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Sample records for atomistic kinetic monte

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

    CERN Document Server

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

    2014-01-01

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

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

    Science.gov (United States)

    Shirazi, Mahdi; Elliott, Simon D

    2014-01-30

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

  3. Long and double hop kinetic Monte Carlo: Techniques to speed up atomistic modeling without losing accuracy

    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.

  4. Mobility and stability of large vacancy and vacancy-copper clusters in iron: An atomistic kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    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.

  5. Modelling radiation-induced phase changes in binary FeCu and ternary FeCuNi alloys using an artificial intelligence-based atomistic kinetic Monte Carlo approach

    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.

  6. Synchronous Parallel Kinetic Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Mart?nez, E; Marian, J; Kalos, M H

    2006-12-14

    A novel parallel kinetic Monte Carlo (kMC) algorithm formulated on the basis of perfect time synchronicity is presented. The algorithm provides an exact generalization of any standard serial kMC model and is trivially implemented in parallel architectures. We demonstrate the mathematical validity and parallel performance of the method by solving several well-understood problems in diffusion.

  7. SPQR: a Monte Carlo reactor kinetics code

    International Nuclear Information System (INIS)

    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

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

    Directory of Open Access Journals (Sweden)

    Darwin B. Putungan

    2010-06-01

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

  9. Protein folding kinetics and thermodynamics from atomistic simulation

    DEFF Research Database (Denmark)

    Piana, Stefano; Lindorff-Larsen, Kresten; Shaw, David E.

    2012-01-01

    simulations of spontaneous folding and unfolding can provide direct access to thermodynamic and kinetic quantities such as folding rates, free energies, folding enthalpies, heat capacities, Φ-values, and temperature-jump relaxation profiles. The quantitative comparison of simulation results with various...

  10. Graphite melting: atomistic kinetics bridges theory and experiment

    Science.gov (United States)

    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.

  11. 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.)

  12. A More Accurate Kinetic Monte Carlo Approach to a Monodimensional Surface Reaction: The Interaction of Oxygen with the RuO2(110) Surface

    OpenAIRE

    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...

  13. Controlling the long-range corrections in atomistic Monte Carlo simulations of two-phase systems.

    Science.gov (United States)

    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

  14. Atomistic Monte Carlo simulations on the influence of sulphur during high-temperature decarburization of molten iron-carbon alloys

    International Nuclear Information System (INIS)

    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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  16. 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)

  17. 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.

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

    Science.gov (United States)

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

    2013-03-01

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

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

    Science.gov (United States)

    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.

  20. 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

  1. 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.

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

    Science.gov (United States)

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

    2003-11-01

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

  3. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-28

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

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

    KAUST Repository

    Shao, Jing

    2015-10-27

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

  6. 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.

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

    Science.gov (United States)

    Joshi, Kaushik; Chaudhuri, Santanu

    2016-10-01

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

  8. Atomistic Molecular Simulations Suggest a Kinetic Model for Membrane Translocation by Arginine-Rich Peptides.

    Science.gov (United States)

    Sun, Delin; Forsman, Jan; Woodward, Clifford E

    2015-11-12

    Arginine-rich cell penetrating peptides (ARCPPs) are known to quickly permeate cell membranes through a non-endocytotic pathway. Potential clinical applications of this facility have prompted enormous effort, both experimental and theoretical, to better understand how ARCPPs manage to overcome the prodigious thermodynamic cost of lipid bilayer permeation by these highly charged peptides. In this work we report the results of all-atom simulations, which suggest that a kinetic (rather than thermodynamic) mechanism may explain how ARCPPs are able to achieve this. Our simulations reveal that octaarginine significantly hinders the closing of membrane pores, either individually or via aggregation in the membrane pore, while octalysine (not an ARCPP) lacks this ability. Our proposed mechanism is an alternative to current attempts to explain pore-mediated translocation of ARCPPs. It asserts that ARCPPs need not lower the equilibrium thermodynamic cost of pore formation. Instead, they can achieve rapid bilayer translocation by instead slowing down the kinetics of naturally occurring thermal pores. Linking the pore lifetime to the characteristic time for peptide diffusion out of the pore, ARCPPs are able to cooperatively permeate the membrane pore. PMID:26485313

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

    Science.gov (United States)

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

    2015-06-01

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

  10. A More Accurate Kinetic Monte Carlo Approach to a Monodimensional Surface Reaction: The Interaction of Oxygen with the RuO2(110) Surface.

    Science.gov (United States)

    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

  11. 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.

