; Hoof, van P.J.C.M.; Suchtelen, van J.; Enckevort, van W.J.P.; Bennema, P.
1998-01-01
Kinetic roughening is not a phase transition and, as such, it lacks an exact definition. Many criteria are used to mark the onset of kinetic roughening. Criteria stemming from the classical two-dimensional nucleation theory are widely used. On the other hand, experimentalists observe a transition fr
Adjoint Weighted Kinetics Parameter Estimation in the Monte Carlo Wielandt Calculations
Energy Technology Data Exchange (ETDEWEB)
Choi, Sung Hoon; Shim, Hyung Jin [Seoul National Univ., Seoul (Korea, Republic of)
2013-10-15
In order to eliminate this huge memory consumption in the current adjoint estimation method, we have developed a new method in which the pedigree of a single history is utilized by applying the MC Wielandt method. The Wielandt method allows the estimations of the adjoint flux and adjoint-weighted parameters within a single cycle neutron simulations. The effectiveness of the new method is demonstrated in the kinetics parameter estimations for an infinite homogeneous two-group problem and the Godiva facility. We have developed an efficient algorithm for the adjoint-weighted kinetics parameter estimation in the MC Wielandt calculations which can significantly reduce the memory usage. From the numerical applications, it is demonstrated that the new method can predict the kinetics parameters with great accuracy.
Energy Technology Data Exchange (ETDEWEB)
Negulyaev, Nikolay N. [Fachbereich Physik, Martin-Luther-Universitaet, Halle-Wittenberg, Halle (Germany); Stepanyuk, Oleg V.; Saletsky, Alexander M. [Faculty of Physics, Moscow State University (Russian Federation); Niebergall, Larissa [Max-Planck-Institut fuer Mikrostrukturphysik, Halle (Germany)
2010-05-15
Performing large-scale atomic simulations by means of kinetic Monte Carlo method we study room temperature self-organization of 3d magnetic atoms (Fe, Co) on fcc (110) surfaces (Pd(110), Cu(110)) in the sub-monolayer regime. The energetics of various diffusion processes relevant for these systems is investigated based on first principles calculations. We reveal that surface-confined atomic intermixing plays a significant role in the formation of nanostructures. Our results lead to the conclusion that the deposited species (Fe, Co) are captured into the topmost surface layer, while the ad-layer structure consists mainly of the expelled substrate atoms (Pd, Cu). Our studies shed a light on recent experimental investigations on the metal-on-metal growth on fcc (110) surfaces. (Abstract Copyright [2010], Wiley Periodicals, Inc.)
Islamuddin Shah, Syed; Nandipati, Giridhar; Karim, Altaf; Rahman, Talat S.
2016-01-01
We studied self-diffusion of small two-dimensional Ag islands, containing up to ten atoms, on the Ag(111) surface using self-learning kinetic Monte Carlo (SLKMC) simulations. Activation barriers are calculated using the semi-empirical embedded atom method (EAM) potential. We find that two- to seven-atom islands primarily diffuse via concerted translation processes with small contributions from multi-atom and single-atom processes, while eight- to ten-atom islands diffuse via single-atom processes, especially edge diffusion, corner rounding and kink detachment, along with a minimal contribution from concerted processes. For each island size, we give a detailed description of the important processes, and their activation barriers, responsible for its diffusion.
Meaningful timescales from Monte Carlo simulations of molecular systems
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.
International Nuclear Information System (INIS)
Kinetic lattice Monte Carlo (KLMC) model is developed for investigating oxygen vacancy diffusion in praseodymium-doped ceria. The current approach uses a database of activation energies for oxygen vacancy migration, calculated using first-principles, for various migration pathways in praseodymium-doped ceria. Since the first-principles calculations revealed significant vacancy-vacancy repulsion, we investigate the importance of that effect by conducting simulations with and without a repulsive interaction. Initially, as dopant concentrations increase, vacancy concentration and thus conductivity increases. However, at higher concentrations, vacancies interfere and repel one another, and dopants trap vacancies, creating a 'traffic jam' that decreases conductivity, which is consistent with the experimental findings. The modeled effective activation energy for vacancy migration slightly increased with increasing dopant concentration in qualitative agreement with the experiment. The current methodology comprising a blend of first-principle calculations and KLMC model provides a very powerful fundamental tool for predicting the optimal dopant concentration in ceria related materials. -- graphical abstract: Ionic conductivity in praseodymium doped ceria as a function of dopant concentration calculated using the kinetic lattice Monte Carlo vacancy-repelling model, which predicts the optimal composition for achieving maximum conductivity. Display Omitted Research highlights: → KLMC method calculates the accurate time-dependent diffusion of oxygen vacancies. → KLMC-VR model predicts a dopant concentration of ∼15-20% to be optimal in PDC. → At higher dopant concentration, vacancies interfere and repel one another, and dopants trap vacancies. → Activation energy for vacancy migration increases as a function of dopant content
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 ...
Garrod, Robin T
2013-01-01
The first off-lattice Monte Carlo kinetics model of interstellar dust-grain surface chemistry is presented. The positions of all surface particles are determined explicitly, according to the local potential minima resulting from the pair-wise interactions of contiguous atoms and molecules, rather than by a pre-defined lattice structure. The model is capable of simulating chemical kinetics on any arbitrary dust-grain morphology, as determined by the user-defined positions of each individual dust-grain atom. A simple method is devised for the determination of the most likely diffusion pathways and their associated energy barriers for surface species. The model is applied to a small, idealized dust grain, adopting various gas densities and using a small chemical network. Hydrogen and oxygen atoms accrete onto the grain, to produce H2O, H2, O2 and H2O2. The off-lattice method allows the ice structure to evolve freely; ice mantle porosity is found to be dependent on the gas density, which controls the accretion ra...
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.
International Nuclear Information System (INIS)
The methods to calculate the kinetics parameters βeff (effective delayed neutron fraction) and Λ (neutron generation time) 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. (author)
Ion beam processing of surfaces and interfaces. Modeling and atomistic simulations
International Nuclear Information System (INIS)
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 general
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
H{sub 2} formation in diffuse clouds: A new kinetic Monte Carlo study
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Iqbal, Wasim; Acharyya, Kinsuk [S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700098 (India); Herbst, Eric [Departments of Chemistry, Astronomy, and Physics, University of Virginia, Charlottesville, VA 22904 (United States)
2014-04-01
We used the continuous-time random-walk Monte Carlo technique to study anew the formation of H{sub 2} on the surfaces of interstellar dust grains in diffuse interstellar clouds. For our study, we considered three different grain materials, olivine (a polycrystalline silicate), amorphous silicate, and amorphous carbon, as well as a grain temperature that depends on granular size. For some runs, we included temperature fluctuations. Four different granular surfaces were used, one 'flat' with one type of binding site due to physisorption, one 'rough' with five different types of physisorption binding sites due to lateral forces, and two with sites for chemisorption, one in which chemisorption sites are entered through precursor physisorption sites, and one in which chemisorption is direct but occurs with a barrier for the adsorption of the first hydrogen atom. We found that on flat and rough olivine surfaces, molecular hydrogen is formed at low efficiencies, with smaller grains contributing very little despite their large numbers due to high temperatures. For flat amorphous carbon and amorphous silicate surfaces, the efficiency increases, reaching unity for the largest grains. For models with barrierless chemisorption, the efficiency of formation of H{sub 2} is near unity at all grain sizes considered, while for direct chemisorption via a barrier, we found efficiencies of 0.13-0.6 depending upon the barrier, but independent of grain size. Treating the flat olivine and amorphous silicate surfaces with temperature fluctuations increases the efficiency of H{sub 2} formation.
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.
Ab initio and atomic kinetic Monte Carlo modelling of segregation in concentrated FeCrNi alloys
International Nuclear Information System (INIS)
Internal structure of pressurised water reactors are made of austenitic materials. Under irradiation, the microstructure of these concentrated alloys evolves and solute segregation on grain boundaries or irradiation defects such as dislocation loops are observed to take place. In order to model and predict the microstructure evolution, a multi-scale modelling approach needs to be developed, which starts at the atomic scale. Atomic Kinetic Monte Carlo (AKMC) modelling is the method we chose to provide an insight on defect mediated diffusion under irradiation. In that approach, we model the concentrated commercial steel as a FeCrNi alloy (γ-Fe70Cr20Ni10). As no reliable empirical potential exists at the moment to reproduce faithfully the phase diagram and the interactions of the elements and point defects, we have adjusted a pair interaction model on large amount of DFT (Density Functional Theory) calculations. The point defect properties in the Fe70Cr20Ni10, and more precisely, how their formation energy depends on the local environment will be presented and some AKMC results on thermal non equilibrium segregation (TNES) and radiation induce segregation will be presented. The effect of Si on the segregation will also be discussed. Preliminary results show that it is the solute- grain boundaries interactions which drive TNES
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The catalytic water formation reaction was investigated by the energy dispersive near-edge x-ray absorption fine structure (dispersive NEXAFS) spectroscopy. An oxygen covered Pt(111) surface with the (2x2) structure was exposed to gaseous hydrogen (5.0x10-9 Torr) at constant surface temperatures (120-140 K). O K-edge NEXAFS spectra were measured during the reaction with a time interval of 35 s. Quantitative analyses of the spectra provided the coverage changes of the adsorbed species (O, OH, and H2O). The reaction is composed of three steps, which are characterized by an induction period (I), fast increase in coverage of OH and H2O with consuming O (II), and slow conversion of OH to H2O after the complete consumption of O (III). It was also found that the maximum OH coverage becomes smaller at a higher temperature. The kinetic Monte Carlo simulation has reproduced the three characteristic reaction steps; in the first step OH domains are created through two-dimensional aggregation of H2O (I), after the nucleation process the second step sets in where the OH domains propagate by the autocatalytic cycle until they contact with each other (II), and finally the merged OH domains convert to H2O (III). The reaction diffusion method was also applied to this system. It explained the reaction behavior in a wide surface area
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A mesoscale modeling framework integrating thermodynamics, kinetic Monte Carlo (KMC) and finite element mechanics (FEM) is developed to simulate displacive thermoelastic transformations between austenite and martensite in shape memory alloys (SMAs). The model is based on a transition state approximation for the energy landscape of the two phases under loading or cooling, which leads to the activation energy and rate for transformation domains incorporating local stress states. The evolved stress state after each domain transformation event is calculated by FEM, and is subsequently used in the stochastic KMC algorithm to determine the next domain to transform. The model captures transformation stochasticity, and predicts internal phase and stress distributions and evolution throughout the entire incubation, nucleation and growth process. It also relates the critical transformation stresses or temperatures to internal activation energies. It therefore enables quantitative exploration of transformation dynamics and transformation–microstructure interactions. The model is used to simulate superelasticity (mechanically induced transformation) under both load control and strain control in single-crystal SMAs under uniaxial tension
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.)
Good, Brian S.
2011-01-01
Yttria-stabilized zirconia s high oxygen diffusivity and corresponding high ionic conductivity, and its structural stability over a broad range of temperatures, have made the material of interest for use in a number of applications, for example, as solid electrolytes in fuel cells. At low concentrations, the stabilizing yttria also serves to increase the oxygen diffusivity through the presence of corresponding oxygen vacancies, needed to maintain charge neutrality. At higher yttria concentration, however, diffusivity is impeded by the larger number of relatively high energy migration barriers associated with yttrium cations. In addition, there is evidence that oxygen vacancies preferentially occupy nearest-neighbor sites around either dopant or Zr cations, further affecting vacancy diffusion. We present the results of ab initio calculations that indicate that it is energetically favorable for oxygen vacancies to occupy nearest-neighbor sites adjacent to Y ions, and that the presence of vacancies near either species of cation lowers the migration barriers. Kinetic Monte Carlo results from simulations incorporating this effect are presented and compared with results from simulations in which the effect is not present.
International Nuclear Information System (INIS)
We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed self-learning KMC (SLKMC) (Trushin et al 2005 Phys. Rev. B 72 115401) is released, leaving atoms free to occupy 'off-lattice' positions to accommodate several processes responsible for small-cluster diffusion, periphery atom motion and heteroepitaxial growth. This technique combines the ideas embedded in the SLKMC method with a new pattern-recognition scheme fitted to an off-lattice model in which relative atomic positions are used to characterize and store configurations. Application of a combination of the 'drag' and the repulsive bias potential (RBP) methods for saddle point searches allows the treatment of concerted cluster, and multiple- and single-atom, motions on an equal footing. This tandem approach has helped reveal several new atomic mechanisms which contribute to cluster migration. We present applications of this off-lattice SLKMC to the diffusion of 2D islands of Cu (containing 2-30 atoms) on Cu and Ag(111), using the interatomic potential from the embedded-atom method. For the hetero-system Cu/Ag(111), this technique has uncovered mechanisms involving concerted motions such as shear, breathing and commensurate-incommensurate occupancies. Although the technique introduces complexities in storage and retrieval, it does not introduce noticeable extra computational cost.
International Nuclear Information System (INIS)
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.)
Atomistic modeling of diffusional phasetransformations with elastic strain
Energy Technology Data Exchange (ETDEWEB)
Mason, D R; Rudd, R E; Sutton, A P
2003-10-31
Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Atomic interactions are modelled by Finnis-Sinclair potentials constructed for these simulations. Vacancy diffusion is modelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of kBT. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r{sup 3} , it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice.
Moura, Alfredo de
2012-01-01
Precipitate structures play a fundamental function in the material science due to the capacity of representing strong obstacles for dislocations movements within the material. This master thesis focuses on the elaboration and application of mechanical statistics knowledge, namely the kinetic Monte Carlo method, on the study and prediction of the phenomenon of precipitation in an aluminum alloy. The alloy under analysis is the aluminum scandium alloy. This thesis tackles subjects such as...
Rieger, M.(RWTH Aachen University, III. Physikalisches Institut A, Aachen, Germany); Rogal, J.; Reuter, K.
2008-01-01
Using the catalytic CO oxidation at RuO2(110) as a showcase, we employ first-principles kinetic Monte Carlo simulations to illustrate the intricate effects on temperature programmed reaction spectroscopy data brought about by the mere correlations between the locations of the active sites at a nanostructured surface. Even in the absence of lateral interactions, this nanostructure alone can cause inhomogeneities that cannot be grasped by prevalent mean-field data analysis procedures, which thu...
Further development of large-scale atomistic modelling techniques for Fe-Cr alloys
International Nuclear Information System (INIS)
In this paper we review the current status of our efforts to model the Fe-Cr system, which is a model alloy for high-Cr ferritic-martensitic steels, using large-scale atomistic methods. The core of such methods are semi-empirical interatomic potentials. Here we discuss their performance with respect to the features that are important for an accurate description of radiation effects in Fe-Cr alloys. We describe their most recent improvements regarding macroscopic thermodynamic properties as well as microscopic point-defect properties. Furthermore we describe a new type of large-scale atomistic kinetic Monte Carlo (AKMC) approach driven by an artificial neural network (ANN) regression method to generate the local migration barrier for a defect accounting for the local chemistry around it. The results of the thermal annealing of the Fe-20Cr alloy modelled using this AKMC approach, parameterized by our newly developed potential, were found to be in very good agreement with experimental data. Furthermore the interaction of a 1/2 screw dislocation with Cr precipitates as obtained from the AKMC simulations was studied using the same potential. In summary, we critically discuss our current achievements, findings and outline issues to be addressed in the near future development.
Comparison of atomistic and elasticity approaches for carbon diffusion near line defects in α-iron
International Nuclear Information System (INIS)
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.
Energy Technology Data Exchange (ETDEWEB)
Gamez, L.; Gamez, B. [Instituto de Fusion, Universidad Politecnica de Madrid (Belgium); Caturla, M.J., E-mail: mj.caturla@ua.es [Departamento de Fisica Aplicada, Universidad de Alicante, Alicante E-03690 (Spain); Terentyev, D. [SCK-CEN, Mol (Belgium); Perlado, J.M. [Instituto de Fusion, Universidad Politecnica de Madrid (Belgium)
2011-07-15
Object Kinetic Monte Carlo models allow for the study of the evolution of the damage created by irradiation to time scales that are comparable to those achieved experimentally. Therefore, the essential Object Kinetic Monte Carlo parameters can be validated through comparison with experiments. However, this validation is not trivial since a large number of parameters is necessary, including migration energies of point defects and their clusters, binding energies of point defects in clusters, as well as the interaction radii. This is particularly cumbersome when describing an alloy, such as the Fe-Cr system, which is of interest for fusion energy applications. In this work we describe an Object Kinetic Monte Carlo model for Fe-Cr alloys in the dilute limit. The parameters used in the model come either from density functional theory calculations or from empirical interatomic potentials. This model is used to reproduce isochronal resistivity recovery experiments of electron irradiated dilute Fe-Cr alloys performed by Abe and Kuramoto. The comparison between the calculated results and the experiments reveal that an important parameter is the capture radius between substitutional Cr and self-interstitial Fe atoms. A parametric study is presented on the effect of the capture radius on the simulated recovery curves.
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.
International Nuclear Information System (INIS)
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
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.
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.
International Nuclear Information System (INIS)
In the present study, the mechanism of free radical production by light-reflective agents in sunscreens (TiO2, ZnO and ZrO2) 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 TiO2 (rutile and anatase), ZnO and ZrO2. • 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
Energy Technology Data Exchange (ETDEWEB)
Yang, Judith C. [University of Pittsburgh
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.
Moura, Alfredo de; Esteves, António
2013-01-01
This paper describes the simulation of the phenomenon of nucleation of the precipitate Al3Sc in an Aluminum Scandium alloy using the kinetic Monte Carlo (kMC) method and the density-based clustering with noise (DBSCAN) method to filter the simulation data. To conduct this task, kMC and DBSCAN algorithms were implemented in C language. The study covers a range of temperatures, concentrations, and dimensions, going from 573K to 873K, 0.25% to 5%, and 50x50x50 to 100x100x100. The Al3Sc precipita...
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An energy-dependent kinetic Monte Carlo approach was proposed to simulate the multilayer growth of BaTiO3 thin films via pulsed laser deposition, in which the four steps, such as the deposition of atoms, the diffusion of adatoms, the bonding of adatoms, and the surface migration of adatoms, were considered. Distinguishing with the traditional solid-on-solid (SOS) model, the adatom bonding and the overhanging of atoms, according to the perovskite structure, were specially adopted to describe the ferroelectric thin film growth. The activation energy was considered from the interactions between the ions, which were calculated by Born-Mayer-Huggins (BMH) potential. From the simulation the relative curves of the each layer coverage and roughness vs total coverage were obtained by varying the parameter values of the incident kinetic energy, laser repetition rate and mean deposition rate. The relationship between growth modes and the different parameters was also acquired.
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In this work, we present a comprehensive quasi-atomistic Object Kinetic Monte Carlo (OKMC) model for diffusion-mediated decomposition in binary alloys, which is applied to the particular case of phase nucleation and spinodal decomposition in the iron–chromium system. The model describes atomistically the defects driving diffusion, while following the evolution of alloy concentrations by tracking the number of alloy atoms in the elements of an uniform mesh. Input parameters are defect diffusivities, tracer diffusivity ratios, and mixing energies, and they have been calibrated according to reported experiments and ab-initio calculations. Simulations based on this model are able to reproduce both phase nucleation in the metastable composition region and spontaneous phase decomposition and coarsening within the spinodal composition region. The convergence into the correct thermodynamics has been shown by comparing the simulation results to theoretical predictions, while the time evolution has been validated with experimental data for different alloy compositions. The simulation approach has proven to be suitable for extended annealing times and for domain sizes up to hundreds of nanometers
Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers
Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter
2014-01-01
Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DM...
Geneste, Grégory; Bellaiche, L.; Kiat, Jean-Michel
2016-06-01
The radio-frequency dielectric response of the lead-free Ba (Zr0.5Ti0.5)O3 relaxor ferroelectric is simulated using a coarse-grained Hamiltonian. This concept, taken from real-space renormalization group theories, allows us to depict the collective behavior of correlated local modes gathered in blocks. Free-energy barriers for their thermally activated collective hopping are deduced from this ab initio-based approach, and used as input data for kinetic Monte Carlo simulations. The resulting numerical scheme allows us to simulate the dielectric response for external field frequencies ranging from kHz up to a few tens of MHz for the first time and to demonstrate, e.g., that local (electric or elastic) random fields lead to the dielectric relaxation in the radio-frequency range that has been observed in relaxors.
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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.
Li, Yun; Jiang, Hai; Lun, Zhiyuan; Wang, Yijiao; Huang, Peng; Hao, Hao; Du, Gang; Zhang, Xing; Liu, Xiaoyan
2016-04-01
Degradation behaviors in the high-k/metal gate stacks of nMOSFETs are investigated by three-dimensional (3D) kinetic Monte-Carlo (KMC) simulation with multiple trap coupling. Novel microscopic mechanisms are simultaneously considered in a compound system: (1) trapping/detrapping from/to substrate/gate; (2) trapping/detrapping to other traps; (3) trap generation and recombination. Interacting traps can contribute to random telegraph noise (RTN), bias temperature instability (BTI), and trap-assisted tunneling (TAT). Simulation results show that trap interaction induces higher probability and greater complexity in trapping/detrapping processes and greatly affects the characteristics of RTN and BTI. Different types of trap distribution cause largely different behaviors of RTN, BTI, and TAT. TAT currents caused by multiple trap coupling are sensitive to the gate voltage. Moreover, trap generation and recombination have great effects on the degradation of HfO2-based nMOSFETs under a large stress.
Energy Technology Data Exchange (ETDEWEB)
Wang, Tongyu [Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching (Germany); Reuter, Karsten, E-mail: karsten.reuter@ch.tum.de [Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching (Germany); SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory and Stanford University, 443 Via Ortega, Stanford, California 94035-4300 (United States)
2015-11-28
We present a density-functional theory based kinetic Monte Carlo study of CO oxidation at the (111) facet of RuO{sub 2}. We compare the detailed insight into elementary processes, steady-state surface coverages, and catalytic activity to equivalent published simulation data for the frequently studied RuO{sub 2}(110) facet. Qualitative differences are identified in virtually every aspect ranging from binding energetics over lateral interactions to the interplay of elementary processes at the different active sites. Nevertheless, particularly at technologically relevant elevated temperatures, near-ambient pressures and near-stoichiometric feeds both facets exhibit almost identical catalytic activity. These findings challenge the traditional definition of structure sensitivity based on macroscopically observable turnover frequencies and prompt scrutiny of the applicability of structure sensitivity classifications developed for metals to oxide catalysis.
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We present a density-functional theory based kinetic Monte Carlo study of CO oxidation at the (111) facet of RuO2. We compare the detailed insight into elementary processes, steady-state surface coverages, and catalytic activity to equivalent published simulation data for the frequently studied RuO2(110) facet. Qualitative differences are identified in virtually every aspect ranging from binding energetics over lateral interactions to the interplay of elementary processes at the different active sites. Nevertheless, particularly at technologically relevant elevated temperatures, near-ambient pressures and near-stoichiometric feeds both facets exhibit almost identical catalytic activity. These findings challenge the traditional definition of structure sensitivity based on macroscopically observable turnover frequencies and prompt scrutiny of the applicability of structure sensitivity classifications developed for metals to oxide catalysis
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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.
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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
Hong, Qi-Jun; Liu, Zhi-Pan
2010-10-01
It has been a goal consistently pursued by chemists to understand and control the catalytic process over composite materials. In order to provide deeper insight on complex interfacial catalysis at the experimental conditions, we performed an extensive analysis on CO 2 hydrogenation over a Cu/ZrO 2 model catalyst by employing density functional theory (DFT) calculations and kinetic Monte Carlo (kMC) simulations based on the continuous stirred tank model. The free energy profiles are determined for the reaction at the oxygen-rich Cu/m-ZrO 2 (2̅12) interface, where all interfacial Zr are six-coordinated since the interface accumulates oxidative species at the reaction conditions. We show that not only methanol but also CO are produced through the formate pathway dominantly, whilst the reverse-water-gas-shift (RWGS) channel has only a minor contribution. H 2CO is a key intermediate species in the reaction pathway, the hydrogenation of which dictates the high temperature of CO 2 hydrogenation. The kinetics simulation shows that the CO 2 conversion is 1.20%, the selectivity towards methanol is 68% at 500 K and the activation energies for methanol and CO formation are 0.79 and 1.79 eV, respectively. The secondary reactions due to the product readsorption lower the overall turnover frequency (TOF) but increase the selectivity towards methanol by 16%. We also show that kMC is a more reliable tool for simulating heterogeneous catalytic processes compared to the microkinetics approach.
Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics
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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.
Material fields in atomistics as pull-backs of spatial distributions
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
Montoya, M.; E. Saettone; Rojas, J.
2007-01-01
Mediante la simulación con el método Monte Carlo, fue estudiada la distribución de masas y energía cinética de los fragmentos de la fisión inducida por neutrones térmicos del 235U. Además de reproducir el ensanchamiento pronunciado en la desviación estándar de la distribución de la energía cinética de los fragmentos finales (¾e(m)) alrededor del número másico m = 109, nuestra simulación también produce un segundo ensanchamiento alrededor de m = 125, en concordancia con los datos expe...
Including Long-range Interactions in Atomistic Modelling of Diffusional Phase Changes
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Mason, D R; Rudd, R E; Sutton, A P
2005-08-25
Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Vacancy diffusion is modeled by comparing the energies of trial states, where the system is partially relaxed for each trial state. Only a limited precision is required for the energy of each trial state, determined by the value of k{sub B}T. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r{sup 3}, it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centered on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice. However on a flexible lattice vacancy trapping by Mg atoms in the ternary Al-Cu-Mg system makes clustering slower than the corresponding rigid lattice calculation.
Atomistic surface erosion and thin film growth modelled over realistic time scales
International Nuclear Information System (INIS)
We present results of atomistic modelling of surface growth and sputtering using a multi-time scale molecular dynamics-on-the-fly kinetic Monte Carlo scheme which allows simulations to be carried out over realistic experimental times. The method uses molecular dynamics to model the fast processes and then calculates the diffusion barriers for the slow processes on-the-fly, without any preconceptions about what transitions might occur. The method is applied to the growth of metal and oxide materials at impact energies typical for both vapour deposition and magnetron sputtering. The method can be used to explain growth processes, such as the filling of vacancies and the formation of stacking faults. By tuning the variable experimental parameters on the computer, a parameter set for optimum crystalline growth can be determined. The method can also be used to model sputtering where the particle interactions with the surface occur at a higher energy. It is shown how a steady state can arise in which interstitial clusters are continuously being formed below the surface during an atom impact event which also recombine or diffuse to the surface between impact events. For fcc metals the near surface region remains basically crystalline during the erosion process with a pitted topography which soon attains a steady state roughness.
Kinetics of niobium carbide precipitation in ferrite
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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
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A three-dimensional kinetic Monte Carlo model (kMC) is proposed for the simulation of deposition and evolution of surface structures at elevated temperatures. The code includes deposition of one given type of atom and main thermally driven events such as surface diffusion, diffusion along island edges, detachment from islands, and movement of atoms on deposited surfaces. It can be used not only for simulating nucleation and growth of thin films but also for simulating time evolution of a given structure when annealed. It is a specific event kMC code, and the rates of the events are used as inputs. It allows the simulation of thousands of incident particles and the simulation of a system at high temperature without suffering large computational time. The code runs on a PC and is freely available. Results of modeling various situations like atomic deposition (Pd on SiO2), islands coalescence (Cu on Cu), Ostwald and inverse Ostwald ripening (Co/C and Co/SiO2) were tested against existing experimental and theoretical data and show a good agreement for all those cases.
Behera, Rakesh K.; Watanabe, Taku; Andersson, David A.; Uberuaga, Blas P.; Deo, Chaitanya S.
2016-04-01
Oxygen interstitials in UO2+x significantly affect the thermophysical properties and microstructural evolution of the oxide nuclear fuel. In hyperstoichiometric Urania (UO2+x), these oxygen interstitials form different types of defect clusters, which have different migration behavior. In this study we have used kinetic Monte Carlo (kMC) to evaluate diffusivities of oxygen interstitials accounting for mono- and di-interstitial clusters. Our results indicate that the predicted diffusivities increase significantly at higher non-stoichiometry (x > 0.01) for di-interstitial clusters compared to a mono-interstitial only model. The diffusivities calculated at higher temperatures compare better with experimental values than at lower temperatures (analysis to estimate the effect of input di-interstitial binding energies on the predicted diffusivities and activation energies. While this article only discusses mono- and di-interstitials in evaluating oxygen diffusion response in UO2+x, future improvements to the model will primarily focus on including energetic definitions of larger stable interstitial clusters reported in the literature. The addition of larger clusters to the kMC model is expected to improve the comparison of oxygen transport in UO2+x with experiment.
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In this work we investigate the formation of Ge clusters on stepped Si substrate at elevated temperatures (≤ 300 °C) with the help of the kinetic Monte-Carlo (kMC) method. The modeling was performed for the case of low surface coverage in order to examine the process of Ge cluster growth at early stages. The temperature dependence of the development of Ge structures was explored and the transition from the growth in the middle of the steps to the growth at step edges was traced. Modeling shows that the formation of Ge clusters at the step edges begins at temperatures higher than 60 °C, whereas at temperatures below 60 °C clusters grow at the middle of the steps, and at 300 °C all Ge atoms are gathered at the bottom of the Si step edges. Results of the kMC simulations were compared to experiments and analytical evaluations. A cluster formation diagram linking deposition rate, terrace width, and transition temperature between different cluster formation modes is presented. - Highlights: • Modeling of the development of Ge structures at stepped Si substrate was performed. • It was shown that morphology of Ge clusters depends on the temperature. • The temperature ranges for each type of morphology were found. • A predictive cluster formation diagram is provided
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Hadron-therapy is a cancer treatment method based on the use of heavy charged particles. The physical characteristics of these particles allow more precise targeting of tumours and offer higher biological efficiency than photons and electrons. This thesis addresses the problem of modelling the biological effects induced by such particles. One part of this work is devoted to the analysis of the Monte-Carlo simulation tool-kit 'Geant4' used to simulate the physical stage of the particle interactions with the biological medium. We evaluated the ability of 'Geant4' to simulate the microscopic distribution of energy deposition produced by charged particles and we compared these results with those of another simulation code dedicated to radiobiological applications. The other part of the work is dedicated to the study of two radiobiological models that are the LEM (Local Effect Model) based on an amorphous track structure approach and the MKM (Microdosimetric Kinetic Model) based on microdosimetric approach. A theoretical analysis of both models and a comparison of their concepts are presented. Then we focused on a detailed analysis of the microdosimetric model 'MKM'. Finally, we applied the MKM to reproduce the experimental results obtained at GANIL by irradiation of two tumour cell lines (cell line SCC61 and SQ20B) of different radiosensitivity with carbon and argon ions. (author)
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Ammonia (NH3) nitridation on an Fe surface was studied by combining density functional theory (DFT) and kinetic Monte Carlo (kMC) calculations. A DFT calculation was performed to obtain the energy barriers (Eb) of the relevant elementary processes. The full mechanism of the exact reaction path was divided into five steps (adsorption, dissociation, surface migration, penetration, and diffusion) on an Fe (100) surface pre-covered with nitrogen. The energy barrier (Eb) depended on the N surface coverage. The DFT results were subsequently employed as a database for the kMC simulations. We then evaluated the NH3 nitridation rate on the N pre-covered Fe surface. To determine the conditions necessary for a rapid NH3 nitridation rate, the eight reaction events were considered in the kMC simulations: adsorption, desorption, dissociation, reverse dissociation, surface migration, penetration, reverse penetration, and diffusion. This study provides a real-time-scale simulation of NH3 nitridation influenced by nitrogen surface coverage that allowed us to theoretically determine a nitrogen coverage (0.56 ML) suitable for rapid NH3 nitridation. In this way, we were able to reveal the coverage dependence of the nitridation reaction using the combined DFT and kMC simulations
Islamuddin Shah, Syed; Nandipati, Giridhar; Kara, Abdelkader; Rahman, Talat S.
2012-02-01
We have applied a modified Self-Learning Kinetic Monte Carlo (SLKMC) method [1] to examine the self-diffusion of small Ag and Ni islands, containing up to 10 atom, on the (111) surface of the respective metal. The pattern recognition scheme in this new SLKMC method allows occupancy of the fcc, hcp and top sites on the fcc(111) surface and employs them to identify the local neighborhood around a central atom. Molecular static calculations with semi empirical interatomic potential and reliable techniques for saddle point search revealed several new diffusion mechanisms that contribute to the diffusion of small islands. For comparison we have also evaluated the diffusion characteristics of Cu clusters on Cu(111) and compared results with previous findings [2]. Our results show a linear increase in effective energy barriers scaling almost as 0.043, 0.051 and 0.064 eV/atom for the Cu/Cu(111), Ag/Ag(111), and Ni/Ni(111) systems, respectively. For all three systems, diffusion of small islands proceeds mainly through concerted motion, although several multiple and single atom processes also contribute. [1] Oleg Trushin et al. Phys. Rev. B 72, 115401 (2005) [2] Altaf Karim et al. Phys. Rev. B 73, 165411 (2006)
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Duplex stainless steels (DSS) are largely used for industrial purposes due to their good corrosion resistance, mechanical properties and also due to their ability to be cast. They are notably used as cast elbows in primary circuits of pressurized water reactors. However these steels are subject to ageing at service temperature (285 C degrees - 323 C degrees). 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
Atomistic Simulations of Nanotube Fracture
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.
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. PMID:26952143
Mohn, Chris E.; Kob, Walter
2008-01-01
We present a genetic algorithm for the atomistic design and global optimisation of substitutionally disordered bulk materials and surfaces. Premature convergence which hamper conventional genetic algorithms due to problems with synchronisation is avoided using a symmetry adapted crossover. The algorithm outperforms previously reported Monte Carlo and genetic algorithm simulations for finding low energy minima of two simple alloy models without the need for any redesign.
Annealing kinetics of single displacement cascades in Ni: An atomic scale computer simulation
International Nuclear Information System (INIS)
In order to describe the long term evolution of the defects produced by a displacement cascade, Molecular dynamics (MD) and Kinetic Monte Carlo (KMC) methods are employed. Using an empirical Ni interatomic potential in MD, the damage resulting from primary knock-on atom (PKA) energies up to 30 keV has been simulated. The annealing kinetics and the fraction of freely migrating defects (FMD) are determined for each single displacement cascade, by a KMC code which is based on a set of parameters extracted mainly from MD simulations. It allows an atomistic study of the evolution of the initial damage over a time scale up to 100s and the determination of the fraction of the defects that escape the KMC box, compared to those obtained by MD, as function of temperature and PKA energy. It has been found that this fraction depends strongly on the temperature but reaches a saturation value above stage V
Atomistic stimulation of defective oxides
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...
Tan, R. P.; Carrey, J.; Respaud, M.
2014-12-01
Understanding the influence of dipolar interactions in magnetic hyperthermia experiments is of crucial importance for fine optimization of nanoparticle (NP) heating power. In this study we use a kinetic Monte Carlo algorithm to calculate hysteresis loops that correctly account for both time and temperature. This algorithm is shown to correctly reproduce the high-frequency hysteresis loop of both superparamagnetic and ferromagnetic NPs without any ad hoc or artificial parameters. The algorithm is easily parallelizable with a good speed-up behavior, which considerably decreases the calculation time on several processors and enables the study of assemblies of several thousands of NPs. The specific absorption rate (SAR) of magnetic NPs dispersed inside spherical lysosomes is studied as a function of several key parameters: volume concentration, applied magnetic field, lysosome size, NP diameter, and anisotropy. The influence of these parameters is illustrated and comprehensively explained. In summary, magnetic interactions increase the coercive field, saturation field, and hysteresis area of major loops. However, for small amplitude magnetic fields such as those used in magnetic hyperthermia, the heating power as a function of concentration can increase, decrease, or display a bell shape, depending on the relationship between the applied magnetic field and the coercive/saturation fields of the NPs. The hysteresis area is found to be well correlated with the parallel or antiparallel nature of the dipolar field acting on each particle. The heating power of a given NP is strongly influenced by a local concentration involving approximately 20 neighbors. Because this local concentration strongly decreases upon approaching the surface, the heating power increases or decreases in the vicinity of the lysosome membrane. The amplitude of variation reaches more than one order of magnitude in certain conditions. This transition occurs on a thickness corresponding to approximately
Atomistic simulation of static magnetic properties of bit patterned media
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.
International Nuclear Information System (INIS)
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
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
Atomistic simulations of Au-silica nanocomposite film growth
Khan, Saif A.; Heinig, K.-H.; Avasthi, D. K.
2011-05-01
The growth of Au-silica nanocomposite film is simulated in the framework of kinetic three dimensional lattice Monte Carlo simulations considering the basic phenomena in the deposition process. In case of co-sputter deposition, the growth kinetics of nanoparticles has been studied taking into consideration the effect of the energetic sputtered species reaching the surface of the film during deposition. Formation of Au nanorod like structures are predicted under certain growth conditions particularly when surface diffusion assisted phase separation plays the dominant role and bulk kinetics is frozen. The observed dependence of the Au nanoparticle size on Au/silica ratio is in agreement with the experimental results.
Energy Technology Data Exchange (ETDEWEB)
Pryor, Craig E., E-mail: craig-pryor@uiowa.edu [Department of Physics and Astronomy, University of Iowa, Iowa City, Iowa 52242 (United States); Pistol, M.-E., E-mail: mats-erik.pistol@ftf.lth.se [NanoLund and Solid State Physics, Lund University, P.O. Box 118, 221 00 Lund (Sweden)
2015-12-14
Pseudopotentials, tight-binding models, and k ⋅ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ⋅ p theory. In its usual formulation, k ⋅ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ⋅ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp{sup 3} tight-binding model. We can thus directly derive the parameters in the sp{sup 3} tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III–V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ⋅ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ⋅ p models to be combined in the same system.
International Nuclear Information System (INIS)
Pseudopotentials, tight-binding models, and k ⋅ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ⋅ p theory. In its usual formulation, k ⋅ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ⋅ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp3 tight-binding model. We can thus directly derive the parameters in the sp3 tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III–V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ⋅ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ⋅ p models to be combined in the same system
Atomistic modeling of dropwise condensation
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.
Atomistic computer simulations a practical guide
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
International Nuclear Information System (INIS)
A kinetic gelation model that incorporates the kinetics of free radical homo polymerization is implemented to determine the effects of kinetics on polymerization statistics and microstructures. The simulation is performed on a simple cubic lattice that has 100 sites in each direction. A new algorithm for random selecting of the next step in a self-avoiding random walk and very efficient mechanisms of mobility of components are introduced to improve the generality of the predictions by removing commonly accruing deficiencies due to early trapping of radicals. A first order kinetics is considered for decomposition of initiator that enables us to consider the effect of temperature on polymerization reaction. Better understanding of microstructural evolution during polymerization and providing a framework to produce a realistic system of highly packed random chains within polymer network are among the benefits of model
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
Protein folding kinetics and thermodynamics from atomistic simulation
DEFF Research Database (Denmark)
Piana, Stefano; Lindorff-Larsen, Kresten; Shaw, David E.
2012-01-01
Advances in simulation techniques and computing hardware have created a substantial overlap between the timescales accessible to atomic-level simulations and those on which the fastest-folding proteins fold. Here we demonstrate, using simulations of four variants of the human villin headpiece, how......¦-values, and folding pathways provides support for the notion that a norleucine double mutant of villin folds five times faster than the wild-type sequence, but following a slightly different pathway. This work showcases how computer simulation has now developed into a mature tool for the quantitative computational...
Czech Academy of Sciences Publication Activity Database
Tarasenko, Alexander; Jastrabík, Lubomír
Berlin Heidelberg : Springer-Verlag, 2012 - (Delgado, J.; Barbosa de Lima, A.; Vázquez da Silva, M.), s. 63-83 ISBN 978-3-642-30531-3. - (Advanced Structured Materials. 27) R&D Projects: GA TA ČR TA01010517; GA ČR GAP108/12/1941 Institutional research plan: CEZ:AV0Z10100522 Keywords : zeolites * lattice-gas model * Monte Carlo Subject RIV: BM - Solid Matter Physics ; Magnetism
International Nuclear Information System (INIS)
The Cupidon 2 CODE aims to calculate the mono-kinetic neutrons flux in an assembly of cubes cavities jointed by rectangular holes. This report is a partial description of the code Cupidon 2 which explains the calculation procedure: data entry, code limits...). (A.L.B.)
Thomas, R S; Yang, R S; Morgan, D G; Moorman, M P; Kermani, H R; Sloane, R A; O'Connor, R W; Adkins, B; Gargas, M L; Andersen, M E
1996-01-01
During a 2-year chronic inhalation study on methylene chloride (2000 or 0 ppm; 6 hr/day, 5 days/week), gas-uptake pharmacokinetic studies and tissue partition coefficient determinations were conducted on female B6C3F1, mice after 1 day, 1 month, 1 year, and 2 years of exposure. Using physiologically based pharmacokinetic (PBPK) modeling coupled with Monte Carlo simulation and bootstrap resampling for data analyses, a significant induction in the mixed function oxidase (MFO) rate constant (Vma...
Atomistic spin dynamics and surface magnons
International Nuclear Information System (INIS)
Atomistic spin dynamics simulations have evolved to become a powerful and versatile tool for simulating dynamic properties of magnetic materials. It has a wide range of applications, for instance switching of magnetic states in bulk and nano-magnets, dynamics of topological magnets, such as skyrmions and vortices and domain wall motion. In this review, after a brief summary of the existing investigation tools for the study of magnons, we focus on calculations of spin-wave excitations in low-dimensional magnets and the effect of relativistic and temperature effects in such structures. In general, we find a good agreement between our results and the experimental values. For material specific studies, the atomistic spin dynamics is combined with electronic structure calculations within the density functional theory from which the required parameters are calculated, such as magnetic exchange interactions, magnetocrystalline anisotropy, and Dzyaloshinskii–Moriya vectors. (topical review)
Quantum corrections to the `atomistic' MOSFET simulation
Asenov, A.
2000-01-01
In this paper we study the influence of the quantum effects in the inversion layer on the parameter fluctuation in decanano MOSFETs. The quantum mechanical effects are incorporated in our previously published 3D 'atomistic' simulation approach using a full 3D implementation of the density gradient formalism. This results in a consistent, fully 3D, quantum mechanical picture which incorporates the vertical inversion layer quantization, lateral confinement effects associated with the current fi...
Diffusive-to-ballistic transition in grain boundary motion studied by atomistic simulations
International Nuclear Information System (INIS)
An adapted simulation method is used to systematically study grain boundary motion at velocities and driving forces across more than five orders of magnitude. This analysis reveals that grain boundary migration can occur in two modes, depending upon the temperature (T) and applied driving force (P). At low P and T, grain boundary motion is diffusional, exhibiting the kinetics of a thermally activated system controlled by grain boundary self-diffusion. At high P and T, grain boundary migration exhibits the characteristic kinetic scaling behavior of a ballistic process. A rather broad transition range in both P and T lies between the regimes of diffusive and ballistic grain boundary motion, and is charted here in detail. The recognition and delineation of these two distinct modes of grain boundary migration also leads to the suggestion that many prior atomistic simulations might have probed a different kinetic regime of grain boundary motion (ballistic) as compared to that revealed in most experimental studies (diffusional).
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...... stability of screw dislocation dipoles is discussed. We show that the presence of jogs will strongly influence cross slip barriers and dipole stability. We furthermore present some new results on jogged edge dislocations and edge dislocation dipoles. The jogs are found to be extended, and simulations of...
Monte Carlo Calculation as an Aid to Teaching Solid-State Diffusion.
Murch, G. E.
1979-01-01
A simple Monte Carlo method is used to simulate an atomistic model of solid-state diffusion. This approach illustrates some of the principles of diffusion and in particular verifies a solution to Fick's second law. The role and calculation of the diffusion correlation factor is also discussed. (Author/BB)
Monte Carlo Demonstration of Solid-State Diffusion in an Electric Field.
Murch, G. E.
1979-01-01
Describes the phenomenological and microscopic aspects of solid-state diffusion in an electric field and presents a Monte Carlo method which is used to stimulate an atomistic model of diffusion in an electric field. The Nernst-Einstein relation is also discussed. (HM)
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.
Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides
International Nuclear Information System (INIS)
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
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
An atomistic vision of the Mass Action Law: Prediction of carbon/oxygen defects in silicon
International Nuclear Information System (INIS)
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
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.
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.
Multi-scale modelling of ions in solution: from atomistic descriptions to chemical engineering
International Nuclear Information System (INIS)
Ions in solution play a fundamental role in many physical, chemical, and biological processes. The PUREX process used in the nuclear industry to the treatment of spent nuclear fuels is considered as an example. For industrial applications these systems are usually described using simple analytical models which are fitted to reproduce the available experimental data. In this work, we propose a multi-scale coarse graining procedure to derive such models from atomistic descriptions. First, parameters for classical force-fields of ions in solution are extracted from ab-initio calculations. Effective (McMillan-Mayer) ion-ion potentials are then derived from radial distribution functions measured in classical molecular dynamics simulations, allowing us to define an implicit solvent model of electrolytes. Finally, perturbation calculations are performed to define the best possible representation for these systems, in terms of charged hard-sphere models. Our final model is analytical and contains no free 'fitting' parameters. It shows good agreement with the exact results obtained from Monte-Carlo simulations for the thermodynamic and structural properties. Development of a similar model for the electrolyte viscosity, from information derived from atomistic descriptions, is also introduced. (author)
Kolb, Brian; Zhao, Bin; Li, Jun; Jiang, Bin; Guo, Hua
2016-06-14
The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H2 → H2 + H, H + H2O → H2 + OH, and H + CH4 → H2 + CH3. A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggest this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved. PMID:27305992
Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins
Savol, Andrej J.; Chennubhotla, Chakra S.
2014-01-01
Experiments and atomistic simulations of polypeptides have revealed structural intermediates that promote or inhibit conformational transitions to the native state during folding. We invoke a concept of “kinetic frustration” to quantify the prevalence and impact of these behaviors on folding rates within a large set of atomistic simulation data for 10 fast-folding proteins, where each protein’s conformational space is represented as a Markov state model of conformational transitions. Our grap...
International Nuclear Information System (INIS)
1 - Description of problem or function: The PREP/KITT computer program package obtains system reliability information from a system fault tree. The PREP program finds the minimal cut sets and/or the minimal path sets of the system fault tree. (A minimal cut set is a smallest set of components such that if all the components are simultaneously failed the system is failed. A minimal path set is a smallest set of components such that if all of the components are simultaneously functioning the system is functioning.) The KITT programs determine reliability information for the components of each minimal cut or path set, for each minimal cut or path set, and for the system. Exact, time-dependent reliability information is determined for each component and for each minimal cut set or path set. For the system, reliability results are obtained by upper bound approximations or by a bracketing procedure in which various upper and lower bounds may be obtained as close to one another as desired. The KITT programs can handle independent components which are non-repairable or which have a constant repair time. Any assortment of non-repairable components and components having constant repair times can be considered. Any inhibit conditions having constant probabilities of occurrence can be handled. The failure intensity of each component is assumed to be constant with respect to time. The KITT2 program can also handle components which during different time intervals, called phases, may have different reliability properties. 2 - Method of solution: The PREP program obtains minimal cut sets by either direct deterministic testing or by an efficient Monte Carlo algorithm. The minimal path sets are obtained using the Monte Carlo algorithm. The reliability information is obtained by the KITT programs from numerical solution of the simple integral balance equations of kinetic tree theory. 3 - Restrictions on the complexity of the problem: The PREP program will obtain the minimal cut and
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.