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

    Science.gov (United States)

    Jonane, Inga; Timoshenko, Janis; Kuzmin, Alexei

    2016-10-01

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

  13. Kinetic Monte Carlo Studies of Hydrogen Abstraction from Graphite

    CERN Document Server

    Cuppen, H M

    2008-01-01

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

  14. Stability and mobility of small vacancy–solute complexes in Fe–MnNi and dilute Fe–X alloys: A kinetic Monte Carlo study

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-09-01

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

  16. Interacting multiagent systems kinetic equations and Monte Carlo methods

    CERN Document Server

    Pareschi, Lorenzo

    2014-01-01

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

  17. 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...

  18. Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study

    Science.gov (United States)

    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.

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

    OpenAIRE

    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...

  20. Stochastic method for accommodation of equilibrating basins in kinetic Monte Carlo simulations

    OpenAIRE

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-30

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

  2. 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

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

    CERN Document Server

    Yasuda, Shugo

    2015-01-01

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

  4. 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.

  5. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-11-06

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

  7. The Lattice Kinetic Monte Carlo Simulation of Atomic Diffusion and Structural Transition for Gold

    Science.gov (United States)

    He, Xiang; Cheng, Feng; Chen, Zhao-Xu

    2016-01-01

    For the kinetic simulation of metal nanoparticles, we developed a self-consistent coordination-averaged energies for Au atoms based on energy properties of gold bulk phases. The energy barrier of the atom pairing change is proposed and holds for the microscopic reversibility principle. By applying the lattice kinetic Monte Carlo simulation on gold films, we found that the atomic diffusion of Au on the Au(111) surface undergoes a late transition state with an energy barrier of about 0.2 eV and a prefactor between 40~50 Å2/ps. This study also investigates the structural transition from spherical to faceted gold nanoparticles upon heating. The temperatures of structural transition are in agreement with the experimental melting temperatures of gold nanoparticles with diameters ranging from 2 nm to 8 nm. PMID:27629538

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

    CERN Document Server

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

    2016-01-01

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

  9. The Lattice Kinetic Monte Carlo Simulation of Atomic Diffusion and Structural Transition for Gold.

    Science.gov (United States)

    He, Xiang; Cheng, Feng; Chen, Zhao-Xu

    2016-01-01

    For the kinetic simulation of metal nanoparticles, we developed a self-consistent coordination-averaged energies for Au atoms based on energy properties of gold bulk phases. The energy barrier of the atom pairing change is proposed and holds for the microscopic reversibility principle. By applying the lattice kinetic Monte Carlo simulation on gold films, we found that the atomic diffusion of Au on the Au(111) surface undergoes a late transition state with an energy barrier of about 0.2 eV and a prefactor between 40~50 Å(2)/ps. This study also investigates the structural transition from spherical to faceted gold nanoparticles upon heating. The temperatures of structural transition are in agreement with the experimental melting temperatures of gold nanoparticles with diameters ranging from 2 nm to 8 nm. PMID:27629538

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-15

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

  11. 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

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

    Science.gov (United States)

    Good, Brian

    2013-01-01

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

  13. Kinetic Monte Carlo Simulation of Oxygen and Cation Diffusion in Yttria-Stabilized Zirconia

    Science.gov (United States)

    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.

  14. 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.

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

    Science.gov (United States)

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

    2016-07-14

    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. PMID:27421395

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  18. 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.

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

    Science.gov (United States)

    Franz, T; Mittendorfer, F

    2010-05-21

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

  20. 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.

  1. Diffusion and growth of metal clusters in nanocomposites: a Kinetic Monte Carlo study

    CERN Document Server

    Rosenthal, L; Bonitz, M; Zaporojtchenko, V; Faupel, F

    2011-01-01

    Nobel metals that are deposited on a polymer surface exhibit surface diffusion and diffusion into the bulk. At the same time the metal atoms tend to form clusters because their cohesive energy is about two orders of magnitude higher than the cohesive energy of polymers. To selfconsistently simulate these coupled processes, we present in this paper a Kinetic Monte Carlo approach. Using a simple model with diffusion coefficients taken as input parameters allows us to perform a systematic study of the behavior of a large ensemble of metal atoms on a polymer surface eventually leading to polymer nanocomposites. Special emphasis is placed on the cluster growth, cluster size distribution and the penetration of clusters into the substrate. We also study the influence of surface defects and analyze how the properties of the resulting material can be controlled by variation of the deposition rate.

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

    Science.gov (United States)

    Arampatzis, Georgios; Katsoulakis, Markos A.

    2014-03-01

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

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

    Science.gov (United States)

    Neumann, Martin; Zoppi, Marco

    2002-03-01

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

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

    Science.gov (United States)

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

    2014-01-01

    The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance. PMID:25628567

  5. Markov chain Monte Carlo based analysis of post-translationally modified VDAC1 gating kinetics

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    CERN Document Server

    Montoya, M; Rojas, J

    2007-01-01

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

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

    Science.gov (United States)

    Linse, Björn; Linse, Sara

    2011-07-01

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

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

    Science.gov (United States)

    Liu, Baoshun

    2016-04-28

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

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

    Science.gov (United States)

    Liu, Baoshun

    2016-04-28

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

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

    Science.gov (United States)

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

    2013-12-01

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

  12. Monte Carlo simulation for calculation of kinetic parameters in an Accelerator Driven Subcritical TRIGA reactor

    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

  13. Monte Carlo simulation of domain growth in the kinetic Ising model on the connection machine

    Science.gov (United States)

    Amar, Jacques G.; Sullivan, Francis

    1989-10-01

    A fast multispin algorithm for the Monte Carlo simulation of the two-dimensional spin-exchange kinetic Ising model, previously described by Sullivan and Mountain and used by Amar et al. has been adapted for use on the Connection Machine and applied as a first test in a calculation of domain growth. Features of the code include: (a) the use of demon bits, (b) the simulation of several runs simultaneously to improve the efficiency of the code, (c) the use of virtual processors to simulate easily and efficiently a larger system size, (d) the use of the (NEWS) grid for last communication between neighbouring processors and updating of boundary layers, (e) the implementation of an efficient random number generator much faster than that provided by Thinking Machines Corp., and (f) the use of the LISP function "funcall" to select which processors to update. Overall speed of the code when run on a (128x128) processor machine is about 130 million attempted spin-exchanges per second, about 9 times faster than the comparable code, using hardware vectorised-logic operations and 64-bit multispin coding on the Cyber 205. The same code can be used on a larger machine (65 536 processors) and should produce speeds in excess of 500 million attempted spin-exchanges per second.

  14. Calculation of kinetic parameters for mixed TRIGA cores with Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Snoj, Luka, E-mail: luka.snoj@ijs.s [Reactor Physics Division, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Kavcic, Andrej [Nuclear Training Centre, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Zerovnik, Gasper; Ravnik, Matjaz [Reactor Physics Division, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia)

    2010-02-15

    Modern Monte Carlo transport codes in combination with fast computer clusters enable very accurate calculations of the most important reactor kinetic parameters. Such are the effective delayed neutron fraction, beta{sub eff}, and mean neutron generation time, LAMBDA. We calculate beta{sub eff} and LAMBDA for various realistic and hypothetical annular TRIGA Mark II cores with different types and amount of fuel. It is observed that the effective delayed neutron fraction strongly depends on the number of fuel elements in the core or on the core size. beta{sub eff} varies for 12 wt.% uranium standard fuel with 20% enrichment from 0.0080 for a small core (43 fuel rods) to 0.0070 for a full core (90 fuel rods). It is found that calculated value of beta{sub eff} strongly depends also on the nuclear data set used in calculations. The prompt neutron lifetime mainly depends on the amount (due to either content or enrichment) of {sup 235}U in the fuel as it is approximately inversely proportional to the average absorption cross-section. It varies from 28 mus for 30 wt.% uranium content fuelled core to 48 mus for 8.5 wt.% uranium content LEU fuelled core. Description of the calculation method and detailed results are presented in the paper.

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

    Institute of Scientific and Technical Information of China (English)

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

    2006-01-01

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

  16. Centrality measures highlight proton traps and access points to proton highways in kinetic Monte Carlo trajectories

    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.

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

    CERN Document Server

    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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-09-05

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

  19. First principles kinetic Monte Carlo study on the growth patterns of WSe2 monolayer

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  3. Modeling the atomistic growth behavior of gold nanoparticles in solution

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-09-01

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

  5. Energy and momentum preserving Coulomb collision model for kinetic Monte Carlo simulations of plasma steady states in toroidal fusion devices

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Leetmaa, Mikael; Skorodumova, Natalia V.

    2014-09-01

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

  7. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-01

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

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

    Science.gov (United States)

    Huang, Chen-Hsi; Marian, Jaime

    2016-10-01

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

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

    Science.gov (United States)

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

    2012-06-01

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

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

    Science.gov (United States)

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

    2012-06-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    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 an...