Atomistic simulation of damage accumulation and amorphization in Ge
International Nuclear Information System (INIS)
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 × 1022 cm−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
Free energy of steps using atomistic simulations
Freitas, Rodrigo; Frolov, Timofey; Asta, Mark
The properties of solid-liquid interfaces are known to play critical roles in solidification processes. Particularly special importance is given to thermodynamic quantities that describe the equilibrium state of these surfaces. For example, on the solid-liquid-vapor heteroepitaxial growth of semiconductor nanowires the crystal nucleation process on the faceted solid-liquid interface is influenced by the solid-liquid and vapor-solid interfacial free energies, and also by the free energies of associated steps at these faceted interfaces. Crystal-growth theories and mesoscale simulation methods depend on quantitative information about these properties, which are often poorly characterized from experimental measurements. In this work we propose an extension of the capillary fluctuation method for calculation of the free energy of steps on faceted crystal surfaces. From equilibrium atomistic simulations of steps on (111) surfaces of Copper we computed accurately the step free energy for different step orientations. We show that the step free energy remains finite at all temperature up to the melting point and that the results obtained agree with the more well established method of thermodynamic integration if finite size effects are taken into account. The research of RF and MA at UC Berkeley were supported by the US National Science Foundation (Grant No. DMR-1105409). TF acknowledges support through a postdoctoral fellowship from the Miller Institute for Basic Research in Science.
Robust atomistic calculation of dislocation line tension
Szajewski, B. A.; Pavia, F.; Curtin, W. A.
2015-12-01
The line tension Γ of a dislocation is an important and fundamental property ubiquitous to continuum scale models of metal plasticity. However, the precise value of Γ in a given material has proven difficult to assess, with literature values encompassing a wide range. Here results from a multiscale simulation and robust analysis of the dislocation line tension, for dislocation bow-out between pinning points, are presented for two widely-used interatomic potentials for Al. A central part of the analysis involves an effective Peierls stress applicable to curved dislocation structures that markedly differs from that of perfectly straight dislocations but is required to describe the bow-out both in loading and unloading. The line tensions for the two interatomic potentials are similar and provide robust numerical values for Al. Most importantly, the atomic results show notable differences with singular anisotropic elastic dislocation theory in that (i) the coefficient of the \\text{ln}(L) scaling with dislocation length L differs and (ii) the ratio of screw to edge line tension is smaller than predicted by anisotropic elasticity. These differences are attributed to local dislocation core interactions that remain beyond the scope of elasticity theory. The many differing literature values for Γ are attributed to various approximations and inaccuracies in previous approaches. The results here indicate that continuum line dislocation models, based on elasticity theory and various core-cut-off assumptions, may be fundamentally unable to reproduce full atomistic results, thus hampering the detailed predictive ability of such continuum models.
Atomistic simulations of caloric effects in ferroelectrics
Lisenkov, Sergey; Ponomareva, Inna
2013-03-01
The materials that exhibit large caloric effects have emerged as promising candidates for solid-state refrigeration which is an energy-efficient and environmentally friendly alternative to the conventional refrigeration technology. However, despite recent ground breaking discoveries of giant caloric effects in some materials they appear to remain one of nature's rarities. Here we use atomistic simulations to study electrocaloric and elastocaloric effects in Ba0.5Sr0.5TiO3 and PbTiO3 ferroelectrics. Our study reveals the intrinsic features of such caloric effects in ferroelectrics and their potential to exhibit giant caloric effects. Some of the findings include the coexistence of negative and positive electrocaloric effects in one material and an unusual field-driven transition between them as well as the coexistence of multiple giant caloric effects in Ba0.5Sr0.5TiO3 alloys. These findings could potentially lead to new paradigms for cooling devices. This work is partially supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0005245.
Atomistic mechanisms of fatigue in nanotwinned metals
International Nuclear Information System (INIS)
We investigate the fatigue behavior of nanotwinned Cu using a combination of molecular statics and molecular dynamics simulations. The presence of nanoscale twins is found to enhance fatigue crack growth resistance. For the twin-free nanocrystalline samples, the fatigue crack propagates by linking the nanovoids that are formed ahead of the crack tip. In the case of the nanotwinned samples, however, it advances as the crack tip alternately blunts and re-sharpens due to dislocation emission and slip. Both detwinning and crack closure are observed in the path of the fatigue crack in nanotwinned samples with a high density of twin boundaries. As the twin number per grain (quantified by the ratio of the mean grain size to the twin boundary spacing d/λ) increases, detwinning increases the dissipated energy of fatigue cracking, leading to enhanced fatigue resistance. The atomistic simulations show that fatigue crack growth in nanotwinned Cu conforms to Paris’ law. In conjunction with the experimental results, we obtain a quantitative estimation of the Paris’ law exponent (∼4.0), which is in agreement with the theoretical predictions from the damage accumulation model
The Moment Guided Monte Carlo Method
Degond, Pierre; Dimarco, Giacomo; Pareschi, Lorenzo
2009-01-01
In this work we propose a new approach for the numerical simulation of kinetic equations through Monte Carlo schemes. We introduce a new technique which permits to reduce the variance of particle methods through a matching with a set of suitable macroscopic moment equations. In order to guarantee that the moment equations provide the correct solutions, they are coupled to the kinetic equation through a non equilibrium term. The basic idea, on which the method relies, consists in guiding the p...
International Nuclear Information System (INIS)
This paper outlines an atomistic-level framework for modeling the non-equilibrium behavior of chemically reactive systems. The framework called steepest- entropy-ascent quantum thermodynamics (SEA-QT) is based on the paradigm of intrinsic quantum thermodynamic (IQT), which is a theory that unifies quantum mechanics and thermodynamics into a single discipline with wide applications to the study of non-equilibrium phenomena at the atomistic level. SEA-QT is a novel approach for describing the state of chemically reactive systems as well as the kinetic and dynamic features of the reaction process without any assumptions of near-equilibrium states or weak-interactions with a reservoir or bath. Entropy generation is the basis of the dissipation which takes place internal to the system and is, thus, the driving force of the chemical reaction(s). The SEA-QT non-equilibrium model is able to provide detailed information during the reaction process, providing a picture of the changes occurring in key thermodynamic properties (e.g., the instantaneous species concentrations, entropy and entropy generation, reaction coordinate, chemical affinities, reaction rate, etc). As an illustration, the SEA-QT framework is applied to an atomistic-level chemically reactive system governed by the reaction mechanism F + H2 ↔ FH + H
A comparison of finite element and atomistic modelling of fracture
International Nuclear Information System (INIS)
Are the cohesive laws of interfaces sufficient for modelling fracture in polycrystals using the cohesive zone model? We examine this question by comparing a fully atomistic simulation of a silicon polycrystal with a finite element simulation with a similar overall geometry. The cohesive laws used in the finite element simulation are measured atomistically. We describe in detail how to convert the output of atomistic grain boundary fracture simulations into the piecewise linear form needed by a cohesive zone model. We discuss the effects of grain boundary microparameters (the choice of section of the interface, the translations of the grains relative to one another and the cutting plane of each lattice orientation) on the cohesive laws and polycrystal fracture. We find that the atomistic simulations fracture at lower levels of external stress, indicating that the initiation of fracture in the atomistic simulations is likely dominated by irregular atomic structures at external faces, internal edges, corners and junctions of grains. Thus, the cohesive properties of interfaces alone are not likely to be sufficient for modelling the fracture of polycrystals using continuum methods
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.
Atomistic Method Applied to Computational Modeling of Surface Alloys
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
Atomistic Modeling of the U-Zr System
International Nuclear Information System (INIS)
Atomistic modeling using the BFS method for alloys and ab initio based parameters is proposed for the study of fundamental properties of U-Zr metallic nuclear fuels. Due to its basic atomistic nature and the universal character of the parametrization, the approach can be used for diverse problems such as the interaction between fuel and cladding and temperature gradient fuel constituent redistribution. In the first case, preliminary results for the formation of an interaction layer using large scale simulations are presented. For the second case, a mean field formalism is introduced in order to determine concentration profiles for arbitrary changes in temperature in the radial direction. (author)
An object oriented Python interface for atomistic simulations
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.
Atomistic calculation of the thermoelectric properties of Si nanowires
Bejenari, Igor; Kratzer, Peter
2014-01-01
The thermoelectric properties of 1.6 nm-thick Si square nanowires with [100] crystalline orientation are calculated over a wide temperature range from 0 K to 1000 K, taking into account atomistic electron-phonon interaction. In our model, the [010] and [001] facets are passivated by hydrogen and there are Si-Si dimers on the nanowire surface. The electronic structure was calculated by using the sp^3 spin-orbit-coupled atomistic second-nearest-neighbor tight-binding model. The phonon dispersio...
Hierarchical approach to 'atomistic' 3-D MOSFET simulation
Asenov, A.; Brown, A. R.; J. H. Davies; S Saini
1999-01-01
We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1-Î¼m MOSFETs. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have de...
The Moment Guided Monte Carlo Method
Degond, Pierre; Pareschi, Lorenzo
2009-01-01
In this work we propose a new approach for the numerical simulation of kinetic equations through Monte Carlo schemes. We introduce a new technique which permits to reduce the variance of particle methods through a matching with a set of suitable macroscopic moment equations. In order to guarantee that the moment equations provide the correct solutions, they are coupled to the kinetic equation through a non equilibrium term. The basic idea, on which the method relies, consists in guiding the particle positions and velocities through moment equations so that the concurrent solution of the moment and kinetic models furnishes the same macroscopic quantities.
Nanostructured surfaces described by atomistic simulation methods
International Nuclear Information System (INIS)
Three separate simulation techniques have been applied to study different problems involving nanostructured surfaces. In the first investigation the bonding of fullerene molecules on silicon and Ag adatoms and dimers on graphite are investigated using the PLATO density functional code. It is shown that in the first case there are strong covalent bonds formed whereas in the latter there are relatively weak bonds with small energy barriers between adjacent sites. Classical MD is used to show how energetic (∼ keV) Ag clusters can be pinned on or implanted into a graphite surface and that the pinning thresholds and implantation depths agree with experiment. Finally a Monte Carlo model for cluster motion over a surface is described and related to pattern formation in the early stages of thin film growth
Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics.
Amani, Ehsan; Movahed, Saeid
2016-06-01
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. PMID:27155300
Adaptive resolution simulation of an atomistic protein in MARTINI water
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
Bridging the Macroscopic and Atomistic Descriptions of the Electrocaloric Effect
Ponomareva, I.; Lisenkov, S.
2012-04-01
First-principles-based simulations are used to simulate the electrocaloric effect (ECE) in Ba0.5Sr0.5TiO3 alloys. In analogy with experimental studies we simulate the effect directly and indirectly (via the use of Maxwell thermodynamics). Both direct and indirect simulations utilize the same atomistic framework that allows us to compare them in a systematic way and with an atomistic precision for the very first time. Such precise comparison allows us to provide a bridge between the atomistic and macroscopic descriptions of the ECE and identify the factors that may critically compromise or even destroy their equivalence. Our computational data reveal the intrinsic features of ECE in ferroelectrics with multiple ferroelectric transitions and confirm the potential of these materials to exhibit giant electrocaloric response. The coexistence of negative and positive ECE in one material as well as an unusual field-driven transition between them is predicted, explained at an atomistic level, and proposed as a potential way to enhance the electrocaloric efficiency.
Definition and detection of contact in atomistic simulations
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,
Using atomistic simulations to model cadmium telluride thin film growth
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.
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.
Long-time atomistic simulations with the Parallel Replica Dynamics method
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.
Cashman, Derek J; Bhatt, Divesh; Zuckerman, Daniel M
2009-01-01
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale interdomain movements that contribute to the receptor's mechanism of action, as well as smaller scale motions, using two different computational methods. We employ extremely fast, "semi-atomistic" Library-Based Monte Carlo (LBMC) simulations, which include all backbone atoms but "implicit" side chains. Our results were compared with previous experiments and an all-atom Langevin dynamics simulation. Both LBMC and Langevin dynamics simulations were performed using both the apo and glucose-bound form of the protein, with LBMC exhibiting significantly larger fluctuations. The LBMC simulations are also in general agreement with the disulfide trapping experiments of Careaga & Falke (JMB, 1992; Biophys. J., 1992), which indicate that distant residues in the crystal structure (i...
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.
Atomistic modeling of carbon Cottrell atmospheres in bcc iron
International Nuclear Information System (INIS)
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.
Atomistic modelling of radiation effects: Towards dynamics of exciton relaxation
Shluger, A. L.; Gavartin, J. L.; Szymanski, M. A.; Stoneham, A. M.
2000-01-01
This brief review is focused on recent results of atomistic modelling and simulation of exciton related processes in ionic materials. We present an analysis of thermal fluctuations of the electrostatic potential in cubic ionic crystals and their relation to formation of a tail in the electron density of states and localisation of electronic states. Then the possible 'fast' mechanism of formation of F-H pairs in KBr as a result of decomposition of relaxing excitons is discussed. We briefly des...
Redox reactions with empirical potentials: Atomistic battery discharge simulations
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 ...
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
Rapaport, D C
2009-01-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Structure identification methods for atomistic simulations of crystalline materials
Stukowski, Alexander
2012-01-01
We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as Common Neighbor Analysis, Centrosymmetry Analysis, Bond Angle Analysis, Bond Order Analysis, and Voronoi Analysis. In addition we propose a simple extension to the Common Neighbor Analysis method that makes it suitable for multi-phase systems...
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
Rapaport, D. C.
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
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...... dislocation is determined. The breakdown of linear elasticity theory for small splitting widths is studied. [S0031-9007(97)04444-X]....
Impacts of Atomistic Coating on Thermal Conductivity of Germanium Nanowires
Chen, Jie; Zhang, Gang; Li, Baowen
2012-01-01
By using non-equilibrium molecular dynamics simulations, we demonstrated that thermal conductivity of Germanium nanowires can be reduced more than 25% at room temperature by atomistic coating. There is a critical coating thickness beyond which thermal conductivity of the coated nanowire is larger than that of the host nanowire. The diameter dependent critical coating thickness and minimum thermal conductivity are explored. Moreover, we found that interface roughness can induce further reducti...
Kinetic Modeling of Divertor Plasma
Ishiguro, Seiji; Hasegawa, Hiroki; Pianpanit, Theerasarn
2015-11-01
Particle-in-Cell (PIC) simulation with the Monte Carlo collisions and the cumulative scattering angle coulomb collision can present kinetic dynamics of divertor plasmas. We are developing two types of PIC codes. The first one is the three dimensional bounded PIC code where three dimensional kinetic dynamics of blob is studied and current flow structures related to sheath formation are unveiled. The second one is the one spatial three velocity space dimensional (1D3V) PIC code with the Monte Carlo collisions where formation of detach plasma is studied. First target of our research is to construct self-consistent full kinetic simulation modeling of the linear divertor simulation experiments. This work is performed with the support and under the auspices of NIFS Collaboration Research program (NIFS15KNSS059, NIFS14KNXN279, and NIFS13KNSS038) and the Research Cooperation Program on Hierarchy and Holism in Natural Science at NINS.
Wu, C. -J.; Chou, C. -Y.; Han, C. -N.; Chiang, K.-N.
2006-01-01
This paper the utilizes atomistic-continuum mechanics (ACM) to investigate the mechanical properties of single-walled carbon nanotubes (SWCNTs). By establishing a linkage between structural mechanics and molecular mechanics, not only the Young's moduli could be obtained but also the modal analysis could be achieved. In addition, according to atomistic-continuum mechanics and finite element method, an effective atomistic-continuum model is constructed to investigate the above two mechanical pr...
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
Energetics and kinetics unveiled on helium cluster growth in tungsten
Wang, Jinlong; Niu, Liang-Liang; Shu, Xiaolin; Zhang, Ying
2015-09-01
The energetics and kinetics regarding helium (He) cluster growth in bcc tungsten (W) are unveiled using combined techniques of molecular statics and molecular dynamics. The principal mechanisms accounting for the decrease of system potential energy are identified to be trap mutation, → 1/2 cluster transformation, loop punching, coalescence between 1/2[1 1-1] and 1/2[1-1-1] loops, and loop capturing. The kinetic barriers associated with these key atomistic events are estimated. This work provides new insights into the complex yet intriguing atomistic evolution sequence of the He cluster and interstitial loop in W-based nuclear fusion materials under irradiation.
Savic, Ivana
2012-02-01
Decreasing the thermal conductivity of bulk materials by nanostructuring and dimensionality reduction, or by introducing some amount of disorder represents a promising strategy in the search for efficient thermoelectric materials [1]. For example, considerable improvements of the thermoelectric efficiency in nanowires with surface roughness [2], superlattices [3] and nanocomposites [4] have been attributed to a significantly reduced thermal conductivity. In order to accurately describe thermal transport processes in complex nanostructured materials and directly compare with experiments, the development of theoretical and computational approaches that can account for both anharmonic and disorder effects in large samples is highly desirable. We will first summarize the strengths and weaknesses of the standard atomistic approaches to thermal transport (molecular dynamics [5], Boltzmann transport equation [6] and Green's function approach [7]) . We will then focus on the methods based on the solution of the Boltzmann transport equation, that are computationally too demanding, at present, to treat large scale systems and thus to investigate realistic materials. We will present a Monte Carlo method [8] to solve the Boltzmann transport equation in the relaxation time approximation [9], that enables computation of the thermal conductivity of ordered and disordered systems with a number of atoms up to an order of magnitude larger than feasible with straightforward integration. We will present a comparison between exact and Monte Carlo Boltzmann transport results for small SiGe nanostructures and then use the Monte Carlo method to analyze the thermal properties of realistic SiGe nanostructured materials. This work is done in collaboration with Davide Donadio, Francois Gygi, and Giulia Galli from UC Davis.[4pt] [1] See e.g. A. J. Minnich, M. S. Dresselhaus, Z. F. Ren, and G. Chen, Energy Environ. Sci. 2, 466 (2009).[0pt] [2] A. I. Hochbaum et al, Nature 451, 163 (2008).[0pt
Atomistic simulations of jog migration on extended screw dislocations
DEFF Research Database (Denmark)
Vegge, T.; Leffers, T.; Pedersen, O.B.; Jacobsen, K.W.
Effective Medium Theory, The minimum energy path through configuration space and the corresponding transition state energy are obtained using the Nudged Elastic Band path technique. We find very similar migration properties for elementary jogs on the (110){110} octahedral slip systems and the (110){110} non......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...
Atomistic simulations of Mg-Cu metallic glasses: Mechanical properties
DEFF Research Database (Denmark)
Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel
2004-01-01
The atomistic mechanisms of plastic deformation in amorphous metals are far from being understood. We have derived potential parameters for molecular dynamics simulations of Mg-Cu amorphous alloys using the Effective Medium Theory. We have simulated the formation of alloys by cooling from the melt......, and have used these glassy configurations to carry out simulations of plastic deformation. These involved different compositions, temperatures (including zero), and types of deformation (uniaxial strain/pure shear), and yielded stress-strain curves and values of flow stress. Separate simulations were...
Energy Technology Data Exchange (ETDEWEB)
PI: Yang, Judith C., Mechanical Eng. & Materials Science, University of Pittsburgh; Co-PI: McGaughey, Alan, Mechanical Eng., Carnegie Mellon University; Sinnott, Susan and Phillpot, Simon, Materials Science & Eng., University of Florida
2007-09-30
, and calculations of these values are part of the ongoing effort with University of Florida (UF) and proposed activity with Carnegie Mellon University (CMU). Brief highlights of our progress to date are summarized below: - Development of TFOx-2D, a versatile kinetic Monte Carlo code that can simulate atomistic transport, nucleation and growth, and includes potential gradients to simulate medium-range substrate mediated effects (e.g., strain). - Systematic study of TFOx-2D input parameters to reveal a variety of nano-structures that resemble those seen experimentally. - Parallelization of the Streitz-Mintmire potential and Rappe-Goddard approach for determining dynamic charge transfer at a metal-oxide interface, which is the critical step required for molecular dynamic simulations of oxygen-metal interactions. - Benchmark calculations of Cu and Cu2O physical properties to determine the most accurate electronic structure approach. - Demonstration of the greater universality of the Tersoff-Tromp elastic strain relief model of nano-rod formation to a gas-surface reaction. Hence, we have established the ground work for a truly comprehensive and multi-scale theoretical tool that can simulate any gas-surface reaction, including oxidation, from the atomic level to the mesoscale, from first principles. The direct comparison between these simulations and in situ experiments of metal nano-oxidation will lead to new knowledge of this important surface reaction.
DEFF Research Database (Denmark)
van Leeuwen, Theo; Djonov, Emilia
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....
Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene
Guin, Laurent; Raphanel, Jean L.; Kysar, Jeffrey W.
2016-06-01
Pristine single crystal graphene is the strongest known two-dimensional material, and its nonlinear anisotropic mechanical properties are well understood from the atomic length scale up to a continuum description. However, experiments indicate that grain boundaries in the polycrystalline form reduce the mechanical behavior of polycrystalline graphene. Herein, we perform atomistic-scale molecular dynamics simulations of the deformation and fracture of graphene grain boundaries and express the results as continuum cohesive zone models (CZMs) that embed notions of the grain boundary ultimate strength and fracture toughness. To facilitate energy balance, we employ a new methodology that simulates a quasi-static controlled crack propagation which renders the kinetic energy contribution to the total energy negligible. We verify good agreement between Griffith's critical energy release rate and the work of separation of the CZM, and we note that the energy of crack edges and fracture toughness differs by about 35%, which is attributed to the phenomenon of bond trapping. This justifies the implementation of the CZM within the context of the finite element method (FEM). To enhance computational efficiency in the FEM implementation, we discuss the use of scaled traction-separation laws (TSLs) for larger element sizes. As a final result, we have established that the failure characteristics of pristine graphene and high tilt angle bicrystals differ by less than 10%. This result suggests that one could use a unique or a few typical TSLs as a good approximation for the CZMs associated with the mechanical simulations of the polycrystalline graphene.
Pan, Xiaoliang; Schwartz, Steven
2015-03-01
It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.
International Nuclear Information System (INIS)
In cellular environments, two protein molecules on their way to form a specific complex encounter many bystander macromolecules. The latter molecules, or crowders, affect both the energetics of the interaction between the test molecules and the dynamics of their relative motion. In earlier work (Zhou and Szabo 1991 J. Chem. Phys. 95 5948–52), it has been shown that, in modeling the association kinetics of the test molecules, the presence of crowders can be accounted for by their energetic and dynamic effects. The recent development of the transient-complex theory for protein association in dilute solutions makes it possible to easily incorporate the energetic and dynamic effects of crowders. The transient complex refers to a late on-pathway intermediate, in which the two protein molecules have near-native relative separation and orientation, but have yet to form the many short-range specific interactions of the native complex. The transient-complex theory predicts the association rate constant as ka = ka0exp( − ΔG*el/kBT), where ka0 is the ‘basal’ rate constant for reaching the transient complex by unbiased diffusion, and the Boltzmann factors captures the influence of long-range electrostatic interactions between the protein molecules. Crowders slow down the diffusion, therefore reducing the basal rate constant (to kac0), and induce an effective interaction energy ΔGc. We show that the latter interaction energy for atomistic proteins in the presence of spherical crowders is ‘long’-ranged, allowing the association rate constant under crowding to be computed as kac = kac0exp[ − (ΔG*el + ΔG*c)/kBT]. Applications demonstrate that this computational method allows for realistic modeling of protein association kinetics under crowding. (paper)
Atomistic view in the initial stages of growth of epitaxial graphene on metal substrates
Zhang, Zhenyu
2011-03-01
For both fundamental studies and potential development of graphene electronics, it is pressing to search for reliable methods for mass production of quality graphene. Epitaxial growth of graphene on catalytic metal substrates combined with post-growth transfer has become a promising route towards this goal [1,2]. However, to better control the quality and yield of graphene, a comprehensive understanding of the growth kinetics is essential. In particular, how the carbon atoms adsorbed on the metal surface (or dissolved into the metal) meet to nucleate into stable carbon islands will greatly influence both the growth rate and quality of larger carbon entities such as graphene sheets. In this talk, we first show that the delicate competition between carbon-carbon bonding and carbon-metal bonding dictates the initial nucleation sites of graphene on metal surfaces. These results are discussed in connection with the experimental findings that on Ir(111) and Ru(0001) substrates graphene nucleates from the step edges [4,5]. We also predict that on Cu(111) nucleation should take place everywhere on a terrace. Next we study larger carbon clusters on Cu(111) and explicitly compare the stability of linear and compact structures. We find that the linear carbon ``nanoarches'' are more stable than compact islands consisting of up to 13 carbon atoms, and these nanoarched structures may serve as the missing bridge between carbon dimers and larger graphene nanodomes. Based on these improved understanding of the atomistic rate processes involved, we propose a few kinetic pathways that may lead to better growth control of bilayer graphene and graphene nanoribbons as elemental building blocks for developing graphene electronics. Work done in collaboration with Hua Chen, Wenguang Zhu, Robert Van Wesep, Wei Chen, Ping Cui, and Haiping Lan, and supported by USDOE, USNSF, and NNSF of China.
Atomistically-informed Dislocation Dynamics in fcc Crystals
Energy Technology Data Exchange (ETDEWEB)
Martinez, E; Marian, J; Arsenlis, T; Victoria, M; Perlado, J M
2006-09-06
We develop a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our findings to the plastic behavior of monocrystalline fcc metals.
Adaptive resolution simulation of an atomistic protein in MARTINI water
International Nuclear Information System (INIS)
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
Testing continuum concepts for hydrogen embrittlement in metals using atomistics
International Nuclear Information System (INIS)
Hydrogen embrittlement is a pervasive mode of degradation in many metallic systems that can occur via several mechanisms. Here, the competition between dislocation emission and cleavage at a crack tip is evaluated in the presence of H. At this level, embrittlement is predicted when the critical stress intensity required for emission rises above that needed for cleavage, eliminating crack tip plasticity and blunting as toughening mechanisms. Continuum predictions for emission and cleavage are made using computed generalized stacking fault energies and surface energies in a model Ni–H system, and embrittlement is predicted at a critical H concentration. An atomistic model is then used to investigate actual crack tip behavior in the presence of controlled arrays of H atoms around the crack tip. The continuum models are accurate at low H concentrations, below the embrittlement point, but at higher H concentrations the models deviate from the atomistic behavior due to alternative dislocation emission modes. Additional H configurations are investigated to understand controlling features of the emission process. In no cases does crack propagation occur in preference to dislocation emission in geometries where emission is possible, indicating that embrittlement can be more complicated than envisioned by the basic brittle–ductile transition
Atomistic Simulation of High-Density Uranium Fuels
Directory of Open Access Journals (Sweden)
Jorge Eduardo Garcés
2011-01-01
Full Text Available We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1 the trend indicating formation of interfacial compounds, (2 much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3 Si depletion in the Al matrix, (4 an unexpected interaction between Mo and Si which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5 the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.
Atomistic calculation of the thermoelectric properties of Si nanowires
Bejenari, I.; Kratzer, P.
2014-07-01
The thermoelectric properties of 1.6-nm-thick Si square nanowires with [100] crystalline orientation are calculated over a wide temperature range from 0 K to 1000 K, taking into account atomistic electron-phonon interaction. In our model, the [010] and [001] facets are passivated by hydrogen and there are Si-Si dimers on the nanowire surface. The electronic structure was calculated by using the sp3 spin-orbit-coupled atomistic second-nearest-neighbor tight-binding model. The phonon dispersion was calculated from a valence force field model of the Brenner type. A scheme for calculating electron-phonon matrix elements from a second-nearest-neighbor tight-binding model is presented. Based on Fermi's golden rule, the electron-phonon transition rate was obtained by combining the electron and phonon eigenstates. Both elastic and inelastic scattering processes are taken into consideration. The temperature dependence of transport characteristics was calculated by using a solution of the linearized Boltzmann transport equation obtained by means of the iterative orthomin method. At room temperature, the electron mobility is 195 cm2 V-1 s-1 and increases with temperature, while a figure of merit ZT =0.38 is reached for n-type doping with a concentration of n =1019 cm-3.
Monte Carlo Radiative Transfer
Whitney, Barbara A
2011-01-01
I outline methods for calculating the solution of Monte Carlo Radiative Transfer (MCRT) in scattering, absorption and emission processes of dust and gas, including polarization. I provide a bibliography of relevant papers on methods with astrophysical applications.
Monte Carlo transition probabilities
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...
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 which serves as lecture material for the Parallel Computing summer school. It goes over the fundamentals of Monte Carlo. Welcome to Los Alamos, the birthplace of “Monte Carlo” for computational physics. Stanislaw Ulam, John von Neumann, and Nicholas Metropolis are credited as the founders of modern Monte Carlo methods. The name “Monte Carlo” was chosen in reference to the Monte Carlo Casino in Monaco (purportedly a place where Ulam’s uncle went to gamble). The central idea (for us) – to use computer-generated “random” numbers to determine expected values or estimate equation solutions – has since spread to many fields. "The first thoughts and attempts I made to practice [the Monte Carlo Method] were suggested by a question which occurred to me in 1946 as I was convalescing from an illness and playing solitaires. The question was what are the chances that a Canfield solitaire laid out with 52 cards will come out successfully? After spending a lot of time trying to estimate them by pure combinatorial calculations, I wondered whether a more practical method than “abstract thinking” might not be to lay it out say one hundred times and simply observe and count the number of successful plays... Later [in 1946], I described the idea to John von Neumann, and we began to plan actual calculations." - Stanislaw Ulam.
Wang-Landau Monte Carlo formalism applied to ferroelectrics
Bin-Omran, S.; Kornev, Igor A.; Bellaiche, L.
2016-01-01
The Wang-Landau Monte Carlo algorithm is implemented within an effective Hamiltonian approach and applied to BaTiO3 bulk. The density of states obtained by this approach allows a highly accurate and straightforward calculation of various thermodynamic properties, including phase transition temperatures, as well as polarization, dielectric susceptibility, specific heat, and electrocaloric coefficient at any temperature. This approach yields rather smooth data even near phase transitions and provides direct access to entropy and free energy, which allow us to compute properties that are typically unaccessible by atomistic simulations. Examples of such latter properties are the nature (i.e., first order versus second order) of the phase transitions for different supercell sizes and the thermodynamic limit of the Curie temperature and latent heat.
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.
Degenerate Ising model for atomistic simulation of crystal-melt interfaces.
Schebarchov, D; Schulze, T P; Hendy, S C
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. PMID:24559357
Variational Monte Carlo Calculations of Energy per Particle Nuclear Matter
Manisa, K.
2004-01-01
In this paper, symmetrical nuclear matter has been investigated. Total, kinetic and potential energies per particle were obtained for nuclear matter by Variational Monte Carlo method. We have observed that the results are in good agreement with those obtained by various authors who used different potentials and techniques.
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.
Monte-carlo calculations for some problems of quantum mechanics
International Nuclear Information System (INIS)
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.
Atomistic simulation of mineral surfaces: Their structure, hydration and growth
International Nuclear Information System (INIS)
In this thesis, we have used atomistic simulation techniques to investigate the surface structure and stability of the biomineral barium sulfate and a number of important iron oxides, namely hematite, magnetite and goethite. We have studied the effect of the molecular adsorption of water on the surface structures and stabilities of all four minerals, and dissociative adsorption of water on the iron oxides. In addition, we have investigated the segregation of foreign ions to the surfaces of barium sulfate. Chapter 1 gives an overview of some previous studies of surfaces, employing both atomistic simulations and electronic structure calculations. Also discussed are some popular experimental analysis techniques used in surface characterisation. Chapter 2 describes the theoretical methods used in atomistic simulations and the mathematical methods used in the calculations, including the evaluation of surface energies. Chapter 3 introduces the potential model and discusses their reliability and transferability between structures. The potential parameters used in chapters 4-7 are given and where possible, compared with experiment. Chapter 4 describes the structures and stabilities of the pure surfaces of barium sulfate, and after the overgrowth of segregation of a layer of impurity ions at the surface. The modified crystal morphologies are discussed. Chapter 5 follows the work in the previous chapter by discussing the effect of the molecular adsorption of water at different coverages on the structure and stabilities of barium sulfate surfaces. The hydrated energies and surface energies are calculated. The second section of chapter 5 investigates structural influences on the growth of barium sulfate. In Chapter 6, the pure surfaces of hematite, magnetite and goethite are described. The surface relaxation are studied and equilibrium crystal morphologies compared with experimental findings. The surface structure of Fe2O3(00.1) under reducing conditions is also investigated
Grand canonical Monte Carlo simulations of hydrogen adsorption in carbon cones
International Nuclear Information System (INIS)
The Monte Carlo method in its grand ensemble variant (GCMC) is used in order to study the hydrogen adsorption (77 K) characteristics of novel carbon structures, namely Carbon Cones (CCs). CCs are conical shaped curved graphitic sheets, with five different apex angles. CC structures with correct bonding topology were developed via atomistic-molecular simulations, while GCMC simulations of hydrogen adsorption were carried out on the five different apex angle structures. Emphasis has been given on the adsorption properties inside the cones and it was found that cone tips are characterized by enhanced adsorbability. The results were also compared with similar calculations on carbon nanotubes.
Atomistic simulations of material damping in amorphous silicon nanoresonators
Mukherjee, Sankha; Song, Jun; Vengallatore, Srikar
2016-06-01
Atomistic simulations using molecular dynamics (MD) are emerging as a valuable tool for exploring dissipation and material damping in nanomechanical resonators. In this study, we used isothermal MD to simulate the dynamics of the longitudinal-mode oscillations of an amorphous silicon nanoresonator as a function of frequency (2 GHz–50 GHz) and temperature (15 K–300 K). Damping was characterized by computing the loss tangent with an estimated uncertainty of 7%. The dissipation spectrum displays a sharp peak at 50 K and a broad peak at around 160 K. Damping is a weak function of frequency at room temperature, and the loss tangent has a remarkably high value of ~0.01. In contrast, at low temperatures (15 K), the loss tangent increases monotonically from 4× {{10}-4} to 4× {{10}-3} as the frequency increases from 2 GHz to 50 GHz. The mechanisms of dissipation are discussed.
An experimentally consistent atomistic structural model of silica glass
International Nuclear Information System (INIS)
Empirical potential structure refinement is used to build an atomistic model of silica glass based on neutron scattering data. This model is tested against X-ray diffraction and extended X-ray absorption fine structure (EXAFS) spectroscopy data to establish its local and intermediate range structural veracity. The chemical specificity of the silicon and oxygen K-edge spectroscopic information allows us to confirm that the neutron scattering derived model represents a reasonable representation of the three partial structure factors that are required to characterise this binary glass and subsequently give confidence in the Faber-Ziman and Bhatia-Thornton partial structure factors and pair distribution functions that are extracted from the model
Protein displacements under external forces: An atomistic Langevin dynamics approach
Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten
2009-02-01
We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.
Effective Transparency: A Test of Atomistic Laser-Cluster Models
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).
Atomistic modelling of the hydration of CaSO 4
Adam, Craig D.
2003-08-01
Atomistic modelling techniques, using empirical potentials, have been used to simulate a range of structures formed by the hydration of γ-CaSO 4 and described as CaSO 4· nH 2O (0commercial importance and has been subjected to much experimental study. These simulation studies demonstrate significant water-matrix interactions that influence the crystallography of the hydrated phase. The existence of two types of hydration site has been predicted, including one within the Ca 2+coordination sphere. Close correlation between water molecule bonding energy, Ca 2+-O w bond length and unit-cell volume have been established. This shows that as the number of water molecules within the unit cell increases, the bonding energy increases and the unit cell contracts. However around n=0.5, this process reaches a turning point with the incorporation of further waters resulting in reduced binding energy and an expanding unit cell.
Atomistic processes during nanoindentation of amorphous silicon carbide
International Nuclear Information System (INIS)
Atomistic mechanisms of nanoindentation of a-SiC have been studied by molecular dynamics simulations. The load displacement curve exhibits a series of load drops, reflecting the short-range topological order similar to crystalline 3C-SiC. In contrast to 3C-SiC, the load drops are irregularly spaced and less pronounced. The damage is spatially more extended than in 3C-SiC, and it exhibits long-range oscillations consistent with the indenter size. Hardness is ∼60% lower than in 3C-SiC and is in agreement with experiment. The onset of plastic deformation occurs at depth ∼75% lower than in 3C-SiC
Atomistic simulations for multiscale modeling in bcc metal
Energy Technology Data Exchange (ETDEWEB)
Belak, J.; Moriarty, J.A.; Soderlind, P.; Xu, W.; Yang, L.H.; Zhu
1998-09-25
Quantum-based atomistic simulations are being used to study fundamental deformation and defect properties relevant to the multiscale modeling of plasticity in bcc metals at both ambient and extreme conditions. Ab initio electronic-structure calculations on the elastic and ideal-strength properties of Ta and Mo help constrain and validate many-body interatomic potentials used to study grain boundaries and dislocations. The predicted C(capital Sigma)5 (310)[100] grain boundary structure for Mo has recently been confirmed in HREM measurements. The core structure, (small gamma) surfaces, Peierls stress, and kink-pair formation energies associated with the motion of a/2(111) screw dislocations in Ta and Mo have also been calculated. Dislocation mobility and dislocation junction formation and breaking are currently under investigation.
An Atomistic Statistically Effective Energy Function for Computational Protein Design.
Topham, Christopher M; Barbe, Sophie; André, Isabelle
2016-08-01
Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical
Experimentally driven atomistic model of 1,2 polybutadiene
International Nuclear Information System (INIS)
We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results
Institute of Scientific and Technical Information of China (English)
熊海灵; 杨志敏; 李航
2014-01-01
The effects of the diffusive (Ds(γ)=D0×sγ) and sticking (Pij(σ)=P0×(i×j)σ) models on the colloidal suspension evolution, cluster-size distribution and scaling, time dependence of weight-averaged cluster size, and the fractal dimensions of aggregates are investigated. Simulations of the aggregation kinetics are carried out for a wide range of diffusivity exponentγand sticking-probability exponentσvalues.γ0 have similar effects on the col oidal aggregation kinetics. The mechanism of transition from slow to fast aggregation is quantitatively analyzed. The physical significance of a cluster-cluster aggregation model, leading to a diffusion-limited aggregation model, is proposed.γ>>0 corresponds to the directional movement of clusters or primary particles, rather than random Brownian motion. The driving force for this directional movement may be a strong long-range van der Waals force, electric force of the largest cluster, or external force from the boundary.σ0, but a negative-feedback process asσ0对胶体的凝聚动力学过程有相似的影响。本文在较宽的γ和σ取值范围内，对胶体的凝聚动力学进行了模拟研究，对慢速凝聚向快速凝聚的转化机理作了定量分析，并进一步分析了在团簇-团簇凝聚(CCA)模型下，得到类似扩散置限凝聚(DLA)模型的凝聚体的物理意义，结果表明：(1)γ>>0代表了体系中团簇或单粒做“定向运动”而非无规则的布朗运动的情况。这种“定向运动”的推动力可能来自于大团簇产生的强“长程范德华力”、“电场力”等，或来自于体系边界处的外力场的作用。(2)当σ0时是一个存在正反馈机制的非线性动力学过程，而在σ<0时则体现出负反馈的特征。
International Nuclear Information System (INIS)
The author has studied the kinetics of heparin and heparin fractions after intravenous administration in humans and in this thesis the results of this study are reported. Basic knowledge about the physico-chemical properties of heparin and its interactions with proteins resulting in anticoagulant and lipolytic effects are discussed in a review (chapter II), which also comprises some clinical aspects of heparin therapy. In chapter III the kinetics of the anticoagulant effect are described after intravenous administration of five commercial heparin preparations. A mathematical model is presented that fits best to these kinetics. The kinetics of the anticoagulant and lipolytic effects after intravenous injection of various 35S-radiolabelled heparin fractions and their relationship with the disappearance of the radiolabel are described in chapter IV. Chapter V gives a description of the kinetics of two radiolabels after injection of in vitro formed complexes consisting of purified, 125I-radiolabelled antithrombin III and various 35S-radiolabelled heparin fractions. (Auth.)
Panzarino, Jason F.; Rupert, Timothy J.
2014-03-01
Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. To understand the fundamental principles that govern material behavior at the atomic scale and directly connect to experimental works, it is necessary to quantify the microstructure of materials simulated with atomistics. Specifically, quantitative tools for identifying crystallites, their crystallographic orientation, and overall sample texture do not currently exist. Here, we develop a post-processing algorithm capable of characterizing such features, while also documenting their evolution during a simulation. In addition, the data is presented in a way that parallels the visualization methods used in traditional experimental techniques. The utility of this algorithm is illustrated by analyzing several types of simulation cells that are commonly found in the atomistic modeling literature but could also be applied to a variety of other atomistic studies that require precise identification and tracking of microstructure.
Parallelization of Kinetic Theory Simulations
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.
Self-consistent simulations of nanowire transistors using atomistic basis sets
NEOPHYTOU, Neophytos; Paul, Abhijeet; Lundstrom, Mark S.; Klimeck, Gerhard
2007-01-01
As device sizes shrink towards the nanoscale, CMOS development investigates alternative structures and devices. Existing CMOS devices will evolve from planar to 3D non-planar devices at nanometer sizes. These devices will operate under strong confinement and strain, regimes where atomistic effects are important. This work investigates atomistic effects in the transport properties of nanowire devices by using a nearest-neighbor tight binding model (sp3s*d5-SO) for electronic structure calculat...
Zelovich, Tamar; Kronik, Leeor; Hod, Oded
2014-01-01
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 S\\'anchez et al. [J. Chem. Phys., 124, 214708 (2006)]. 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 defi...
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.
International Nuclear Information System (INIS)
An atomistically informed mesoscale model is developed for the deposition of a discharge product in a Li-O2 battery. This mescocale model includes particle growth and coarsening as well as a simplified nucleation model. The model involves LiO2 formation through reaction of O2− 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-O2 batteries and nucleation and growth in Li-S batteries
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
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. PMID:27054098
Nanosculpt: A methodology for generating complex realistic configurations for atomistic simulations
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 nanosculpt 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. PMID:27054098
Institute of Scientific and Technical Information of China (English)
C.S. Chang
2007-01-01
@@ The ITER relevant edge plasmas in the present day experiments are in the kinetic regime,with the pedestalions in the long-mean-free-path banans collisionality regime and the pedestal electrons in the banana-plateau regime.
MONTE-4 for Monte Carlo simulations with high performance
International Nuclear Information System (INIS)
The Monte Carlo machine MONTE-4, has been developed based on the architecture of existing supercomputer with a design philosophy to realize high performance in vector-parallel processing of Monte Carlo codes for particle transport problems. The effective performance of this Monte Carlo machine is presented through practical applications of multi-group criticality safety code KENO-IV and continuous-energy neutron/photon transport code MCNP. Ten times speedup has been obtained on MONTE-4 compared with the execution time in the scalar processing. (K.A.)
Monte Carlo photon benchmark problems
International Nuclear Information System (INIS)
Photon benchmark calculations have been performed to validate the MCNP Monte Carlo computer code. These are compared to both the COG Monte Carlo computer code and either experimental or analytic results. The calculated solutions indicate that the Monte Carlo method, and MCNP and COG in particular, can accurately model a wide range of physical problems. 8 refs., 5 figs
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....
International Nuclear Information System (INIS)
This book gives descriptions of chemical kinetics. It starts summary of chemical kinetics and reaction mechanism, and explains basic velocity law, experiment method for determination of reaction velocity, temperature dependence of reaction velocity, theory of reaction velocity, theory on reaction of unimolecular, process of atom and free radical, reaction in solution, catalysis, photochemical reaction, such as experiment and photochemical law and rapid reaction like flame, beam of molecule and shock tube.
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.
Collective translational and rotational Monte Carlo moves for attractive particles
RÅ¯žička, Štěpán; Allen, Michael P.
2014-03-01
Virtual move Monte Carlo is a Monte Carlo (MC) cluster algorithm forming clusters via local energy gradients and approximating the collective kinetic or dynamic motion of attractive colloidal particles. We carefully describe, analyze, and test the algorithm. To formally validate the algorithm through highlighting its symmetries, we present alternative and compact ways of selecting and accepting clusters which illustrate the formal use of abstract concepts in the design of biased MC techniques: the superdetailed balance and the early rejection scheme. A brief and comprehensive summary of the algorithms is presented, which makes them accessible without needing to understand the details of the derivation.
Monte Carlo studies of domain growth in two dimensions
International Nuclear Information System (INIS)
Monte Carlo simulations have been carried out to study the effect of temperature on the kinetics of domain growth. The concept of ''spatial entropy'' is introduced. It is shown that ''spatial entropy'' of the domain can be used to give a measure of the roughening of the domain. Most of the roughening is achieved during the initial time (t< or approx. 10 Monte Carlo cycles), the rate of roughening being greater for higher temperatures. For later times the roughening of the domain for different temperatures proceeds at essentially the same rate. (author)
The Metropolis Monte Carlo method with CUDA enabled Graphic Processing Units
International Nuclear Information System (INIS)
We present a CPU–GPU system for runtime acceleration of large molecular simulations using GPU computation and memory swaps. The memory architecture of the GPU can be used both as container for simulation data stored on the graphics card and as floating-point code target, providing an effective means for the manipulation of atomistic or molecular data on the GPU. To fully take advantage of this mechanism, efficient GPU realizations of algorithms used to perform atomistic and molecular simulations are essential. Our system implements a versatile molecular engine, including inter-molecule interactions and orientational variables for performing the Metropolis Monte Carlo (MMC) algorithm, which is one type of Markov chain Monte Carlo. By combining memory objects with floating-point code fragments we have implemented an MMC parallel engine that entirely avoids the communication time of molecular data at runtime. Our runtime acceleration system is a forerunner of a new class of CPU–GPU algorithms exploiting memory concepts combined with threading for avoiding bus bandwidth and communication. The testbed molecular system used here is a condensed phase system of oligopyrrole chains. A benchmark shows a size scaling speedup of 60 for systems with 210,000 pyrrole monomers. Our implementation can easily be combined with MPI to connect in parallel several CPU–GPU duets. -- Highlights: •We parallelize the Metropolis Monte Carlo (MMC) algorithm on one CPU—GPU duet. •The Adaptive Tempering Monte Carlo employs MMC and profits from this CPU—GPU implementation. •Our benchmark shows a size scaling-up speedup of 62 for systems with 225,000 particles. •The testbed involves a polymeric system of oligopyrroles in the condensed phase. •The CPU—GPU parallelization includes dipole—dipole and Mie—Jones classic potentials.
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.
International Nuclear Information System (INIS)
The contributon Monte Carlo method is based on a new recipe to calculate target responses by means of volume integral of the contributon current in a region between the source and the detector. A comprehensive description of the method, its implementation in the general-purpose MCNP code, and results of the method for realistic nonhomogeneous, energy-dependent problems are presented. 23 figures, 10 tables
Atomistic Simulations of Poly(N-isopropylacrylamide) Surfactants in Water
Abbott, Lauren J.; Stevens, Mark J.
2015-03-01
The amphiphilic polymer poly(N-isopropylacrylamide) (PNIPAM) displays a sharp phase transition at its LCST around 32 °C, which results from competing interactions of the hydrophobic and hydrophilic groups with water. This thermoresponsive behavior can be exploited in more complex architectures, such as block copolymers or surfactants, to provide responsive PNIPAM head groups. In these systems, however, changes to the hydrophobic/hydrophilic balance can alter the transition behavior. In this work, we perform atomistic simulations of PNIPAM-alkyl surfactants to study the temperature dependence of their structures. A single chain of the surfactant does not show temperature-responsive behavior. Instead, below and above the LCST of PNIPAM, the surfactant folds to bring the hydrophobic alkyl tail in contact with the PNIPAM backbone, shielding it from water. In addition to single chains, we explore the self-assembly of multiple surfactants into micelles and how the temperature-dependent behavior is changed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Atomistic Hydrodynamics and the Dynamical Hydrophobic Effect in Porous Graphene.
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. PMID:27139634
Atomistic modeling of phonon transport in turbostratic graphitic structures
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.
Optimization Algorithms in Optimal Predictions of Atomistic Properties by Kriging.
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. PMID:26930135
Atomistic Molecular Dynamics Simulations of Shock Compressed Quartz
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...