  14. Kinetic roughening of the Kossel (100) surface: comparison of classical criteria with Monte Carlo results

    NARCIS (Netherlands)

    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

  15. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    . We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule......, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential...

  16. Meaningful timescales from Monte Carlo simulations of molecular systems

    CERN Document Server

    Costa, Liborio I

    2016-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

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

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

    CERN Document Server

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

    2009-01-01

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

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

    CERN Document Server

    Ko, Hyunseok; Szlufarska, Izabela; Morgan, Dane

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

    Sinha, Indrajit; Mukherjee, Ashim K.

    2014-03-01

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

  2. 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.

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

    Science.gov (United States)

    Nagaya, Yasunobu

    2014-06-01

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

  4. H{sub 2} formation in diffuse clouds: A new kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    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.

  5. 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

  6. 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

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

    Science.gov (United States)

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

    2011-03-01

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

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

    Science.gov (United States)

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

    2010-12-01

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

  9. Study on formation of step bunching on 6H-SiC (0001) surface by kinetic Monte Carlo method

    Science.gov (United States)

    Li, Yuan; Chen, Xuejiang; Su, Juan

    2016-05-01

    The formation and evolution of step bunching during step-flow growth of 6H-SiC (0001) surfaces were studied by three-dimensional kinetic Monte Carlo (KMC) method and compared with the analytic model based on the theory of Burton-Cabera-Frank (BCF). In the KMC model the crystal lattice was represented by a structured mesh which fixed the position of atoms and interatomic bonding. The events considered in the model were adatoms adsorption and diffusion on the terrace, and adatoms attachment, detachment and interlayer transport at the step edges. In addition, effects of Ehrlich-Schwoebel (ES) barriers at downward step edges and incorporation barriers at upwards step edges were also considered. In order to obtain more elaborate information for the behavior of atoms in the crystal surface, silicon and carbon atoms were treated as the minimal diffusing species. KMC simulation results showed that multiple-height steps were formed on the vicinal surface oriented toward [ 1 1 bar 00 ] or [ 11 2 bar 0 ] directions. And then the formation mechanism of the step bunching was analyzed. Finally, to further analyze the formation processes of step bunching, a one-dimensional BCF analytic model with ES and incorporation barriers was used, and then it was solved numerically. In the BCF model, the periodic boundary conditions (PBC) were applied, and the parameters were corresponded to those used in the KMC model. The evolution character of step bunching was consistent with the results obtained by KMC simulation.

  10. 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

  11. Water formation reaction on Pt(111): Near edge x-ray absorption fine structure experiments and kinetic Monte Carlo simulations

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-01

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

  13. Kinetic Monte Carlo Investigation of the Effects of Vacancy Pairing on Oxygen Diffusivity in Yttria-Stabilized Zirconia

    Science.gov (United States)

    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.

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

    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.)

  15. Effect of surface nanostructure on temperature programmed reaction spectroscopy: First-principles kinetic Monte Carlo simulations of CO oxidation at RuO2(110)

    OpenAIRE

    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...

  16. Atomistic simulations of fracture

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-31

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

  17. Object Kinetic Monte Carlo calculations of irradiated Fe-Cr dilute alloys: The effect of the interaction radius between substitutional Cr and self-interstitial Fe

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-10-15

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

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

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

    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

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

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 詹晓力; 陈丰秋; 阳永荣

    2003-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-01

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

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

    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

  5. Atomistic Properties of Solids

    CERN Document Server

    Sirdeshmukh, Dinker B; Subhadra, K G

    2011-01-01

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

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

    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.

  7. Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

    OpenAIRE

    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...

  8. Structure sensitivity in oxide catalysis: First-principles kinetic Monte Carlo simulations for CO oxidation at RuO2(111)

    International Nuclear Information System (INIS)

    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

  9. Reliability investigation of high-k/metal gate in nMOSFETs by three-dimensional kinetic Monte-Carlo simulation with multiple trap interactions

    Science.gov (United States)

    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.

  10. Structure sensitivity in oxide catalysis: First-principles kinetic Monte Carlo simulations for CO oxidation at RuO{sub 2}(111)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    王冠博; 刘汉刚; 王侃; 刘永康; 曾和荣; 杨鑫

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-15

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

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

    International Nuclear Information System (INIS)

    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

  14. Mechanism of CO 2 hydrogenation over Cu/ZrO 2(2̅12) interface from first-principles kinetics Monte Carlo simulations

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Chandra Admal, Nikhil; Tadmor, Ellad B.

    2016-04-01

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

  16. 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.