Equilibrium and Kinetics: Water Confined in Carbon Nanotube as 1D Lattice Gas
Zhou, Xin; Li, Cheng-Quan; Iwamoto, Mitsumasa
2002-01-01
A simple 1D lattice gas model is presented, which very well describes the equilibrium and kinetic behaviors of water confined in a thin carbon nanotube found in an atomistic molecular dynamics(MD) simulation {[} Nature {\\bf 414}, 188 (2001) {]}. The model parameters are corresponding to various physical interactions and can be calculated or estimated in statistic mechanics. The roles of every interaction in the water filling, emptying and transporting processes are clearly understood. Our res...
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
MontePython: Implementing Quantum Monte Carlo using Python
J.K. Nilsen
2006-01-01
We present a cross-language C++/Python program for simulations of quantum mechanical systems with the use of Quantum Monte Carlo (QMC) methods. We describe a system for which to apply QMC, the algorithms of variational Monte Carlo and diffusion Monte Carlo and we describe how to implement theses methods in pure C++ and C++/Python. Furthermore we check the efficiency of the implementations in serial and parallel cases to show that the overhead using Python can be negligible.
Wan Ahmad Tajuddin Wan Abdullah; Sidiq Mohamad Khidzir
2007-01-01
We study a minimalist kinetic model for economies. A system of agents with local trading rules display emergent demand behaviour. We examine the resulting wealth distribution to look for non-thermal behaviour. We compare and contrast this model with other similar models.
Construction of Monte Carlo operators in collisional transport theory
International Nuclear Information System (INIS)
A Monte Carlo approach for investigating the dynamics of quiescent collisional magnetoplasmas is presented, based on the discretization of the gyrokinetic equation. The theory applies to a strongly rotating multispecies plasma, in a toroidally axisymmetric configuration. Expressions of the Monte Carlo collision operators are obtained for general v-space nonorthogonal coordinates systems, in terms of approximate solutions of the discretized gyrokinetic equation. Basic features of the Monte Carlo operators are that they fullfill all the required conservation laws, i.e., linear momentum and kinetic energy conservation, and in addition that they take into account correctly also off-diagonal diffusion coefficients. The present operators are thus potentially useful for describing the dynamics of a multispecies toroidal magnetoplasma. In particular, strict ambipolarity of particle fluxes is ensured automatically in the limit of small departures of the unperturbed particle trajectories from some initial axisymmetric toroidal magnetic surfaces
Atomistic theory of transport in organic and inorganic nanostructures
International Nuclear Information System (INIS)
As the size of modern electronic and optoelectronic devices is scaling down at a steady pace, atomistic simulations become necessary for an accurate modelling of their structural, electronic, optical and transport properties. Such microscopic approaches are important in order to account correctly for quantum-mechanical phenomena affecting both electronic and transport properties of nanodevices. Effective bulk parameters cannot be used for the description of the electronic states since interfacial properties play a crucial role and semiclassical methods for transport calculations are not suitable at the typical scales where the device behaviour is characterized by coherent tunnelling. Quantum-mechanical computations with atomic resolution can be achieved using localized basis sets for the description of the system Hamiltonian. Such methods have been extensively used to predict optical and electronic properties of molecules and mesoscopic systems. The most important approaches formulated in terms of localized basis sets, from empirical tight-binding (TB) to first principles methods, are here reviewed. Being a full band approach, even the simplest TB overcomes the limitations of envelope function approximations, such as the well-known k · p, and allows to retain atomic details and realistic band structures. First principles calculations, on the other hand, can give a very accurate description of the electronic and structural properties. Transport in nanoscale devices cannot neglect quantum effects such as coherent tunnelling. In this context, localized basis sets are well-suited for the formal treatment of quantum transport since they provide a simple mathematical framework to treat open-boundary conditions, typically encountered when the system eigenstates carry a steady-state current. We review the principal methods used to formulate quantum transport based on local orbital sets via transfer matrix and Green's function (GF) techniques. We start from a general
Atomistic theory of transport in organic and inorganic nanostructures
Pecchia, Alessandro; Di Carlo, Aldo
2004-08-01
As the size of modern electronic and optoelectronic devices is scaling down at a steady pace, atomistic simulations become necessary for an accurate modelling of their structural, electronic, optical and transport properties. Such microscopic approaches are important in order to account correctly for quantum-mechanical phenomena affecting both electronic and transport properties of nanodevices. Effective bulk parameters cannot be used for the description of the electronic states since interfacial properties play a crucial role and semiclassical methods for transport calculations are not suitable at the typical scales where the device behaviour is characterized by coherent tunnelling. Quantum-mechanical computations with atomic resolution can be achieved using localized basis sets for the description of the system Hamiltonian. Such methods have been extensively used to predict optical and electronic properties of molecules and mesoscopic systems. The most important approaches formulated in terms of localized basis sets, from empirical tight-binding (TB) to first principles methods, are here reviewed. Being a full band approach, even the simplest TB overcomes the limitations of envelope function approximations, such as the well-known k · p, and allows to retain atomic details and realistic band structures. First principles calculations, on the other hand, can give a very accurate description of the electronic and structural properties. Transport in nanoscale devices cannot neglect quantum effects such as coherent tunnelling. In this context, localized basis sets are well-suited for the formal treatment of quantum transport since they provide a simple mathematical framework to treat open-boundary conditions, typically encountered when the system eigenstates carry a steady-state current. We review the principal methods used to formulate quantum transport based on local orbital sets via transfer matrix and Green's function (GF) techniques. We start from a general
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.
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.
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!
An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations
Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.
2013-12-01
In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations
Optimization of Monte Carlo simulations
Bryskhe, Henrik
2009-01-01
This thesis considers several different techniques for optimizing Monte Carlo simulations. The Monte Carlo system used is Penelope but most of the techniques are applicable to other systems. The two mayor techniques are the usage of the graphics card to do geometry calculations, and raytracing. Using graphics card provides a very efficient way to do fast ray and triangle intersections. Raytracing provides an approximation of Monte Carlo simulation but is much faster to perform. A program was ...
Quantum Gibbs ensemble Monte Carlo
International Nuclear Information System (INIS)
We present a path integral Monte Carlo method which is the full quantum analogue of the Gibbs ensemble Monte Carlo method of Panagiotopoulos to study the gas-liquid coexistence line of a classical fluid. Unlike previous extensions of Gibbs ensemble Monte Carlo to include quantum effects, our scheme is viable even for systems with strong quantum delocalization in the degenerate regime of temperature. This is demonstrated by an illustrative application to the gas-superfluid transition of 4He in two dimensions
A Note on Automatic Kernel Carpentry for Atomistic Support of Continuum Stress
Ulz, Manfred H
2015-01-01
Research within the field of multiscale modelling seeks, amongst other questions, to reconcile atomistic scale interactions with thermodynamical quantities (such as stress) on the continuum scale. The estimation of stress at a continuum point on the atomistic scale requires a pre-defined kernel function. This kernel function derives the stress at a continuum point by averaging the contribution from atoms within a region surrounding the continuum point. Commonly the kernel weight assignment is isotropic: an identical weight is assigned to atoms at the same spatial distance, which is tantamount to a local constant regression model. In this paper we employ a local linear regression model and leverage the mechanism of automatic kernel carpentry to allow for spatial averaging adaptive to the local distribution of atoms. As a result, different weights may be assigned to atoms at the same spatial distance. This is of interest for determining atomistic stress at stacking faults, interfaces or surfaces. It is shown in...
Accelerating a hybrid continuum-atomistic fluidic model with on-the-fly machine learning
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...
Limitations of reactive atomistic potentials in describing defect structures in oxides
Hynninen, Teemu; Musso, Tiziana; Foster, Adam S.
2016-03-01
It is difficult to achieve low expense and high accuracy in computational methods, yet it remains a key objective in atomistic approaches. In solid state physics, advanced atomistic potentials using reactive force fields have shown promise in delivering both. However, these methods have not been applied widely beyond their development environment and thus their strengths and weaknesses are not fully understood. In this work we present benchmark calculations on silica (SiO2) and hafnia (HfO2) structures, comparing a leading charge optimized many-body potential to a more advanced density functional calculation. We find that although the atomistic potential gives excellent results for bulk structures, it has severe shortcomings when applied to small systems with low coordinated atoms. We also establish clearly the components of the many-body potential and how these relate to predicted physical properties.
Local stress and heat flux in atomistic systems involving three-body forces.
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. PMID:16468857
First principles view on chemical compound space: Towards atomistic control of molecular properties
von Lilienfeld, O A
2012-01-01
A well-defined notion of chemical space is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we revisit the atomistic first principles perspective on chemical compound space. First, we review chemical space in terms of conceptual density functional and molecular grand-canonical ensemble theory. Subsequently, compound-pairs, "alchemical" interpolation and reference compounds, and the relevance of property non-linearity are discussed. Thereafter, we will focus on recent contributions for accelerating atomistic simulations based on modern statistical data analysis methods (artificial intelligence). The crucial role of good descriptors for chemical compounds will be addressed.
Atomistic modeling of BN nanofillers for mechanical and thermal properties: a review
Kumar, Rajesh; Parashar, Avinash
2015-12-01
Due to their exceptional mechanical properties, thermal conductivity and a wide band gap (5-6 eV), boron nitride nanotubes and nanosheets have promising applications in the field of engineering and biomedical science. Accurate modeling of failure or fracture in a nanomaterial inherently involves coupling of atomic domains of cracks and voids as well as a deformation mechanism originating from grain boundaries. This review highlights the recent progress made in the atomistic modeling of boron nitride nanofillers. Continuous improvements in computational power have made it possible to study the structural properties of these nanofillers at the atomistic scale.
Turneaure, Stefan J; Sinclair, N; Gupta, Y M
2016-07-22
The experimental determination of atomistic mechanisms linking crystal structures during a compression-driven solid-solid phase transformation is a long-standing and challenging scientific objective. Using new capabilities at the Dynamic Compression Sector at the Advanced Photon Source, the structure of shocked Si at 19 GPa was identified as simple hexagonal, and the lattice orientations between ambient cubic diamond and simple hexagonal structures were related. The approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes. PMID:27494481
Turneaure, Stefan J.; Sinclair, N.; Gupta, Y. M.
2016-07-01
The experimental determination of atomistic mechanisms linking crystal structures during a compression-driven solid-solid phase transformation is a long-standing and challenging scientific objective. Using new capabilities at the Dynamic Compression Sector at the Advanced Photon Source, the structure of shocked Si at 19 GPa was identified as simple hexagonal, and the lattice orientations between ambient cubic diamond and simple hexagonal structures were related. The approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes.
Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K
2013-01-21
The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses. PMID:23343292
Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I.; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K.
2013-01-01
The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.
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...
Atomistic theory of transport in organic and inorganic nanostructures
Energy Technology Data Exchange (ETDEWEB)
Pecchia, Alessandro; Di Carlo, Aldo [INFM-Department of Electronic Engineering, University of Rome, Tor Vergata, Rome (Italy)
2004-08-01
As the size of modern electronic and optoelectronic devices is scaling down at a steady pace, atomistic simulations become necessary for an accurate modelling of their structural, electronic, optical and transport properties. Such microscopic approaches are important in order to account correctly for quantum-mechanical phenomena affecting both electronic and transport properties of nanodevices. Effective bulk parameters cannot be used for the description of the electronic states since interfacial properties play a crucial role and semiclassical methods for transport calculations are not suitable at the typical scales where the device behaviour is characterized by coherent tunnelling. Quantum-mechanical computations with atomic resolution can be achieved using localized basis sets for the description of the system Hamiltonian. Such methods have been extensively used to predict optical and electronic properties of molecules and mesoscopic systems. The most important approaches formulated in terms of localized basis sets, from empirical tight-binding (TB) to first principles methods, are here reviewed. Being a full band approach, even the simplest TB overcomes the limitations of envelope function approximations, such as the well-known k {center_dot} p, and allows to retain atomic details and realistic band structures. First principles calculations, on the other hand, can give a very accurate description of the electronic and structural properties. Transport in nanoscale devices cannot neglect quantum effects such as coherent tunnelling. In this context, localized basis sets are well-suited for the formal treatment of quantum transport since they provide a simple mathematical framework to treat open-boundary conditions, typically encountered when the system eigenstates carry a steady-state current. We review the principal methods used to formulate quantum transport based on local orbital sets via transfer matrix and Green's function (GF) techniques. We start from
Scalable and portable visualization of large atomistic datasets
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
Fundamental aspects of plasma chemical physics kinetics
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...
Monte Carlo Exploration of Warped Higgsless Models
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.
International Nuclear Information System (INIS)
The course of ''Monte Carlo Techniques'' will try to give a general overview of how to build up a method based on a given theory, allowing you to compare the outcome of an experiment with that theory. Concepts related with the construction of the method, such as, random variables, distributions of random variables, generation of random variables, random-based numerical methods, will be introduced in this course. Examples of some of the current theories in High Energy Physics describing the e+e- annihilation processes (QED, Electro-Weak, QCD) will also be briefly introduced. A second step in the employment of this method is related to the detector. The interactions that a particle could have along its way, through the detector as well as the response of the different materials which compound the detector will be quoted in this course. An example of detector at LEP era, in which these techniques are being applied, will close the course. (orig.)
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.
Monte Carlo Methods in Physics
International Nuclear Information System (INIS)
Method of Monte Carlo integration is reviewed briefly and some of its applications in physics are explained. A numerical experiment on random generators used in the monte Carlo techniques is carried out to show the behavior of the randomness of various methods in generating them. To account for the weight function involved in the Monte Carlo, the metropolis method is used. From the results of the experiment, one can see that there is no regular patterns of the numbers generated, showing that the program generators are reasonably good, while the experimental results, shows a statistical distribution obeying statistical distribution law. Further some applications of the Monte Carlo methods in physics are given. The choice of physical problems are such that the models have available solutions either in exact or approximate values, in which comparisons can be mode, with the calculations using the Monte Carlo method. Comparison show that for the models to be considered, good agreement have been obtained
Simulations of kinetically irreversible protein aggregate structure.
Patro, S Y; Przybycien, T M
1994-01-01
We have simulated the structure of kinetically irreversible protein aggregates in two-dimensional space using a lattice-based Monte-Carlo routine. Our model specifically accounts for the intermolecular interactions between hydrophobic and hydrophilic protein surfaces and a polar solvent. The simulations provide information about the aggregate density, the types of inter-monomer contacts and solvent content within the aggregates, the type and extent of solvent exposed perimeter, and the short-...
Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions
Rzepiela, Andrzej J.; Sengupta, Durba; Goga, Nicolae; Marrink, Siewert J.
2010-01-01
Antimicrobial peptides (AMPs) comprise a large family of peptides that include small cationic peptides, such as magainins, which permeabilize lipid membranes. Previous atomistic level simulations of magainin-H2 peptides show that they act by forming toroidal transmembrane pores. However, due to the
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.
Stanzione, Francesca; Jayaraman, Arthi
2016-05-01
In-silico design of polymeric biomaterials requires molecular dynamics (MD) simulations that retain essential atomistic/molecular details (e.g., explicit water around the biofunctional macromolecule) while simultaneously achieving large length and time scales pertinent to macroscale function. Such large-scale atomistically detailed macromolecular MD simulations with explicit solvent representation are computationally expensive. One way to overcome this limitation is to use an adaptive resolution scheme (AdResS) in which the explicit solvent molecules dynamically adopt either atomistic or coarse-grained resolution depending on their location (e.g., near or far from the macromolecule) in the system. In this study we present the feasibility and the limitations of AdResS methodology for studying polyethylene glycol (PEG) in adaptive resolution water, for varying PEG length and architecture. We first validate the AdResS methodology for such systems, by comparing PEG and solvent structure with that from all-atom simulations. We elucidate the role of the atomistic zone size and the need for calculating thermodynamic force correction within this AdResS approach to correctly reproduce the structure of PEG and water. Lastly, by varying the PEG length and architecture, we study the hydration of PEG, and the effect of PEG architectures on the structural properties of water. Changing the architecture of PEG from linear to multiarm star, we observe reduction in the solvent accessible surface area of the PEG, and an increase in the order of water molecules in the hydration shells. PMID:27108869
An atomistically validated continuum model for strain relaxation and misfit dislocation formation
Zhou, X. W.; Ward, D. K.; Zimmerman, J. A.; Cruz-Campa, J. L.; Zubia, D.; Martin, J. E.; van Swol, F.
2016-06-01
In this paper, molecular dynamics (MD) calculations have been used to examine the physics behind continuum models of misfit dislocation formation and to assess the limitations and consequences of approximations made within these models. Without compromising the physics of misfit dislocations below a surface, our MD calculations consider arrays of dislocation dipoles constituting a mirror imaged "surface". This allows use of periodic boundary conditions to create a direct correspondence between atomistic and continuum representations of dislocations, which would be difficult to achieve with free surfaces. Additionally, by using long-time averages of system properties, we have essentially reduced the errors of atomistic simulations of large systems to "zero". This enables us to deterministically compare atomistic and continuum calculations. Our work results in a robust approach that uses atomistic simulation to accurately calculate dislocation core radius and energy without the continuum boundary conditions typically assumed in the past, and the novel insight that continuum misfit dislocation models can be inaccurate when incorrect definitions of dislocation spacing and Burgers vector in lattice-mismatched systems are used. We show that when these insights are properly incorporated into the continuum model, the resulting energy density expression of the lattice-mismatched systems is essentially indistinguishable from the MD results.
Parallelizing Monte Carlo with PMC
Energy Technology Data Exchange (ETDEWEB)
Rathkopf, J.A.; Jones, T.R.; Nessett, D.M.; Stanberry, L.C.
1994-11-01
PMC (Parallel Monte Carlo) is a system of generic interface routines that allows easy porting of Monte Carlo packages of large-scale physics simulation codes to Massively Parallel Processor (MPP) computers. By loading various versions of PMC, simulation code developers can configure their codes to run in several modes: serial, Monte Carlo runs on the same processor as the rest of the code; parallel, Monte Carlo runs in parallel across many processors of the MPP with the rest of the code running on other MPP processor(s); distributed, Monte Carlo runs in parallel across many processors of the MPP with the rest of the code running on a different machine. This multi-mode approach allows maintenance of a single simulation code source regardless of the target machine. PMC handles passing of messages between nodes on the MPP, passing of messages between a different machine and the MPP, distributing work between nodes, and providing independent, reproducible sequences of random numbers. Several production codes have been parallelized under the PMC system. Excellent parallel efficiency in both the distributed and parallel modes results if sufficient workload is available per processor. Experiences with a Monte Carlo photonics demonstration code and a Monte Carlo neutronics package are described.
Mechanical properties of carbon nanostructures investigated by Monte Carlo simulations
International Nuclear Information System (INIS)
Full text: Carbon nanostructures are a fascinating class of materials combining high stiffness with low weight and exceptional toughness that makes carbon a promising candidate for applications in structural mechanics. Understanding the mechanical behavior of carbon structures also on atomistic length scales is inevitable in describing the mechanical performance and stability of large, hierarchical structures like carbon onions and fibers. In the presented work ab initio calculations were used to extract classical potentials describing stretching, bending and torsion deformations of carbon bonds that were used in subsequent Monte Carlo simulations to perform computational mechanical tests on graphene, carbon nanotubes and fullerenes. These tests included the application of hydrostatic pressure, the application of a ring load and the deformation of a fullerene between two plates. We analyzed the elastic response, as well as the stability limits and post buckling behavior of the structures for different sizes. The simulation results were compared to the predictions of nite element methods to evaluate macroscopic parameters like elastic modulus or Poisson ratio of the investigated structures. In fullerenes special attention was paid to the influence of pentagons that are inherently present in these structures. It was observed that the pentagons deform less than the atomic bonds in hexagonal geometry. (author)
Monte Carlo simulations of lattice models for single polymer systems
Energy Technology Data Exchange (ETDEWEB)
Hsu, Hsiao-Ping, E-mail: hsu@mpip-mainz.mpg.de [Max-Planck-Institut für Polymerforschung, Ackermannweg 10, D-55128 Mainz (Germany)
2014-10-28
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length N∼O(10{sup 4}). Based on the standard simple cubic lattice model (SCLM) with fixed bond length and the bond fluctuation model (BFM) with bond lengths in a range between 2 and √(10), we investigate the conformations of polymer chains described by self-avoiding walks on the simple cubic lattice, and by random walks and non-reversible random walks in the absence of excluded volume interactions. In addition to flexible chains, we also extend our study to semiflexible chains for different stiffness controlled by a bending potential. The persistence lengths of chains extracted from the orientational correlations are estimated for all cases. We show that chains based on the BFM are more flexible than those based on the SCLM for a fixed bending energy. The microscopic differences between these two lattice models are discussed and the theoretical predictions of scaling laws given in the literature are checked and verified. Our simulations clarify that a different mapping ratio between the coarse-grained models and the atomistically realistic description of polymers is required in a coarse-graining approach due to the different crossovers to the asymptotic behavior.
International Nuclear Information System (INIS)
Highlights: ► We have studied the coupling among gas, plasma and surface in the divertor region. ► A one-dimensional PIC-DSMC model has been developed. ► Profiles of density and temperature of all the species involved have been provided. ► MAR processes are effective in a region smaller than 1.5 mm from the divertor plate. ► For regions more distant, the ionization of atoms, produced by MAR, starts to occur. - Abstract: The coupled dynamics and kinetics between gas and plasma in the divertor region is studied by means of a one-dimensional Particle in Cell-Direct Simulation Monte Carlo (PIC-DSMC) model. In particular, the collision-induced vibrational excitation/relaxation of H2 molecules and particle–surface interaction (vibrational relaxation and recombinative desorption) have been considered in detail to estimate the importance of plasma volumetric recombination by molecular assisted reaction (MAR). Spatially resolved results show that MAR processes are effective very close to the divertor plate in a region smaller than 1.5 mm from the divertor plate. For regions more distant the ionization of atoms, produced by MAR, starts to make molecular assisted recombination an ineffective reaction.
Monte Carlo Simulation of Linear Polymer Thermal Depolymerization under Isothermal and Dynamic Modes
Bystritskaya, Elena V.; Karpukhin, Oleg N.; Kutsenova, Alla V.
2011-01-01
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 = 1 0 0 and different width (polydispersity index, P D I = / = 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 wid...
International Nuclear Information System (INIS)
Recently, the in vivo processes of platelet function and the reaction and interaction of platelets with components of the blood vessel wall and artificial surfaces have received increasing attention. In this article the focus is placed on two aspects of platelet function and kinetics as revealed by 111In-labelled platelets. First the interaction of platelets with foreign prosthetic surfaces is discussed and some interesting facets of platelet functions that have come to light, are pointed out. Secondly, experiences with the development and refinement of an improved technique, namely the dual-isotope subtraction method, which increases the sensitivity of platelet imaging and allows the detection of relatively small areas of platelet deposition with accuracy, are described
Atomistic study of macroscopic analogs to short-chain molecules
Welch, Kyle J.; Kilmer, Clayton S. G.; Corwin, Eric I.
2015-02-01
We use a bath of chaotic surface waves in water to mechanically and macroscopically mimic the thermal behavior of a short articulated chain with only nearest-neighbor interactions. The chaotic waves provide isotropic and random agitation to which a temperature can be ascribed, allowing the chain to passively explore its degrees of freedom in analogy to thermal motion. We track the chain in real time and infer end-to-end potentials using Boltzmann statistics. We extrapolate our results, by using Monte Carlo simulations of self-avoiding polymers, to lengths not accessible in our system. In the long-chain limit we demonstrate universal scaling of the statistical parameters of all chains in agreement with well-known predictions for self-avoiding walks. However, we find that the behavior of chains below a characteristic length scale fundamentally differs. We find that short chains have much greater compressional stiffness than would be expected. However, chains rapidly soften as length increases to meet with expected scalings.