  17. Simulation at high temperature of atomic deposition, islands coalescence, Ostwald and inverse Ostwald ripening with a general simple kinetic Monte Carlo code

    International Nuclear Information System (INIS)

    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.

  18. Diffusion of oxygen interstitials in UO2+x using kinetic Monte Carlo simulations: Role of O/M ratio and sensitivity analysis

    Science.gov (United States)

    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.

  19. A use of the microdosimetric Kinetic Model (MKM) for the interpretation of cell irradiation in the framework of the hadron-therapy: Application of Monte-Carlo simulations

    International Nuclear Information System (INIS)

    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)

  20. Theoretical study of the ammonia nitridation rate on an Fe (100) surface: A combined density functional theory and kinetic Monte Carlo study

    International Nuclear Information System (INIS)

    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

  1. Kinetics of niobium carbide precipitation in ferrite

    International Nuclear Information System (INIS)

    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

  2. Atomistic Simulations of Nanotube Fracture

    CERN Document Server

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

    2002-01-01

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

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

    Science.gov (United States)

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

    2015-10-01

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

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

    Science.gov (United States)

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

    2016-04-18

    Estragole is a known hepatocarcinogen in rodents at high doses following metabolic conversion to the DNA-reactive metabolite 1'-sulfooxyestragole. The aim of the present study was to model possible levels of DNA adduct formation in (individual) humans upon exposure to estragole. This was done by extending a previously defined PBK model for estragole in humans to include (i) new data on interindividual variation in the kinetics for the major PBK model parameters influencing the formation of 1'-sulfooxyestragole, (ii) an equation describing the relationship between 1'-sulfooxyestragole and DNA adduct formation, (iii) Monte Carlo modeling to simulate interindividual human variation in DNA adduct formation in the population, and (iv) a comparison of the predictions made to human data on DNA adduct formation for the related alkenylbenzene methyleugenol. Adequate model predictions could be made, with the predicted DNA adduct levels at the estimated daily intake of estragole of 0.01 mg/kg bw ranging between 1.6 and 8.8 adducts in 10(8) nucleotides (nts) (50th and 99th percentiles, respectively). This is somewhat lower than values reported in the literature for the related alkenylbenzene methyleugenol in surgical human liver samples. The predicted levels seem to be below DNA adduct levels that are linked with tumor formation by alkenylbenzenes in rodents, which were estimated to amount to 188-500 adducts per 10(8) nts at the BMD10 values of estragole and methyleugenol. Although this does not seem to point to a significant health concern for human dietary exposure, drawing firm conclusions may have to await further validation of the model's predictions. PMID:26952143

  5. Magnetic hyperthermia properties of nanoparticles inside lysosomes using kinetic Monte Carlo simulations: Influence of key parameters and dipolar interactions, and evidence for strong spatial variation of heating power

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2016-09-01

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

  7. Atomistic simulations of dislocation processes in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Jacobsen, K.W.

    2002-01-01

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

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

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Roentzsch, L.

    2007-07-01

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

  10. Atomistic k ⋅ p theory

    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.

  11. Atomistic k ⋅ p theory

    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

  12. Atomistic modeling of dropwise condensation

    Science.gov (United States)

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

    2016-05-01

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

  13. Monte Carlo simulation of non-linear free radical polymerization using a percolation kinetic gelation model (I): free radical homo polymerization

    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

  14. Atomistic computer simulations a practical guide

    CERN Document Server

    Brazdova, Veronika

    2013-01-01

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

  15. 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

  16. Visualization and analysis of atomistic simulation data with OVITO-the Open Visualization Tool

    Science.gov (United States)

    Stukowski, Alexander

    2010-01-01

    The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/.

  17. Contribution to the study by a Monte-Carlo method of mono-kinetic particles propagation in a cavity simulated by rectangular cubes. CODE Cupidon 2 (version 29)

    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.)

  18. 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)

  19. Quantum corrections to the `atomistic' MOSFET simulation

    OpenAIRE

    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...

  20. Atomistic modeling of H absorption in Pd nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-04-16

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

  1. 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).

  2. Monte Carlo Calculation as an Aid to Teaching Solid-State Diffusion.

    Science.gov (United States)

    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)

  3. Monte Carlo Demonstration of Solid-State Diffusion in an Electric Field.

    Science.gov (United States)

    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)

  4. Atomistic Mechanisms of Fatigue in Nanocrystalline Metals

    Science.gov (United States)

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

    2005-04-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  6. Atomistic Modeling of Gas Adsorption in Nanocarbons

    Directory of Open Access Journals (Sweden)

    G. Zollo

    2012-01-01

    Full Text Available Carbon nanostructures are currently under investigation as possible ideal media for gas storage and mesoporous materials for gas sensors. The recent scientific literature concerning gas adsorption in nanocarbons, however, is affected by a significant variation in the experimental data, mainly due to the different characteristics of the investigated samples arising from the variety of the synthesis techniques used and their reproducibility. Atomistic simulations have turned out to be sometimes crucial to study the properties of these systems in order to support the experiments, to indicate the physical limits inherent in the investigated structures, and to suggest possible new routes for application purposes. In consideration of the extent of the theme, we have chosen to treat in this paper the results obtained within some of the most popular atomistic theoretical frameworks without any purpose of completeness. A significant part of this paper is dedicated to the hydrogen adsorption on C-based nanostructures for its obvious importance and the exceptional efforts devoted to it by the scientific community.

  7. Atomistic Method Applied to Computational Modeling of Surface Alloys

    Science.gov (United States)

    Bozzolo, Guillermo H.; Abel, Phillip B.

    2000-01-01

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

  8. 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.

  9. 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

  10. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gendt, D

    2001-07-01

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

  12. 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)

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

    Science.gov (United States)

    Kapfer, Sebastian C.; Krauth, Werner

    2016-09-01

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

  14. The Moment Guided Monte Carlo Method

    OpenAIRE

    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...

  15. Atomistic simulations of caloric effects in ferroelectrics

    Science.gov (United States)

    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.

  16. Robust atomistic calculation of dislocation line tension

    Science.gov (United States)

    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.

  17. Stress in titania nanoparticles: An atomistic study

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-24

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

  18. 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

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

    Institute of Scientific and Technical Information of China (English)

    汪量子; 姚栋; 王侃

    2012-01-01

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

  20. Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins

    OpenAIRE

    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...

  1. 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

  2. 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.

  3. The Moment Guided Monte Carlo Method

    CERN Document Server

    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.

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

    Directory of Open Access Journals (Sweden)

    Sourav Gur

    2016-01-01

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

  5. 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)

  6. An object oriented Python interface for atomistic simulations

    Science.gov (United States)

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

    2016-01-01

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

  7. Hierarchical approach to 'atomistic' 3-D MOSFET simulation

    OpenAIRE

    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-μm 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...

  8. 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

  9. Definition and detection of contact in atomistic simulations

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  11. Atomistic Determination of Cross-Slip Pathway and Energetics

    DEFF Research Database (Denmark)

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

    1997-01-01

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

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

    Science.gov (United States)

    Yu, Miao; Kenny, Steven D.

    2016-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Steven M. Valone

    2012-06-01

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

  14. Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations

    CERN Document Server

    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...

  15. Exploring Monte Carlo methods

    CERN Document Server

    Dunn, William L

    2012-01-01

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

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

    Science.gov (United States)

    Perez, Danny

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-31

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

  18. 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.

  19. Atomistic modeling of carbon Cottrell atmospheres in bcc iron

    Science.gov (United States)

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

    2013-01-01

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

  20. 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.

  1. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    Science.gov (United States)

    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

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

    OpenAIRE

    Dapp, Wolf B.; Müser, Martin H.

    2013-01-01

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

  3. Structure identification methods for atomistic simulations of crystalline materials

    OpenAIRE

    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...

  4. Atomistic modelling of radiation effects: Towards dynamics of exciton relaxation

    OpenAIRE

    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...

  5. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

    CERN Document Server

    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.

  6. Impacts of Atomistic Coating on Thermal Conductivity of Germanium Nanowires

    OpenAIRE

    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...

  7. Large scale atomistic approaches to thermal transport and phonon scattering in nanostructured materials

    Science.gov (United States)

    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

  8. Monte Carlo Radiative Transfer

    CERN Document Server

    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.

  9. Monte Carlo transition probabilities

    OpenAIRE

    Lucy, L. B.

    2001-01-01

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

  10. Fundamentals of Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-06-16

    This is a powerpoint 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.

  11. MULTISCALE ATOMISTIC SIMULATION OF METAL-OXYGEN SURFACE INTERACTIONS: METHODOLOGICAL DEVELOPMENT, THEORETICAL INVESTIGATION, AND CORRELATION WITH EXPERIMENT - FINAL REPORT

    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.