Monte Carlo simulation of local correlation and cluster formation in model fcc binary alloys
International Nuclear Information System (INIS)
Through the simulation with the Monte Carlo method is carried out the atomistic description of structure in a model fcc binary alloys A - B, which present at low-temperature trends to ordering. We use the ABV model of the alloy within the pair interaction approach with nearest neighbors and constant ordering energy. The dynamic was introduced through a vacancy which exchanges places with the atoms of nearest neighbors. The simulation was made on a fcc lattice with 256, 2048, 16,384 and 62,500 sites, using periodic boundary conditions to avoid edge effects. It was determined the probability of formation of different atomic clusters A13 - mBm (m = 0, 1, 2, ...13) consisting of 13 atoms as a function of the concentration and temperature, as well as the first short-range order parameters of Warren-Cowley. We found that in some regions of temperature and concentration is observed compositional and thermal polymorphism of clusters. (author)
Monte Carlo simulation of atomic aggregates formation in model bcc binary alloys. Preliminary report
International Nuclear Information System (INIS)
By means of the Monte Carlo simulation an atomistic description of the structure of model bcc binary alloys was made. We used ABV model of the alloy where the approach of pair interaction to first neighbours with constant ordering energy is assumed. The dynamics was introduced by means of a vacancy that interchanges of place with nearest neighbouring atoms. The simulations were made in a bcc lattice with 128, 1024, 8192 and 16000 sites, applying periodic boundary conditions to avoid edge effects. We calculate the formation probabilities of different atomic aggregate A9-m Bm (m = 0, 1, 2,... 9) as function of concentration of the components and the temperature. In some regions of temperature and concentration, compositional and thermal polymorphism of aggregates is observed. (author)
Frequency-domain deviational Monte Carlo method for linear oscillatory gas flows
Ladiges, Daniel R.; Sader, John E.
2015-10-01
Oscillatory non-continuum low Mach number gas flows are often generated by nanomechanical devices in ambient conditions. These flows can be simulated using a range of particle based Monte Carlo techniques, which in their original form operate exclusively in the time-domain. Recently, a frequency-domain weight-based Monte Carlo method was proposed [D. R. Ladiges and J. E. Sader, "Frequency-domain Monte Carlo method for linear oscillatory gas flows," J. Comput. Phys. 284, 351-366 (2015)] that exhibits superior statistical convergence when simulating oscillatory flows. This previous method used the Bhatnagar-Gross-Krook (BGK) kinetic model and contains a "virtual-time" variable to maintain the inherent time-marching nature of existing Monte Carlo algorithms. Here, we propose an alternative frequency-domain deviational Monte Carlo method that facilitates the use of a wider range of molecular models and more efficient collision/relaxation operators. We demonstrate this method with oscillatory Couette flow and the flow generated by an oscillating sphere, utilizing both the BGK kinetic model and hard sphere particles. We also discuss how oscillatory motion of arbitrary time-dependence can be simulated using computationally efficient parallelization. As in the weight-based method, this deviational frequency-domain Monte Carlo method is shown to offer improved computational speed compared to the equivalent time-domain technique.
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.
Determining anaerobic degradation kinetics from batch tests.
Moreda, Iván López
2016-01-01
Data obtained from a biomethane potential (BMP) test were used in order to obtain the parameters of a kinetic model of solid wastes anaerobic degradation. The proposed model considers a hydrolysis step with a first order kinetic, a Monod kinetic for the soluble organic substrate degradation and a first order decay of microorganisms. The instantaneous release of methane was assumed. The parameters of the model are determined following a direct search optimization procedure. A 'multiple-shooting' technique was used as a first step of the optimization process. The confidence interval of the parameters was determined by using Monte Carlo simulations. Also, the distribution functions of the parameters were determined. Only the hydrolysis first order constant shows a normal distribution. PMID:27191569
Kinetic theory for dilute cohesive granular gases with a square well potential.
Takada, Satoshi; Saitoh, Kuniyasu; Hayakawa, Hisao
2016-07-01
We develop the kinetic theory of dilute cohesive granular gases in which the attractive part is described by a square well potential. We derive the hydrodynamic equations from the kinetic theory with the microscopic expressions for the dissipation rate and the transport coefficients. We check the validity of our theory by performing the direct simulation Monte Carlo. PMID:27575205
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...
Subdiffusion kinetics of nanoprecipitate growth and destruction in solid solutions
Sibatov, R. T.; Svetukhin, V. V.
2015-06-01
Based on fractional differential generalizations of the Ham and Aaron-Kotler precipitation models, we study the kinetics of subdiffusion-limited growth and dissolution of new-phase precipitates. We obtain the time dependence of the number of impurities and dimensions of new-phase precipitates. The solutions agree with the Monte Carlo simulation results.
Monte Carlo simulation of tomography techniques using the platform Gate
International Nuclear Information System (INIS)
Simulations play a key role in functional imaging, with applications ranging from scanner design, scatter correction, protocol optimisation. GATE (Geant4 for Application Tomography Emission) is a platform for Monte Carlo Simulation. It is based on Geant4 to generate and track particles, to model geometry and physics process. Explicit modelling of time includes detector motion, time of flight, tracer kinetics. Interfaces to voxellised models and image reconstruction packages improve the integration of GATE in the global modelling cycle. In this work Monte Carlo simulations are used to understand and optimise the gamma camera's performances. We study the effect of the distance between source and collimator, the diameter of the holes and the thick of the collimator on the spatial resolution, energy resolution and efficiency of the gamma camera. We also study the reduction of simulation's time and implement a model of left ventricle in GATE. (Author). 7 refs
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.
Hybrid continuum–atomistic modelling of swift heavy ion radiation damage in germanium
International Nuclear Information System (INIS)
The response of germanium to swift heavy ion irradiation is simulated using a hybrid continuum–atomistic approach. The continuum part of the model, which characterises the electronic excitations is an extension of the inelastic thermal spike based on an approximation to the Boltzmann transport equation; while the atomistic part is represented with molecular dynamics. This integrated method can realistically account for the non-equilibrium carrier dynamics in band-gap materials under irradiation, unlike earlier developments based on the two-temperature approach. The model is used to obtain temporal and spatial evolution of carrier density, electronic temperature and lattice temperature for germanium irradiated with carbon cluster ions. Good agreement with experimental data of amorphised latent track radii for different stopping powers is obtained by fitting a constant value for the electron–phonon coupling strength – the only parameter treated as free in the model
Atomistic Conversion Reaction Mechanism of WO3 in Secondary Ion Batteries of Li, Na, and Ca.
He, Yang; Gu, Meng; Xiao, Haiyan; Luo, Langli; Shao, Yuyan; Gao, Fei; Du, Yingge; Mao, Scott X; Wang, Chongmin
2016-05-17
Intercalation and conversion are two fundamental chemical processes for battery materials in response to ion insertion. The interplay between these two chemical processes has never been directly seen and understood at atomic scale. Here, using in situ HRTEM, we captured the atomistic conversion reaction processes during Li, Na, Ca insertion into a WO3 single crystal model electrode. An intercalation step prior to conversion is explicitly revealed at atomic scale for the first time for Li, Na, Ca. Nanoscale diffraction and ab initio molecular dynamic simulations revealed that after intercalation, the inserted ion-oxygen bond formation destabilizes the transition-metal framework which gradually shrinks, distorts and finally collapses to an amorphous W and Mx O (M=Li, Na, Ca) composite structure. This study provides a full atomistic picture of the transition from intercalation to conversion, which is of essential importance for both secondary ion batteries and electrochromic devices. PMID:27071488
Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations
Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.
2016-07-01
Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.
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.
Energy Technology Data Exchange (ETDEWEB)
Soppa, E.A., E-mail: ewa.soppa@mpa.uni-stuttgart.de; Kohler, C., E-mail: christopher.kohler@mpa.uni-stuttgart.de; Roos, E., E-mail: eberhard.roos@mpa.uni-stuttgart.de
2014-03-01
Experimental investigations on the austenitic stainless steel X6CrNiNb18-10 (AISI – 347) and concomitant atomistic simulations of a FeNi nanocrystalline model system have been performed in order to understand the basic mechanisms of fatigue damage under cyclic loading. Using electron backscatter diffraction (EBSD) the influence of deformation induced martensitic transformation and NbC size distribution on the fatigue crack formation has been demonstrated. The martensite nucleates prevalently at grain boundaries, triple points and at the specimen free surface and forms small (∼1 µm sized) differently oriented grains. The atomistic simulations show the role of regions of a high density of stacking faults for the martensitic transformation.
International Nuclear Information System (INIS)
Experimental investigations on the austenitic stainless steel X6CrNiNb18-10 (AISI – 347) and concomitant atomistic simulations of a FeNi nanocrystalline model system have been performed in order to understand the basic mechanisms of fatigue damage under cyclic loading. Using electron backscatter diffraction (EBSD) the influence of deformation induced martensitic transformation and NbC size distribution on the fatigue crack formation has been demonstrated. The martensite nucleates prevalently at grain boundaries, triple points and at the specimen free surface and forms small (∼1 µm sized) differently oriented grains. The atomistic simulations show the role of regions of a high density of stacking faults for the martensitic transformation
Electronic states in an atomistic carbon quantum dot patterned in graphene
Craco, L.; Carara, S. S.; da Silva Pereira, T. A.; Milošević, M. V.
2016-04-01
We reveal the emergence of metallic Kondo clouds in an atomistic carbon quantum dot, realized as a single-atom junction in a suitably patterned graphene nanoflake. Using density functional dynamical mean-field theory (DFDMFT) we show how correlation effects lead to striking features in the electronic structure of our device, and how those are enhanced by the electron-electron interactions when graphene is patterned at the atomistic scale. Our setup provides a well-controlled environment to understand the principles behind the orbital-selective Kondo physics and the interplay between orbital and spin degrees of freedom in carbon-based nanomaterials, which indicate new pathways for spintronics in atomically patterned graphene.
Chen, Xing; Moore, Justin E; Zekarias, Meserret; Jensen, Lasse
2015-01-01
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. PMID:26555179
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.
Permittivity of oxidized ultra-thin silicon films from atomistic simulations
Penazzi, G.; KWOK, YH; Aradi, B.; Pecchia, A.; Frauenheim, T.; Chen, G.; Markov, SN
2015-01-01
We establish the dependence of the permittivity of oxidized ultra-thin silicon films on the film thickness by means of atomistic simulations within the density-functional-based tight-binding theory (DFTB). This is of utmost importance for modeling ultra- and extremely-thin silicon-on-insulator MOSFETs, and for evaluating their scaling potential. We demonstrate that electronic contribution to the dielectric response naturally emerges from the DFTB Hamiltonian when coupled to Poisson equation s...
A numerical method for the time coarsening of transport processes at the atomistic scale
Gonzalez-Ferreiro, B.; Romero, I.; Ortiz, M.
2016-05-01
We propose a novel numerical scheme for the simulation of slow transport processes at the atomistic scale. The scheme is based on a model for non-equilibrium statistical thermodynamics recently proposed by the authors, and extends it by formulating a variational integrator, i.e. a discrete functional whose optimality conditions provide all the governing equations of the problem. The method is employed to study surface segregation of AuAg alloys and its convergence is confirmed numerically.
Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension
Muddana, Hari S.; Gullapalli, Ramachandra R.; Manias, Evangelos; Butler, Peter J.
2010-01-01
Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from −2.6 mN m−1 to 15.9 mN m−1. Simulations showed that th...
Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments.
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. PMID:26809025
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...... 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....
International Nuclear Information System (INIS)
The present paper studies the size effects during nanoindentation in Ni thin films using large scale atomistic simulation. The main focus of this paper is to evaluate the available theoretical models of size effects during nanoindentation using atomistic simulation. First, the dislocation nucleation and evolution in the simulated samples are studied. In the next step, the plastic zone size is obtained for each sample at several indentation depths incorporating the dislocation visualization. The results show that the plastic zone size divided by the contact radius is not a constant factor and varies as the indentation depth changes. The total length of dislocations located in the plastic zone is measured in the simulated samples and compared to that of the corresponding theoretical models. The results obtained from the atomistic simulation verify the theoretical predictions of the dislocation length. Next, the variation of hardness obtained directly from the molecular dynamics outputs, which is the indentation force over the contact area, is studied. In the case of conical indenter, the theoretical predictions of hardness have been verified using both experiments and simulations, and the current simulation shows the same trend, i.e. the hardness decreases as the indentation depth increases. However, in the cases of flat indenters, the theoretical models have not been validated using any experiments or simulations. Here, in the cases of flat indenters, the simulation results verify the theoretical predictions of hardness. They show that the hardness increases as the indentation depth increases. The variation of dislocation density as a function of indentation depth is then studied. In the case of nanoindentation experiment, the validity of Taylor hardening model, i.e. the relation between the hardening and dislocation density, which has not been previously studied with full atomistic details, is investigated. Accordingly, the hardness obtained directly from the
Atomistic calculation of the thermal conductance of large scale bulk-nanowire junctions
Duchemin, Ivan; Donadio, Davide
2011-01-01
We have developed an efficient scalable kernel method for thermal transport in open systems, with which we have computed the thermal conductance of a junction between bulk silicon and silicon nanowires with diameter up to 10 nm. We have devised scaling laws for transmission and reflection spectra, which allow us to predict the thermal resistance of bulk-nanowire interfaces with larger cross sections than those achievable with atomistic simulations. Our results indicate the characteristic size...
J. R. Watling; Barker, J R; Asenov, A
2000-01-01
The atomistic modelling of silicon MOSFET devices becomes essential at deep sub-micron scales when it is no longer possible to represent the charged impurities by a continuous charge distribution with a determined doping density. Instead the spatial distribution and the actual number of dopants must be treated as discrete random variables. The present paper addresses the issue of modelling the dynamics of discrete carrier flow in a semiconductor device utilising a simple model of the carrier-...
An atomistic-continuum hybrid simulation of fluid flows over superhydrophobic surfaces
LI Qiang; He, Guo-Wei
2009-01-01
Recent experiments have found that slip length could be as large as on the order of 1 μm for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper, an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces, in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption i...
Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal
Huang, Liangliang; Seredych, Mykola; Bandosz, Teresa J.; van Duin, Adri C. T.; Lu, Xiaohua; Gubbins, Keith E.
2013-11-01
The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O/H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O/H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.
Hybrid Simulation Strategy for Simulating Self-Assembled Morphologies at the Atomistic Length Scales
Sethuraman, Vaidyanathan; Ganesan, Venkat
In the context of Lithium-ion batteries, an enhancement in both ionic conductivity and mechanical properties, were observed for block copolymer electrolytes with increasing MW. On the contrary, when homopolymers were used as electrolytes, the ionic conductivity decreased with increasing MW. However, the origins of such increase in conductivity are unclear and are speculated to be tied to both the morphology and the atomistic details of the copolymer themselves. Motivated by such issues, we present a strategy to create ordered morphologies of block copolymers at the atomistic level using a combination of coarse-graining and inverse coarse-graining techniques. A mapping which is developed using the long-ranged structural mapping in the disordered phases will be utilized to generate self-assembled morphologies. In particular we focus on generating self-assembled morphologies of PS-PEO at the atomistic length scales. Statics and dynamics of such self-assembled morphologies will be presented and the effect of self assembly on the transport properties of ions will also be explored. Funded by NSF.
Theoretical modeling of the PEMFC catalyst layer: A review of atomistic methods
International Nuclear Information System (INIS)
This article reviews recent progress in the catalyst layer modeling of polymer electrolyte membrane fuel cells. Theoretical modeling is important to understand the basic chemical, and physical phenomena at the atomistic level in materials and relating these fundamentals to the properties and performance of the catalyst layer. Two fundamentally important theoretical methods have been chosen to represent atomistic models, namely density functional theory (DFT) and classical molecular dynamics. In addition, some reactive force field models are highlighted, and the mathematical framework is sufficiently described. The literature review includes important contributions that help to understand the oxygen reduction reaction including gas-phase reaction trends, and the solvation effects are also presented. Moreover, the electric field effect is discussed along with the recently established double reference method in the DFT framework. Using two atomistic simulations based on different axiomatic theories, the production of current density in the molecular junctions is considered with respect to voltage, elucidating applications to simple systems. The models of water transportation via polymer electrolyte membrane, as well as the catalyst and support oxidation are described. Epoxidized carbon support, oxidizable metal-oxide support and electron localization function analysis have provided insights for improving catalyst support material and enable characterization of the bonding between the catalyst and support. Conclusions and future outlook are outlined at the end. Thus the present work enlightens the future of the catalyst modeling towards more realistic models
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.
Atomistic modeling of the dislocation dynamics and evaluation of static yield stress
Karavaev, A. V.; Dremov, V. V.; Ionov, G. V.
2015-09-01
Static strength characteristics of structural materials are of great importance for the analysis of the materials behaviour under mechanical loadings. Mechanical characteristics of structural materials such as elastic limit, strength limit, ultimate tensile strength, plasticity are, unlike elastic moduli, very sensitive to the presence of impurities and defects of crystal structure. Direct atomistic modeling of the static mechanical strength characteristics of real materials is an extremely difficult task since the typical time scales available for the direct modeling in the frames of classical molecular dynamics do not exceed a hundred of nanoseconds. This means that the direct atomistic modeling of the material deformation can be done for the regimes with rather high strain rates at which the yield stress and other mechanical strength characteristics are controlled by microscopic mechanisms different from those at low (quasi-static) strain rates. In essence, the plastic properties of structural materials are determined by the dynamics of the extended defects of crystal structure (edge and screw dislocations) and by interactions between them and with the other defects in the crystal. In the present work we propose a method that is capable to model the dynamics of edge dislocations in the fcc and hcp materials at dynamic deformations and to estimate the material static yield stress in the states of interest in the frames of the atomistic approach. The method is based on the numerical characterization of the stress relaxation processes in specially generated samples containing solitary edge dislocations.
Atomistic modeling of the dislocation dynamics and evaluation of static yield stress
Directory of Open Access Journals (Sweden)
Karavaev A.V.
2015-01-01
Full Text Available Static strength characteristics of structural materials are of great importance for the analysis of the materials behaviour under mechanical loadings. Mechanical characteristics of structural materials such as elastic limit, strength limit, ultimate tensile strength, plasticity are, unlike elastic moduli, very sensitive to the presence of impurities and defects of crystal structure. Direct atomistic modeling of the static mechanical strength characteristics of real materials is an extremely difficult task since the typical time scales available for the direct modeling in the frames of classical molecular dynamics do not exceed a hundred of nanoseconds. This means that the direct atomistic modeling of the material deformation can be done for the regimes with rather high strain rates at which the yield stress and other mechanical strength characteristics are controlled by microscopic mechanisms different from those at low (quasi-static strain rates. In essence, the plastic properties of structural materials are determined by the dynamics of the extended defects of crystal structure (edge and screw dislocations and by interactions between them and with the other defects in the crystal. In the present work we propose a method that is capable to model the dynamics of edge dislocations in the fcc and hcp materials at dynamic deformations and to estimate the material static yield stress in the states of interest in the frames of the atomistic approach. The method is based on the numerical characterization of the stress relaxation processes in specially generated samples containing solitary edge dislocations.
Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal
International Nuclear Information System (INIS)
The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O/H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O/H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials
Seoane, N.; Aldegunde, M.; García-Loureiro, A.; Valin, R.; Kalna, K.
2012-03-01
A detailed simulation study of the impact of quantum effects on random dopant induced fluctuations in a 15 nm gate length, implant free In0.75Ga0.25As MOSFET is carried out using parallel 3D finite-element drift-diffusion (DD) device simulations and a mesh with atomistic resolution. The DD device simulations are calibrated against finite element heterostructure ensemble Monte Carlo simulations. Three figures of merit for the off-state have been investigated: threshold voltage, off-current, and sub-threshold slope. Quantum confinement effects are taken into account through the density gradient approximation meticulously calibrating carrier density in the channel against 1D Poisson-Schrödinger solutions. We have shown that the net result of including quantum effects, while considering statistical dopant fluctuations, is a decrease in both threshold voltage fluctuations and threshold voltage shift. These results show the opposite trend generally seen in bulk Si MOSFETs simulated using 3D quantum corrected DD simulations with random discrete dopants in the channel region.
Monte Carlo simulations of neoclassical transport in toroidal plasmas
International Nuclear Information System (INIS)
FORTEC-3D code, which solves the drift-kinetic equation for torus plasmas and radial electric field using the δf Monte Carlo method, has developed to study the variety of issues relating to neoclassical transport phenomena in magnetic confinement plasmas. Here the numerical techniques used in FORTEC-3D are reviewed, and resent progress in the simulation method to simulate GAM oscillation is also explained. A band-limited white noise term is introduced in the equation of time evolution of radial electric field to excite GAM oscillation, which enables us to analyze GAM frequency using FORTEC-3D even in the case the collisionless GAM damping is fast. (author)
Proton Upset Monte Carlo Simulation
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.
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.
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.
Monte Carlo Particle Lists: MCPL
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.
Accelerated Monte Carlo Methods for Coulomb Collisions
Rosin, Mark; Ricketson, Lee; Dimits, Andris; Caflisch, Russel; Cohen, Bruce
2014-03-01
We present a new highly efficient multi-level Monte Carlo (MLMC) simulation algorithm for Coulomb collisions in a plasma. The scheme, initially developed and used successfully for applications in financial mathematics, is applied here to kinetic plasmas for the first time. The method is based on a Langevin treatment of the Landau-Fokker-Planck equation and has a rich history derived from the works of Einstein and Chandrasekhar. The MLMC scheme successfully reduces the computational cost of achieving an RMS error ɛ in the numerical solution to collisional plasma problems from (ɛ-3) - for the standard state-of-the-art Langevin and binary collision algorithms - to a theoretically optimal (ɛ-2) scaling, when used in conjunction with an underlying Milstein discretization to the Langevin equation. In the test case presented here, the method accelerates simulations by factors of up to 100. We summarize the scheme, present some tricks for improving its efficiency yet further, and discuss the method's range of applicability. Work performed for US DOE by LLNL under contract DE-AC52- 07NA27344 and by UCLA under grant DE-FG02-05ER25710.
International Nuclear Information System (INIS)
Recent developments in multiscale modelling include the treatment of atomistic scale interactions via molecular dynamics simulations. The atomistic stress definition at a given continuum point contains a space-averaging volume over nearby atoms to provide an averaged macroscopic stress measure. Previous work on atomistic stress measures introduce the size of this volume as an a priori given parameter. In this contribution we let the atomistic data speak for itself by hypothesizing that the influence between atoms can be effectively estimated from their relative spatial position and stress. Atoms with highly similar spatial position and stress should therefore be contained within the same space-averaging volume. We motivate the application of Gaussian mixture modelling as a principled probabilistic means of estimating this similarity directly from the atomistic data. This model enables the discovery of homogeneous sub-populations of atoms in an entirely data-driven manner. The size of the space-averaging volume then follows naturally from the average maximum extent of the sub-populations. Furthermore, we demonstrate how the model can be used to compute the stress at arbitrary continuum points. Thorough evaluation is conducted on a numerical example of an edge dislocation in a single crystal. We find that our results are in excellent agreement with the corresponding analytical solution. (paper)
Review of neutron noise analysis theory by Monte Carlo simulation
International Nuclear Information System (INIS)
Some debates on the theory of neutron noise analysis for reactor kinetic parameter measurement were found before 1970 but a report firmly clearing these debates has not been found, and a question was raised when neutron noise experiments for the TRIGA and HANARO reactors in Korea were performed. In order to clarify this question, the neutron noise experiment is simulated by the Monte Carlo method. This simulation confirms that the widely used equation is approximately valid and that the confusion was caused from the explanation on the derivation of the equation. Rossi-α technique is one of the representative methods of noise analyses for the reactor kinetic parameter measurement, but different opinions were raised for the chain reaction related term in the equation. The equation originally derived at the Los Alamos National Laboratory (LANL) has been widely accepted. However, the others were supported by strict mathematics and experiments as well, and the reason of discrepancy has not been clarified. Since it is the problem of basic concept before the effect of neutron energy or geometry is included, the Monte Carlo simulation for the simplest reactor model could clarify it. For this purpose, the experiment measuring the neutron noise is simulated, and it results that the original equation is approximately valid. However, it is judged that the explanation on the equation by the authors derived it for the first time is not so correct, but Orndoff who made the first experiment by the Ross-α technique explained it rather correctly
Solute segregation kinetics and dislocation depinning in a binary alloy
Dontsova, E.; Rottler, J.; Sinclair, C. W.