  12. Structural properties of silver nanowires from atomistic descriptions

    Science.gov (United States)

    Jia, Jianming; Shi, Daning; Zhao, Jijun; Wang, Baolin

    2007-10-01

    The structural formation process and physical properties of silver nanowires were investigated via an unbiased genetic algorithm search using empirical potential combined with density-functional theory calculations. Some unexpected structural behaviors resulting from the intrinsic properties of silver were revealed. Two kinds of atomic arrangements, i.e., normal and abnormal configurations, appear alternately during the growth of wire, from which a (111) facet-based formation mechanism was observed. The excellent agreements between theoretical results and experimental observations on the structural motif, Young’s modulus, and shell effects of Ag nanowires indicate the importance of objective and precise atomistic descriptions in the study of nanosystems.

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

    Indian Academy of Sciences (India)

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

    2016-09-01

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

  14. 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...

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

    Science.gov (United States)

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

    2013-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-01

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

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

    Science.gov (United States)

    Sedighi, Sina

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

  18. Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene

    Science.gov (United States)

    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.

  19. Wang-Landau Monte Carlo formalism applied to ferroelectrics

    Science.gov (United States)

    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.

  20. 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

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

    Science.gov (United States)

    Plendl, J N

    1971-05-01

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

  2. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-01-12

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

  3. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-12-31

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

  4. 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.

  5. 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.

  6. Variational Monte Carlo Calculations of Energy per Particle Nuclear Matter

    OpenAIRE

    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.

  7. Kinetic Actviation Relaxation Technique

    CERN Document Server

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

    2011-01-01

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

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

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-02-21

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

  10. 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.

  11. The Virtual Monte Carlo

    CERN Document Server

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

    2003-01-01

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

  12. 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.

  13. 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

  14. Coupling Effects of Diffusive Model and Sticking Model on Aggregation Kinetics of Colloidal Particles:A Monte Carlo Simulation Study%扩散模型和凝聚模型耦合作用下胶体凝聚动力学的Monte Carlo模拟研究

    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。

  15. Atomistic modelling of the hydration of CaSO 4

    Science.gov (United States)

    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.

  16. Atomistic simulations of material damping in amorphous silicon nanoresonators

    Science.gov (United States)

    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.

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

    CERN Document Server

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

    2016-01-01

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

  18. Atomistic simulations of jog migration on extended screw dislocations

    DEFF Research Database (Denmark)

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

    2001-01-01

    We have performed large-scale atomistic simulations of the migration of elementary jogs on dissociated screw dislocations in Cu. The local crystalline configurations, transition paths. effective masses. and migration barriers for the jogs are determined using an interatomic potential based...... on the 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......-octahedral slip systems. with energy barriers in the 15-19 meV range. (C) 2001 Elsevier Science B.V. All rights reserved....

  19. Quantum-based Atomistic Simulation of Transition Metals

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-08-29

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

  20. Protein displacements under external forces: An atomistic Langevin dynamics approach

    Science.gov (United States)

    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.

  1. 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.

  2. An Atomistic Statistically Effective Energy Function for Computational Protein Design.

    Science.gov (United States)

    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

  3. Monte Carlo and nonlinearities

    CERN Document Server

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

    2016-01-01

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

  4. Quantum Monte Carlo Calculations of Neutron Matter

    CERN Document Server

    Carlson, J; Ravenhall, D G

    2003-01-01

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

  5. Fundamentals of Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-06-16

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

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

    CERN Document Server

    Reeves, Kyle G; Kanai, Yosuke

    2016-01-01

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

  7. 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)

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

    Science.gov (United States)

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

    2011-06-14

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

  9. Self-consistent simulations of nanowire transistors using atomistic basis sets

    OpenAIRE

    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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-09-01

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

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

    OpenAIRE

    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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-14

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-14

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

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

  15. 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

  16. The Metropolis Monte Carlo method with CUDA enabled Graphic Processing Units

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Clifford [Computational Materials Science Center, George Mason University, 4400 University Dr., Fairfax, VA 22030 (United States); School of Physics, Astronomy, and Computational Sciences, George Mason University, 4400 University Dr., Fairfax, VA 22030 (United States); Ji, Weixiao [Computational Materials Science Center, George Mason University, 4400 University Dr., Fairfax, VA 22030 (United States); Blaisten-Barojas, Estela, E-mail: blaisten@gmu.edu [Computational Materials Science Center, George Mason University, 4400 University Dr., Fairfax, VA 22030 (United States); School of Physics, Astronomy, and Computational Sciences, George Mason University, 4400 University Dr., Fairfax, VA 22030 (United States)

    2014-02-01

    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.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

    Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nano sculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data. PMID:27054098

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

    Science.gov (United States)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

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

  20. Heparin kinetics

    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.)