2015-06-01
Static strain aging, a phenomenon caused by diffusion of solute atoms to dislocations, is an important contributor to the strength of substitutional alloys. Accurate modeling of this complex process requires both atomic spatial resolution and diffusional time scales, which is very challenging to achieve with commonly used atomistic computational methods. In this paper, we use the recently developed "diffusive molecular dynamics" (DMD) method that is capable of describing the kinetics of the solute segregation process at the atomic level while operating on diffusive time scales in a computationally efficient way. We study static strain aging in the Al-Mg system and calculate the depinning shear stress between edge and screw dislocations and their solute atmospheres formed for various waiting times with different solute content and for a range of temperatures. A simple phenomenological model is also proposed that describes the observed behavior of the critical shear stress as a function of segregation level.
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.
Cholesterol-induced suppression of membrane elastic fluctuations at the atomistic level.
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. PMID:27154600
Energy Technology Data Exchange (ETDEWEB)
Kielpinski, A.L.
1995-03-01
Glass formulation development depends on an understanding of the effects of glass composition on its processibility and product quality. Such compositional effects on properties in turn depend on the microscopic structure of the glass. Historically, compositional effects on macroscopic properties have been explored empirically, e.g., by measuring viscosity at various glass compositions. The relationship of composition to structure has been studied by microstructural experimental methods. More recently, computer simulation has proved a fruitful complement to these more traditional methods of study. By simulating atomic interaction over a period of time using the molecular dynamics method, a direct picture of the glass structure and dynamics is obtained which can verify existing concepts as well as permit ``measurement`` of quantities inaccessible to experiment. Atomistic simulation can be of particular benefit in the development of waste glasses. As vitrification is being considered for an increasing variety of waste streams, process and product models are needed to formulate compositions for an extremely wide variety of elemental species and composition ranges. The demand for process and product models which can predict over such a diverse composition space requires mechanistic understanding of glass behavior; atomistic simulation is ideally suited for providing this understanding. Moreover, while simulation cannot completely eliminate the need for treatability studies, it can play a role in minimizing the experimentation on (and therefore contact handling of) such materials. This paper briefly reviews the molecular dynamics method, which is the primary atomistic simulation tool for studying glass structure. We then summarize the current state of glass simulation, emphasizing areas of importance for waste glass process/product modeling. At SRS, glass process and product models have been formulated in terms of glass structural concepts.
Shell model Monte Carlo methods
International Nuclear Information System (INIS)
We review quantum Monte Carlo methods for dealing with large shell model problems. These methods reduce the imaginary-time many-body evolution operator to a coherent superposition of one-body evolutions in fluctuating one-body fields; resultant path integral is evaluated stochastically. We first discuss the motivation, formalism, and implementation of such Shell Model Monte Carlo methods. There then follows a sampler of results and insights obtained from a number of applications. These include the ground state and thermal properties of pf-shell nuclei, thermal behavior of γ-soft nuclei, and calculation of double beta-decay matrix elements. Finally, prospects for further progress in such calculations are discussed. 87 refs
Kinematics of multigrid Monte Carlo
International Nuclear Information System (INIS)
We study the kinematics of multigrid Monte Carlo algorithms by means of acceptance rates for nonlocal Metropolis update proposals. An approximation formula for acceptance rates is derived. We present a comparison of different coarse-to-fine interpolation schemes in free field theory, where the formula is exact. The predictions of the approximation formula for several interacting models are well confirmed by Monte Carlo simulations. The following rule is found: For a critical model with fundametal Hamiltonian Η(φ), absence of critical slowing down can only be expected if the expansion of (Η(φ+ψ)) in terms of the shift ψ contains no relevant (mass) term. We also introduce a multigrid update procedure for nonabelian lattice gauge theory and study the acceptance rates for gauge group SU(2) in four dimensions. (orig.)
Asynchronous Anytime Sequential Monte Carlo
Paige, Brooks; Wood, Frank; Doucet, Arnaud; Teh, Yee Whye
2014-01-01
We introduce a new sequential Monte Carlo algorithm we call the particle cascade. The particle cascade is an asynchronous, anytime alternative to traditional particle filtering algorithms. It uses no barrier synchronizations which leads to improved particle throughput and memory efficiency. It is an anytime algorithm in the sense that it can be run forever to emit an unbounded number of particles while keeping within a fixed memory budget. We prove that the particle cascade is an unbiased mar...
Neural Adaptive Sequential Monte Carlo
Gu, Shixiang; Ghahramani, Zoubin; Turner, Richard E
2015-01-01
Sequential Monte Carlo (SMC), or particle filtering, is a popular class of methods for sampling from an intractable target distribution using a sequence of simpler intermediate distributions. Like other importance sampling-based methods, performance is critically dependent on the proposal distribution: a bad proposal can lead to arbitrarily inaccurate estimates of the target distribution. This paper presents a new method for automatically adapting the proposal using an approximation of the Ku...
Parallel Monte Carlo reactor neutronics
International Nuclear Information System (INIS)
The issues affecting implementation of parallel algorithms for large-scale engineering Monte Carlo neutron transport simulations are discussed. For nuclear reactor calculations, these include load balancing, recoding effort, reproducibility, domain decomposition techniques, I/O minimization, and strategies for different parallel architectures. Two codes were parallelized and tested for performance. The architectures employed include SIMD, MIMD-distributed memory, and workstation network with uneven interactive load. Speedups linear with the number of nodes were achieved
Adaptive Multilevel Monte Carlo Simulation
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).
Monomial Gamma Monte Carlo Sampling
Zhang, Yizhe; Wang, Xiangyu; Chen, Changyou; Fan, Kai; Carin, Lawrence
2016-01-01
We unify slice sampling and Hamiltonian Monte Carlo (HMC) sampling by demonstrating their connection under the canonical transformation from Hamiltonian mechanics. This insight enables us to extend HMC and slice sampling to a broader family of samplers, called monomial Gamma samplers (MGS). We analyze theoretically the mixing performance of such samplers by proving that the MGS draws samples from a target distribution with zero-autocorrelation, in the limit of a single parameter. This propert...
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.
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.
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.
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
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...
Experimental and atomistic study of the elastic properties of α′ Fe–C martensite
International Nuclear Information System (INIS)
We calculate the elastic constants of Fe–C α′ single crystals and compare them to our own and previously published measurement data on polycrystals. Based on a recently developed interatomic interaction potential, discrepancies between our present experimental results and earlier measurements are discussed, and can be settled with the help of our simulation data. Atomistic data obtained with a different interatomic potential show less satisfactory agreement. Our results demonstrate a strong increase of the elastic anisotropy with carbon content, but only a mild dependence of the Debye temperature.
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.
Investigations on the mechanical behavior of nanowires with twin boundaries by atomistic simulations
International Nuclear Information System (INIS)
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
Tsuru, Tomohito; Aoyagi, Yoshiteru; Kaji, Yoshiyuki; Shimokawa, Tomotsugu
2016-03-01
The effect of the dislocation density on yield strength and subsequent plastic deformation of ultrafine-grained metals was investigated in large-scale atomistic simulations. Polycrystalline models were constructed and uniaxial tension and compression were applied to elucidate the heterogeneous plastic deformation and the Bauschinger effect. The initial yield becomes heterogeneous as the dislocation density decreases owing to a wide range of Schmid factors of activated slip systems in each grain. A different mechanism of the Bauschinger effect was proposed, where the Bauschinger effect of ultrafine-grained metals is caused by the change in dislocation density in the process of forward and backward loadings.
Atomistic investigation of the structure and transport properties of tilt grain boundaries of UO2
International Nuclear Information System (INIS)
We apply atomistic simulation techniques to address whether oxygen shows higher diffusivity at the grain boundary region compared to that in bulk UO2, and whether the relative diffusivity is affected by the choice of the grain boundary. We consider coincident site lattice grain boundaries, Σ3, Σ5, Σ9, Σ11 and Σ19, expressing the {n n 1}, {n 1 1}, and {n 1 0} surfaces, and evaluate the extent that the grain boundary structures affect the diffusion of oxygen. We found that oxygen diffusion is enhanced at all boundaries and in the adjacent regions, with strong dependence on the temperature and local structure
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.
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.
Fu, Yao; Song, Jeong-Hoon
2015-08-01
Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic-continuum bridging.
International Nuclear Information System (INIS)
The glide of edge and screw dislocation in solid solution is modeled through atomistic simulations in two model alloys of Ni(Al) and Al(Mg) described within the embedded atom method. Our approach is based on the study of the elementary interaction between dislocations and solutes to derive solid solution hardening of face centered cubic binary alloys. We identify the physical origins of the intensity and range of the interaction between a dislocation and a solute atom. The thermally activated crossing of a solute atom by a dislocation is studied at the atomistic scale. We show that hardening of edge and screw segments are similar. We develop a line tension model that reproduces quantitatively the atomistic calculations of the flow stress. We identify the universality class to which the dislocation depinning transition in solid solution belongs. (author)
Extending canonical Monte Carlo methods
Velazquez, L.; Curilef, S.
2010-02-01
In this paper, we discuss the implications of a recently obtained equilibrium fluctuation-dissipation relation for the extension of the available Monte Carlo methods on the basis of the consideration of the Gibbs canonical ensemble to account for the existence of an anomalous regime with negative heat capacities C < 0. The resulting framework appears to be a suitable generalization of the methodology associated with the so-called dynamical ensemble, which is applied to the extension of two well-known Monte Carlo methods: the Metropolis importance sampling and the Swendsen-Wang cluster algorithm. These Monte Carlo algorithms are employed to study the anomalous thermodynamic behavior of the Potts models with many spin states q defined on a d-dimensional hypercubic lattice with periodic boundary conditions, which successfully reduce the exponential divergence of the decorrelation time τ with increase of the system size N to a weak power-law divergence \\tau \\propto N^{\\alpha } with α≈0.2 for the particular case of the 2D ten-state Potts model.
International Nuclear Information System (INIS)
We have shown that the transport equation can be solved with particles, like the Monte-Carlo method, but without random numbers. In the Monte-Carlo method, particles are created from the source, and are followed from collision to collision until either they are absorbed or they leave the spatial domain. In our method, particles are created from the original source, with a variable weight taking into account both collision and absorption. These particles are followed until they leave the spatial domain, and we use them to determine a first collision source. Another set of particles is then created from this first collision source, and tracked to determine a second collision source, and so on. This process introduces an approximation which does not exist in the Monte-Carlo method. However, we have analyzed the effect of this approximation, and shown that it can be limited. Our method is deterministic, gives reproducible results. Furthermore, when extra accuracy is needed in some region, it is easier to get more particles to go there. It has the same kind of applications: rather problems where streaming is dominant than collision dominated problems
Raffaini, Giuseppina; Ganazzoli, Fabio; Mazzaglia, Antonino
2016-01-01
Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809
Ganazzoli, Fabio; Mazzaglia, Antonino
2016-01-01
Summary Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809
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...
Mishra, Shawn; Keten, Sinan
2013-01-01
We present an investigation of the retained solvent effect on the glass transition temperature (Tg) of poly(methyl methacrylate) (PMMA) through all-atom molecular dynamics simulations. Addition of a weakly interactive solvent, tetrahydrofuran (THF), causes a depression of the PMMA Tg that can be identified through an analysis of the mean squared displacement of the polymer chains from atomistic trajectories. Our results are in very good agreement with an atomistically informed theoretical model based on free volume theory and demonstrate the applicability of molecular simulation to discern solvent effects on polymer thermomechanical behavior in silico.
International Nuclear Information System (INIS)
Highlights: • We present a Monte Carlo method for computing the adjoint-weighted kinetics parameters via the IFP algorithm. • Extensive verification tests are performed on simple models. • Several validation tests are performed on the measured values of effective delayed neutron fraction and Rossi alpha. - Abstract: The analysis of neutron kinetics relies on the knowledge of adjoint-weighted kinetics parameters, which are key to safety issues in the context of transient or accidental reactor behavior. The Iterated Fission Probability (IFP) method allows the adjoint-weighted mean generation time and delayed neutron fraction to be computed within a Monte Carlo power iteration calculation. In this work we describe the specific features of the implementation of the IFP algorithm in the reference Monte Carlo code TRIPOLI-4® developed at CEA. Several verification and validation tests are discussed, and the impact of nuclear data libraries, IFP cycle length and inter-cycle correlations are analyzed in detail
Leetmaa, Mikael; Pettersson, Lars G M
2009-01-01
We present a novel approach to reverse Monte Carlo (RMC) modeling, SpecSwap-RMC, which makes use of pre-computed property data from a discrete configuration space replacing atomistic moves with swap moves of contributions to a sample-set representing the average, or summed property. The approach is particularly suitable for disordered systems and properties which require significant computer time to compute. We demonstrate the approach by fitting jointly and separately the EXAFS signal and x-ray absorption spectrum (XAS) of ice Ih using as SpecSwap sample-set 80 configurations from a space of 1382 local structures with associated pre-computed spectra. As an additional demonstration we compare SpecSwap and FEFFIT fits of EXAFS data on crystalline copper finding excellent agreement.
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.
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.
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.
International Nuclear Information System (INIS)
Researchers at the National Renewable Energy Laboratory and their collaborators have developed over the past ∼10 years a set of algorithms for an atomistic description of the electronic structure of nanostructures, based on plane-wave pseudopotentials and configurationinteraction. The present contribution describes the first step in assembling these various codes into a single, portable, integrated set of software packages. This package is part of an ongoing research project in the development stage. Components of NanoPSE include codes for atomistic nanostructure generation and passivation, valence force field model for atomic relaxation, code for potential field generation, empirical pseudopotential method solver, strained linear combination of bulk bands method solver, configuration interaction solver for excited states, selection of linear algebra methods, and several inverse band structure solvers. Although not available for general distribution at this time as it is being developed and tested, the design goal of the NanoPSE software is to provide a software context for collaboration. The software package is enabled by fcdev, an integrated collection of best practice GNU software for open source development and distribution augmented to better support FORTRAN
Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations
Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.
2009-01-01
Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.
An atomistic interpretation of Planck's 1900 derivation of his radiation law
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In deriving his radiation law in 1900, Max Planck employed a simple harmonic oscillator to model the exchange of energy between radiation and matter. Traditionally the harmonic oscillator has been viewed as modelling an entity which is itself oscillating, although a suitable oscillating entity has not been forthcoming. (Opinion is divided between a material oscillator, an imaginary oscillator and a need to revise Planck's derivation to apply to cavity modes of oscillation). We offer a novel, atomistic interpretation of Planck's derivation wherein the harmonic oscillator models a transition between the internal quantum states of an atom|not a normal electronic atom characterised by possible energies 0 and hν, but an atom populated by subatomic bosons (such as pions) and characterised by multiple occupancy of quantum states and possible energies nhν (n = 0;1;2; ...). We show how Planck's derivation can be varied to accommodate electronic atoms. A corollary to the atomistic interpretation is that Planck's derivation can no longer be construed as support for the postulate that material oscillating entities can have only those energies that are multiples of hν. Copyright (2000) CSIRO Australia
Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.
Wang, Yong-Lei; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N; Laaksonen, Aatto
2014-07-24
We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions. PMID:25020237
New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation
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.
Comparative study of embedded atom potentials for atomistic simulations of fracture in α-iron
International Nuclear Information System (INIS)
Atomistic simulations play a crucial role in advancing our understanding of the crack-tip processes that take place during fracture of semi-brittle materials like α-iron. As with all atomistic simulations, the results of such simulations however depend critically on the underlying atomic interaction model. Here, we present a systematic study of eight α-iron embedded atom method potentials used to model cracks subjected to plane strain mode-I loading conditions in six different crystal orientations. Molecular statics simulations are used to determine the fracture behavior (cleavage, dislocation emission, twinning) and the critical stress intensity factor KIc. The structural transformations in front of the crack tips, and in particular the occurrence of {1 1 0} planar faults, are analyzed in detail and related to the strain-dependent generalized stacking fault energy curve. The simulation results are discussed in terms of theoretical fracture criteria and compared to recent experimental data. The different potentials are ranked according to their capability to model the experimentally observed fracture behavior. (paper)
Atomistically informed crystal plasticity model for body-centered cubic iron
International Nuclear Information System (INIS)
The glide of screw dislocations with non-planar dislocation cores dominates the plastic deformation behavior in body-centered cubic iron. This yields a strong strain rate and temperature dependence of the flow stress, the breakdown of Schmid’s law and a dependence of dislocation mobility on stress components that do not contribute to the mechanical driving force of dislocation glide. We developed a constitutive plasticity model that takes all these effects into account. The model is based on the crystal plasticity approach and parameterized by performing molecular statics calculations using a semi-empirical potential. The atomistic studies yield quantitative relations between local stress tensor components and the mobility of dislocations. Together with experimental stress–strain curves obtained for two different orientations of iron single crystals taken from the literature, the constitutive law is completely parameterized. The model is validated by comparing numerical single crystal tension tests for a third orientation to the equivalent experimental data from the literature. We also provide results for the temperature and strain rate dependence of the new atomistically informed constitutive model.
An atomistic model for cross-linked HNBR elastomers used in seals
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.
Atomistic nature in band-to-band tunneling in two-dimensional silicon pn tunnel diodes
Tabe, Michiharu; Tan, Hoang Nhat; Mizuno, Takeshi; Muruganathan, Manoharan; Anh, Le The; Mizuta, Hiroshi; Nuryadi, Ratno; Moraru, Daniel
2016-02-01
We study low-temperature transport properties of two-dimensional (2D) Si tunnel diodes, or Si Esaki diodes, with a lateral layout. In ordinary Si Esaki diodes, interband tunneling current is severely limited because of the law of momentum conservation, while nanoscale Esaki diodes may behave differently due to the dopants in the narrow depletion region, by atomistic effects which release such current limitation. In thin-Si lateral highly doped pn diodes, we find clear signatures of interband tunneling between 2D-subbands involving phonon assistance. More importantly, the tunneling current is sharply enhanced in a narrow voltage range by resonance via a pair of a donor- and an acceptor-atom in the pn junction region. Such atomistic behavior is recognized as a general feature showing up only in nanoscale tunnel diodes. In particular, a donor-acceptor pair with deeper ground-state energies is likely to be responsible for such a sharply enhanced current peak, tunable by external biases.
Atomistic cluster alignment method for local order mining in liquids and glasses
International Nuclear Information System (INIS)
An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the 'order mining' idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65, and Zr36Ni64). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.
Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations
Energy Technology Data Exchange (ETDEWEB)
Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner
2013-10-01
In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.
Kooi, BJ
2006-01-01
An analytical theory has been developed, based on Monte Carlo (MC) simulations, describing the kinetics of isothermal phase transformations proceeding by nucleation and subsequent growth for d-1 dimensional growth in d dimensional space (with d 2 or 3). This type of growth is of interest since it is
International Nuclear Information System (INIS)
The neutron generation time Λ plays an important role in the reactor kinetics. However, it is not straightforward nor standard in most continuous energy Monte Carlo codes which are able to calculate the prompt neutron lifetime lp directly. The difference between Λ and lp are sometimes very apparent. As very few delayed neutrons are produced in the reactor, they have little influence on Λ. Thus on the assumption that no delayed neutrons are produced in the system, the prompt kinetics equations for critical system and subcritical system with an external source are proposed. And then the equations are applied to calculating Λ with pulsed neutron technique using Monte Carlo. Only one fission neutron source is simulated with Monte Carlo in critical system while two neutron sources, including a fission source and an external source, are simulated for subcritical system. Calculations are performed on both critical benchmarks and subcritical system with an external source and the results are consistent with the reference values. (author)
Monte Carlo simulation of a sputtering hollow-cathode discharge for laser applications
International Nuclear Information System (INIS)
We report on a kinetic model that computes the electron behaviour in a hollow cathode discharge. It is a part of the PLASIMO toolkit and is based on a Monte-Carlo technique. The model is tested by varying the input parameters and by comparing the output with the output obtained by the freeware Boltzmann equation solver BOLSIG+. The results show that the Monte-Carlo model gives reliable information about the behavior of the electrons in the discharge. The Monte-Carlo module is applied to the case of a hollow cathode discharge for laser applications. Analysis of the output data and its adequateness is done. Future developments of the model are discussed.
General purpose dynamic Monte Carlo with continuous energy for transient analysis
Energy Technology Data Exchange (ETDEWEB)
Sjenitzer, B. L.; Hoogenboom, J. E. [Delft Univ. of Technology, Dept. of Radiation, Radionuclide and Reactors, Mekelweg 15, 2629JB Delft (Netherlands)
2012-07-01
For safety assessments transient analysis is an important tool. It can predict maximum temperatures during regular reactor operation or during an accident scenario. Despite the fact that this kind of analysis is very important, the state of the art still uses rather crude methods, like diffusion theory and point-kinetics. For reference calculations it is preferable to use the Monte Carlo method. In this paper the dynamic Monte Carlo method is implemented in the general purpose Monte Carlo code Tripoli4. Also, the method is extended for use with continuous energy. The first results of Dynamic Tripoli demonstrate that this kind of calculation is indeed accurate and the results are achieved in a reasonable amount of time. With the method implemented in Tripoli it is now possible to do an exact transient calculation in arbitrary geometry. (authors)
Dynamic phase transitions in a ferromagnetic thin film system: A Monte Carlo simulation study
International Nuclear Information System (INIS)
Dynamic phase transition properties of a ferromagnetic thin film system under the influence of both bias and time-dependent magnetic fields have been elucidated by means of kinetic Monte Carlo simulation with local spin update Metropolis algorithm. The obtained results after a detailed analysis suggest that the bias field is the conjugate field to dynamic order parameter, and it also appears to define a phase line between two antiparallel dynamic ordered states depending on the considered system parameters. Moreover, the data presented in this study well qualitatively reproduce the recently published experimental findings where time-dependent magnetic behavior of a uniaxial cobalt films is studied in the neighborhood of dynamic phase transition point. - Highlights: • A ferromagnetic thin film system is examined. • The system is exposed to both bias and time-dependent magnetic fields. • Kinetic Monte Carlo simulation technique is used. • Bias field is the conjugate field to the dynamic order parameter
International Nuclear Information System (INIS)
When a compound is maintained in far for equilibrium configurations by nuclear collisions under irradiation, the steady-state properties of the system can no longer be predicted from equilibrium thermodynamics. Here the authors propose Monte Carlo simulations for addressing the question of phase stability under irradiation. They are based on a kinetic model with two dynamics acting in parallel: thermally activated jumps of vacancies and ballistic events induced by nuclear collisions. Two transformations are studied: the A2-B2 order-disorder transition and the precipitation of copper in iron. In the former case a shift from second to first order of the A2-B2 transition, predicted by the model, has been experimentally checked by 1 MeV electron irradiations of a FeAl alloy. In the latter case, the precipitation kinetics are determined by Monte Carlo simulations and are found to be in very good agreement with available experimental data
Forward physics Monte Carlo (FPMC)
Czech Academy of Sciences Publication Activity Database
Boonekamp, M.; Juránek, Vojtěch; Kepka, Oldřich; Royon, C.
Hamburg : Verlag Deutsches Elektronen-Synchrotron, 2009 - (Jung, H.; De Roeck, A.), s. 758-762 ISBN N. [HERA and the LHC workshop series on the implications of HERA for LHC physics. Geneve (CH), 26.05.2008-30.05.2008] R&D Projects: GA MŠk LC527; GA MŠk LA08032 Institutional research plan: CEZ:AV0Z10100502 Keywords : forward physics * diffraction * two-photon * Monte Carlo Subject RIV: BF - Elementary Particles and High Energy Physics http://arxiv.org/PS_cache/arxiv/pdf/0903/0903.3861v2.pdf
Monte Carlo techniques in radiation therapy
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...
Monte Carlo primer for health physicists
International Nuclear Information System (INIS)
The basic ideas and principles of Monte Carlo calculations are presented in the form of a primer for health physicists. A simple integral with a known answer is evaluated by two different Monte Carlo approaches. Random number, which underlie Monte Carlo work, are discussed, and a sample table of random numbers generated by a hand calculator is presented. Monte Carlo calculations of dose and linear energy transfer (LET) from 100-keV neutrons incident on a tissue slab are discussed. The random-number table is used in a hand calculation of the initial sequence of events for a 100-keV neutron entering the slab. Some pitfalls in Monte Carlo work are described. While this primer addresses mainly the bare bones of Monte Carlo, a final section briefly describes some of the more sophisticated techniques used in practice to reduce variance and computing time
International Nuclear Information System (INIS)
The site-selective occupation of point defects, Y3+ ions (Y′Zr) and O2- vacancies (VÖ), and their associations at a symmetric tilt grain boundary (GB) are studied to understand their competitive contribution to energetically favorable atomic arrangements by using atomistic simulations. It is found that at the GB there are the favorable sites for segregation of an isolated Y′Zr and VÖ. This indicates that the driving force for the site-selective segregation is present. Moreover, our results of Y′Zr-VÖ association at the GB show that the lattice energies are very dispersed despite that a second-nearest neighbor (SNN) vacancy to Y′Zr is favored for bulk Y2O3-doped ZrO2. The result suggests that the site-selective segregation has significant effects on the favorable point defect arrangement at the GB core, competing with the point defect associations. For more realistic cases, Monte Carlo simulations are performed to reveal favorable atomic arrangements for a high dopant concentration, where point defects are crowded at the GB. The results show that the region of GB segregation can be classified with respect to O2- coordination to cation species; at the GB core the favorable configuration is not necessarily a SNN O2- vacancy relative to Y3+. On the other hand, eight-fold O2- coordination is sustained for Y3+ ions more than ∼3 Å distant from the GB plane. The difference in O2- coordination may play an important role in O2- ionic conductivity at GBs via the energetics for O2- migration. (author)
Interacting Particle Markov Chain Monte Carlo
Rainforth, Tom; Naesseth, Christian A.; Lindsten, Fredrik; Paige, Brooks; van de Meent, Jan-Willem; Doucet, Arnaud; Wood, Frank
2016-01-01
We introduce interacting particle Markov chain Monte Carlo (iPMCMC), a PMCMC method that introduces a coupling between multiple standard and conditional sequential Monte Carlo samplers. Like related methods, iPMCMC is a Markov chain Monte Carlo sampler on an extended space. We present empirical results that show significant improvements in mixing rates relative to both non-interacting PMCMC samplers and a single PMCMC sampler with an equivalent total computational budget. An additional advant...
Mean field simulation for Monte Carlo integration
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
Monte Carlo Studies of particle dffusion on a patchwise bivariate surface
Czech Academy of Sciences Publication Activity Database
Tarasenko, Alexander; Jastrabík, Lubomír
Barcelona : ThinkMind IARIA, 2013 - (Priviman, V.; Ovchinnikov, V.), s. 7-12 ISBN 9781629930640. [ International Conference on Quantum, Nano and Micro Technologies /7./ ICQNM 2013. Barcelona (ES), 25.08.2013-31.08.2013] R&D Projects: GA TA ČR TA01010517; GA ČR GAP108/12/1941 Institutional support: RVO:68378271 Keywords : surface diffusion * kinetic Monte Carlo simulations * patchwise lattice Subject RIV: BM - Solid Matter Physics ; Magnetism
Kinetic approach to the cluster liquid-gas transition
Calvo, F
2004-01-01
The liquid-gas transition in free atomic clusters is investigated theoretically based on simple unimolecular rate theories and assuming sequential evaporations. A kinetic Monte Carlo scheme is used to compute the time-dependent properties of clusters undergoing multiple dissociations, and two possible definitions of the boiling point are proposed, relying on the cluster or gas temperature. This numerical approach is supported by molecular dynamics simulations of clusters made of sodium atoms or C60 molecules, as well as simplified rate equation.
The Kinetics of Phase Separation in Asymmetric Membranes
Wallace, Elizabeth J.; Hooper, Nigel M.; Olmsted, Peter D
2005-01-01
Phase separation in a model asymmetric membrane is studied using Monte Carlo techniques. The membrane comprises two species of particles, which mimic different lipids in lipid bilayers and separately possess either zero or non-zero spontaneous curvatures. We study the influence of phase separation on membrane shape and the influence of the coupling of composition and height dynamics on phase separation and domain growth, via both the degree of shape asymmetry and relative kinetic coefficients...
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.
Monte Carlo Application ToolKit (MCATK)
International Nuclear Information System (INIS)
Highlights: • Component-based Monte Carlo radiation transport parallel software library. • Designed to build specialized software applications. • Provides new functionality for existing general purpose Monte Carlo transport codes. • Time-independent and time-dependent algorithms with population control. • Algorithm verification and validation results are provided. - Abstract: The Monte Carlo Application ToolKit (MCATK) is a component-based software library designed to build specialized applications and to provide new functionality for existing general purpose Monte Carlo radiation transport codes. We will describe MCATK and its capabilities along with presenting some verification and validations results
Multidimensional stochastic approximation Monte Carlo.
Zablotskiy, Sergey V; Ivanov, Victor A; Paul, Wolfgang
2016-06-01
Stochastic Approximation Monte Carlo (SAMC) has been established as a mathematically founded powerful flat-histogram Monte Carlo method, used to determine the density of states, g(E), of a model system. We show here how it can be generalized for the determination of multidimensional probability distributions (or equivalently densities of states) of macroscopic or mesoscopic variables defined on the space of microstates of a statistical mechanical system. This establishes this method as a systematic way for coarse graining a model system, or, in other words, for performing a renormalization group step on a model. We discuss the formulation of the Kadanoff block spin transformation and the coarse-graining procedure for polymer models in this language. We also apply it to a standard case in the literature of two-dimensional densities of states, where two competing energetic effects are present g(E_{1},E_{2}). We show when and why care has to be exercised when obtaining the microcanonical density of states g(E_{1}+E_{2}) from g(E_{1},E_{2}). PMID:27415383
Single scatter electron Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Svatos, M.M. [Lawrence Livermore National Lab., CA (United States)|Wisconsin Univ., Madison, WI (United States)
1997-03-01
A single scatter electron Monte Carlo code (SSMC), CREEP, has been written which bridges the gap between existing transport methods and modeling real physical processes. CREEP simulates ionization, elastic and bremsstrahlung events individually. Excitation events are treated with an excitation-only stopping power. The detailed nature of these simulations allows for calculation of backscatter and transmission coefficients, backscattered energy spectra, stopping powers, energy deposits, depth dose, and a variety of other associated quantities. Although computationally intense, the code relies on relatively few mathematical assumptions, unlike other charged particle Monte Carlo methods such as the commonly-used condensed history method. CREEP relies on sampling the Lawrence Livermore Evaluated Electron Data Library (EEDL) which has data for all elements with an atomic number between 1 and 100, over an energy range from approximately several eV (or the binding energy of the material) to 100 GeV. Compounds and mixtures may also be used by combining the appropriate element data via Bragg additivity.
Finite element analysis of an atomistically derived cohesive model for brittle fracture
International Nuclear Information System (INIS)
In order to apply information from molecular dynamics (MD) simulations in problems governed by engineering length and time scales, a coarse graining methodology must be used. In previous work by Zhou et al (2009 Acta Mater. 57 4671–86), a traction-separation cohesive model was developed using results from MD simulations with atomistic-to-continuum measures of stress and displacement. Here, we implement this cohesive model within a combined finite element/cohesive surface element framework (referred to as a finite element approach or FEA), and examine the ability for the atomistically informed FEA to directly reproduce results from MD. We find that FEA shows close agreement of both stress and crack opening displacement profiles at the cohesive interface, although some differences do exist that can be attributed to the stochastic nature of finite temperature MD. The FEA methodology is then used to study slower loading rates that are computationally expensive for MD. We find that the crack growth process initially exhibits a rate-independent relationship between crack length and boundary displacement, followed by a rate-dependent regime where, at a given amount of boundary displacement, a lower applied strain rate produces a longer crack length. Our method is also extended to larger length scales by simulating a compact tension fracture-mechanics specimen with sub-micrometer dimensions. Such a simulation shows a computational speedup of approximately four orders of magnitude over conventional atomistic simulation, while exhibiting the expected fracture-mechanics response. Finally, differences between FEA and MD are explored with respect to ensemble and temperature effects in MD, and their impact on the cohesive model and crack growth behavior. These results enable us to make several recommendations to improve the methodology used to derive cohesive laws from MD simulations. In light of this work, which has critical implications for efforts to derive continuum laws
Guo, Hui-Jun; Huang, Wei; Liu, Xi; Gao, Pan; Zhuo, Shi-Yi; Xin, Jun; Yan, Cheng-Feng; Zheng, Yan-Qing; Yang, Jian-Hua; Shi, Er-Wei
2014-09-01
Polytype stability is very important for high quality SiC single crystal growth. However, the growth conditions for the 4H, 6H and 15R polytypes are similar, and the mechanism of polytype stability is not clear. The kinetics aspects, such as surface-step nucleation, are important. The kinetic Monte Carlo method is a common tool to study surface kinetics in crystal growth. However, the present lattice models for kinetic Monte Carlo simulations cannot solve the problem of the competitive growth of two or more lattice structures. In this study, a competitive lattice model was developed for kinetic Monte Carlo simulation of the competition growth of the 4H and 6H polytypes of SiC. The site positions are fixed at the perfect crystal lattice positions without any adjustment of the site positions. Surface steps on seeds and large ratios of diffusion/deposition have positive effects on the 4H polytype stability. The 3D polytype distribution in a physical vapor transport method grown SiC ingot showed that the facet preserved the 4H polytype even if the 6H polytype dominated the growth surface. The theoretical and experimental results of polytype growth in SiC suggest that retaining the step growth mode is an important factor to maintain a stable single 4H polytype during SiC growth.
Directory of Open Access Journals (Sweden)
Hui-Jun Guo
2014-09-01
Full Text Available Polytype stability is very important for high quality SiC single crystal growth. However, the growth conditions for the 4H, 6H and 15R polytypes are similar, and the mechanism of polytype stability is not clear. The kinetics aspects, such as surface-step nucleation, are important. The kinetic Monte Carlo method is a common tool to study surface kinetics in crystal growth. However, the present lattice models for kinetic Monte Carlo simulations cannot solve the problem of the competitive growth of two or more lattice structures. In this study, a competitive lattice model was developed for kinetic Monte Carlo simulation of the competition growth of the 4H and 6H polytypes of SiC. The site positions are fixed at the perfect crystal lattice positions without any adjustment of the site positions. Surface steps on seeds and large ratios of diffusion/deposition have positive effects on the 4H polytype stability. The 3D polytype distribution in a physical vapor transport method grown SiC ingot showed that the facet preserved the 4H polytype even if the 6H polytype dominated the growth surface. The theoretical and experimental results of polytype growth in SiC suggest that retaining the step growth mode is an important factor to maintain a stable single 4H polytype during SiC growth.
Introduction to chemical kinetics
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
Difference in aggregation between functional and toxic amyloids studied by atomistic simulations
Carballo Pacheco, Martin; Ismail, Ahmed E.; Strodel, Birgit
Amyloids are highly structured protein aggregates, normally associated with neurodegenerative diseases such as Alzheimer's disease. In recent years, a number of nontoxic amyloids with physiologically normal functions, called functional amyloids, have been found. It is known that soluble small oligomers are more toxic than large fibrils. Thus, we study with atomistic explicit-solvent molecular dynamics simulations the oligomer formation of the amyloid- β peptide Aβ25 - 35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Our simulations show that monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations. In addition, we observe faster aggregation by functional amyloids than toxic amyloids, which could explain their lack of toxicity.
Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers.
Upadhyay, Sanjay K; Wang, Yukun; Zhao, Tangzhen; Ulmschneider, Jakob P
2015-06-01
The membrane disruption and pore-forming mechanism of melittin has been widely explored by experiments and computational studies. However, the precise mechanism is still enigmatic, and further study is required to turn antimicrobial peptides into future promising drugs against microbes. In this study, unbiased microsecond (µs) time scale (total 17 µs) atomistic molecular dynamics simulation were performed on multiple melittin systems in 1,2-dimyristoyl-sn-glycero-3-phosphocholine membrane to capture the various events during the membrane disorder produced by melittin. We observed bent U-shaped conformations of melittin, penetrated deeply into the membrane in all simulations, and a special double U-shaped structure. However, no peptide transmembrane insertion, nor pore formation was seen, indicating that these processes occur on much longer timescales, and suggesting that many prior computational studies of melittin were not sufficiently unbiased. PMID:25963936
Study of the embedded atom method of atomistic calculations for metals and alloys
International Nuclear Information System (INIS)
Two projects were completed in the past year. The stability of a series of binary alloys was calculated using the embedded-atom method (EAM) with an analytic form for two-body potentials derived previously. Both disordered alloys and intermetallic compounds with the L10 and L12 structures were studied. The calculated heats of solution of alloys of Cu, Ag, Au, Ni, and Pt were satisfactory, while results for alloys containing Pd were too high. Atomistic calculations using the EAM were also carried out for point defects in hcp metals. By comparison with results in the literature, it was found that many body effects from the EAM significantly alter predicted physical properties of hcp metals. For example, the EAM calculations yield anisotropic vacancy diffusion with greater vacancy mobility in the basal plane, and imply that diffusion will start at a lower fraction of the melting temperature
Laktionov, Andrey; Chemineau-Chalaye, Emilie; Wesolowski, Tomasz A
2016-08-21
Besides molecular electron densities obtained within the Born-Oppenheimer approximation (ρB(r)) to represent the environment, the ensemble averaged density (〈ρB〉(r)) is also admissible in frozen-density embedding theory (FDET) [Wesolowski, Phys. Rev. A, 2008, 77, 11444]. This makes it possible to introduce an approximation in the evaluation of the solvent effect on quantum mechanical observables consisting of replacing the ensemble averaged observable by the observable evaluated at ensemble averaged ρB(r). This approximation is shown to affect negligibly the solvatochromic shift in the absorption of hydrated acetone. The proposed model provides a continuum type of representation of the solvent, which reflects nevertheless its local structure, and it is to be applied as a post-simulation analysis tool in atomistic level simulations. PMID:26984532
Directory of Open Access Journals (Sweden)
Giuseppina Raffaini
2015-12-01
Full Text Available 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.
Raffaini, Giuseppina; Mazzaglia, Antonino; Ganazzoli, Fabio
2015-01-01
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
Energy Technology Data Exchange (ETDEWEB)
Zanjani, Mehdi B.; Lukes, Jennifer R., E-mail: jrlukes@seas.upenn.edu [Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States)
2014-04-14
A computational study of thermal conductivity and phonon dispersion of gold nanocrystal superlattices is presented. Phonon dispersion curves, reported here for the first time from combined molecular dynamics and lattice dynamics calculations, show multiple phononic band gaps and consist of many more dispersion branches than simple atomic crystals. Fully atomistic three dimensional molecular dynamics calculations of thermal conductivity using the Green Kubo method are also performed for the first time on these materials. Thermal conductivity is observed to increase for increasing nanocrystal core size and decrease for increasing surface ligand density. Our calculations predict values in the range 0.1–1 W/m K that are consistent with reported experimental results.
Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.
Directory of Open Access Journals (Sweden)
Andrew T Fenley
Full Text Available Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS, an open-source software package for computing atomic resolution stresses from molecular dynamics (MD simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.
Atomistic study of deposition process of Al thin film on Cu substrate
International Nuclear Information System (INIS)
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.
Trigg, Edward B.; Stevens, Mark J.; Winey, Karen I.
Layered crystal structures have been observed in linear poly(ethylene-co-acrylic acid) in which the carboxylic acid groups are placed precisely every 21 carbon atoms along the backbone. The alkane segments form structures resembling orthorhombic polyethylene crystals, while the acid groups form continuous domains that may act as pathways for ion conduction. Further details of the crystal structure have been difficult to elucidate experimentally, but could be important for understanding structure-property relationships. Here, two classes of crystal structures are evaluated via atomistic molecular dynamics: extended chain structures, wherein the polymer backbones are highly extended in near-trans conformations, and adjacent reentry structures, wherein the polymer backbones conform in adjacent reentry loops near the site of each covalently-bonded acid group. Energies of relaxed structures and hydrogen bonding states are compared, and X-ray scattering and other experimental data is compared with the simulation results.
International Nuclear Information System (INIS)
In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO2 and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature
B and N ion implantation into carbon nanotubes: Insight from atomistic simulations
International Nuclear Information System (INIS)
By employing atomistic computer simulations with empirical potential and density functional force models, we study B/N ion implantation onto carbon nanotubes. We simulate irradiation of single-walled nanotubes with B and N ions and show that up to 40% of the impinging ions can occupy directly the sp2 positions in the nanotube atomic network. We further estimate the optimum ion energies for direct substitution. Ab initio simulations are used to get more insight into the structure of the typical atomic configurations which appear under the impacts of the ions. As annealing should further increase the number of sp2 impurities due to dopant atom migration and annihilation with vacancies, we also study migration of impurity atoms over the tube surface. Our results indicate that irradiation-mediated doping of nanotubes is a promising way to control the nanotube electronic and even mechanical properties due to impurity-stimulated crosslinking of nanotubes
Orientation dependence of the solid–liquid interface stress: atomistic calculations for copper
International Nuclear Information System (INIS)
We present an atomistic study of the solid–liquid interface stress in copper for four different interface orientations: (1 0 0), (1 1 0), (1 1 1) and (3 1 0). For the (1 1 0) and (3 1 0) orientations, the interface stress is found to be anisotropic, while for the (1 0 0) and (1 1 1) orientations it is isotropic by crystal symmetry. The magnitude and sign of the interface stress depend on the interface orientation. Examination of stress profiles across the interfaces reveals competition between the compression of a narrow solid layer and tension of the adjacent liquid layer within the interface region. The sign of the interface stress is dictated by balance between these tensile and compressive contributions
A Spectral Multiscale Method for Wave Propagation Analysis: Atomistic-Continuum Coupled Simulation
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 ...
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.
Computer code for the atomistic simulation of lattice defects and dynamics
International Nuclear Information System (INIS)
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
Atomistic-Continuum Hybrid Simulation of Heat Transfer between Argon Flow and Copper Plates
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.
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
Atomistic studies of nucleation of He clusters and bubbles in bcc iron
Yang, L.; Deng, H. Q.; Gao, F.; Heinisch, H. L.; Kurtz, R. J.; Hu, S. Y.; Li, Y. L.; Zu, X. T.
2013-05-01
Atomistic simulations of the nucleation of He clusters and bubbles in bcc iron at 800 K have been carried out using the newly developed Fe-Fe interatomic potential, along with Ackland potential for the Fe-Fe interactions. Microstructure changes were analyzed in detail. We found that a He cluster with four He atoms is able to push out an iron interstitial from the cluster, creating a Frenkel pair. Small He clusters and self-interstitial atom (SIA) can migrate in the matrix, but He-vacancy (He-V) clusters are immobile. Most SIAs form clusters, and only the dislocation loops with a Burgers vector of b = 1/2 appear in the simulations. SIA clusters (or loops) are attached to He-V clusters for He implantation up to 1372 appm, while the He-V cluster-loop complexes with more than one He-V cluster are formed at the He concentration of 2057 appm and larger.
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. PMID:20557090
Atomistic simulation of twin boundaries effect on nanoindentation of Ag(1 1 1) films
International Nuclear Information System (INIS)
Atomistic simulations were employed to study the effect of a single twin boundary parallel with the indented surface on nanoindentation of Ag(1 1 1) films. The results show that the twin boundary has little influence on the elastic modulus of films. The load for the initial yield is observably reduced when the twin boundary is very near the indented surface due to the nucleation of the glissile dislocations on the slip plane parallel to the surface, rather than the formation of the tetrahedral sessile lock when nanoindentation on the perfect film. Twin boundaries are effective obstacles to the motion of dislocations, and change the dislocation patterns dominating the deformation, resulting in the hardening of films. In addition, twin boundaries can act as dislocation sources before losing their coherency.
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.
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.
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Dumpala, Santoshrupa; Broderick, Scott R.; Rajan, Krishna, E-mail: krajan@iastate.edu [Department of Materials Science and Engineering and Institute for Combinatorial Discovery, Iowa State University, 2220 Hoover Hall, Ames, Iowa 50011 (United States); Khalilov, Umedjon; Neyts, Erik C. [Department of Chemistry, PLASMANT Research Group, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk-Antwerp (Belgium); Duin, Adri C. T. van [Department of Mechanical and Nuclear Engineering, Penn State University, University Park, Pennsylvania 16801 (United States); Provine, J; Howe, Roger T. [Department of Electrical Engineering, Stanford University, 420 Via Palou Mall, Stanford, California 94305 (United States)
2015-01-05
In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO{sub 2} and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature.
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...... electrostatic 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...
Atomistic features in the electrochemical potential drop across a graphene grain boundary
International Nuclear Information System (INIS)
A recent publication presents a new computational approach to the local electrochemical potential in the vicinity of a graphene grain boundary subject to an in-plane electric current [1]. The local electrochemical potential can be measured using scanning tunneling potentiometry, a method related to scanning tunneling microscopy. The paper predicts that atomistic features should be measurable. These features reflect the local electrochemical potential drop caused by the opaque grain boundary which is non-transparent to ballistic electrons. The paper has implications not only for scanning tunneling potentiometry, but also for Kelvin probe-force microscopy which can also measure the local electrochemical potential. In addition it could help to understand electronic transport across metallic nanocontacts. (viewpoint)
Atomistic mechanisms of amorphization during nanoindentation of SiC: A molecular dynamics study
Szlufarska, Izabela; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2005-05-01
Atomistic mechanisms underlying the nanoindentation-induced amorphization in SiC crystal has been studied by molecular dynamics simulations on parallel computers. The calculated load-displacement curve consists of a series of load drops, corresponding to plastic deformation, in addition to a shoulder at a smaller displacement, which is fully reversible upon unloading. The peaks in the load-displacement curve are shown to reflect the crystalline structure and dislocation activities under the surface. The evolution of indentation damage and defect accumulation are also discussed in terms of bond angles, local pressure, local shear stress, and spatial rearrangements of atoms. These structural analyses reveal that the defect-stimulated growth and coalescence of dislocation loops are responsible for the crystalline-to-amorphous transition. The shortest-path-ring analysis is effectively employed to characterize nanoindentation-induced structural transformations and dislocation activities.
A fully atomistic computer simulation study of cold denaturation of a β-hairpin
Yang, Changwon; Jang, Soonmin; Pak, Youngshang
2014-12-01
Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in molecular details can provide a new insight into the detailed natures of hydrophobic forces governing the stability of proteins in water. We show that the cold-denaturation-like phenomenon can be directly observed at low temperatures using a fully atomistic molecular dynamics simulation method. Using a highly optimized protein force field in conjunction with three different explicit water models, a replica exchange molecular dynamics simulation scheme at constant pressures allows for the computation of the melting profile of an experimentally well-characterized β-hairpin peptide. For all three water models tested, the simulated melting profiles are indicative of possible cold denaturation. From the analysis of simulation ensembles, we find that the most probable cold-denatured structure is structurally compact, with its hydrogen bonds and native hydrophobic packing substantially disrupted.
Atomistic modeling of the self-diffusion in γ-U and γ-U-Mo
Smirnova, D. E.; Kuksin, A. Yu.; Starikov, S. V.; Stegailov, V. V.
2015-05-01
Results of investigations of the self-diffusion in gamma-uranium and metallic U-Mo alloys are presented. Calculations are performed using the method of atomistic modeling with the help of interatomic potentials based on the embedded-atom model and its modifications. Proposed potentials are verified by calculating thermodynamic and mechanical properties of uranium and U-Mo alloys. The formation energies of point defects and atomic diffusivities due to the diffusion of defects are calculated for gamma-uranium and alloy containing 9 wt % molybdenum. Self-diffusion coefficients of uranium and molybdenum are evaluated. Based on the data obtained, it has been concluded that the experimentally observed features of the self-diffusion in gamma-uranium can be explained by the prevalence of the interstitial mechanism.
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.
Structures, nanomechanics, and disintegration of single-walled GaN nanotubes: atomistic simulations
International Nuclear Information System (INIS)
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.
Atomistic study of energy funneling in the light-harvesting complex of green sulfur bacteria
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...