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

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

    2011-10-01

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

  3. Parallelization of Kinetic Theory Simulations

    CERN Document Server

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

    2013-01-01

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

  4. MontePython: Implementing Quantum Monte Carlo using Python

    OpenAIRE

    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.

  5. The non-uniqueness of the atomistic stress tensor and its relationship to the generalized Beltrami representation

    Science.gov (United States)

    Admal, Nikhil Chandra; Tadmor, E. B.

    2016-08-01

    The non-uniqueness of the atomistic stress tensor is a well-known issue when defining continuum fields for atomistic systems. In this paper, we study the non-uniqueness of the atomistic stress tensor stemming from the non-uniqueness of the potential energy representation. In particular, we show using rigidity theory that the distribution associated with the potential part of the atomistic stress tensor can be decomposed into an irrotational part that is independent of the potential energy representation, and a traction-free solenoidal part. Therefore, we have identified for the atomistic stress tensor a discrete analog of the continuum generalized Beltrami representation (a version of the vector Helmholtz decomposition for symmetric tensors). We demonstrate the validity of these analogies using a numerical test. A program for performing the decomposition of the atomistic stress tensor called MDStressLab is available online at

  6. Monts Jura Jazz Festival

    CERN Multimedia

    2012-01-01

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

  7. Monts Jura Jazz Festival

    CERN Multimedia

    Jazz Club

    2012-01-01

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

  8. Computer Science Techniques Applied to Parallel Atomistic Simulation

    Science.gov (United States)

    Nakano, Aiichiro

    1998-03-01

    Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

  9. Atomistic modeling of phonon transport in turbostratic graphitic structures

    Science.gov (United States)

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

    2016-05-01

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

  10. An efficient fully atomistic potential model for dense fluid methane

    Science.gov (United States)

    Jiang, Chuntao; Ouyang, Jie; Zhuang, Xin; Wang, Lihua; Li, Wuming

    2016-08-01

    A fully atomistic model aimed to obtain a general purpose model for the dense fluid methane is presented. The new optimized potential for liquid simulation (OPLS) model is a rigid five site model which consists of five fixed point charges and five Lennard-Jones centers. The parameters in the potential model are determined by a fit of the experimental data of dense fluid methane using molecular dynamics simulation. The radial distribution function and the diffusion coefficient are successfully calculated for dense fluid methane at various state points. The simulated results are in good agreement with the available experimental data shown in literature. Moreover, the distribution of mean number hydrogen bonds and the distribution of pair-energy are analyzed, which are obtained from the new model and other five reference potential models. Furthermore, the space-time correlation functions for dense fluid methane are also discussed. All the numerical results demonstrate that the new OPLS model could be well utilized to investigate the dense fluid methane.

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

    Science.gov (United States)

    Strong, Steven E; Eaves, Joel D

    2016-05-19

    Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For numerical simulation to play a predictive and descriptive role, one must have theoretically sound methods that span orders of magnitude in physical scales, from the atomistic motions of particles inside the channels to the large-scale hydrodynamic gradients that drive transport. Here, we use constraint dynamics to derive a nonequilibrium molecular dynamics method for simulating steady-state mass flow of a fluid moving through the nanoscopic spaces of a porous solid. After validating our method on a model system, we use it to study the hydrophobic effect of water moving through pores of electrically doped single-layer graphene. The trend in permeability that we calculate does not follow the hydrophobicity of the membrane but is instead governed by a crossover between two competing molecular transport mechanisms. PMID:27139634

  12. Atomistic Simulations of Poly(N-isopropylacrylamide) Surfactants in Water

    Science.gov (United States)

    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.

  13. Atomistic Molecular Dynamics Simulations of Shock Compressed Quartz

    CERN Document Server

    Farrow, Matthew R

    2011-01-01

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

  14. Optimization of Monte Carlo simulations

    OpenAIRE

    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 ...

  15. 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

  16. Kinetic simulation

    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.

  17. Kinetic Interface

    DEFF Research Database (Denmark)

    2009-01-01

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

  18. Monte Carlo simulation of hydrogen adsorption on Ni surfaces

    Institute of Scientific and Technical Information of China (English)

    WANG Rui; DENG Hui-qiu; YUAN Xiao-jian; HU Wang-yu

    2007-01-01

    In the present paper the adsorption kinetics of the hydrogen molecule on the(111)and(100)surfaces have been studied with the model proposed by Panczyk and the grand canonical Monte Carlo simulation method.The equilibrium adsorption isotherms are calculated at five different temperatures ranging from 314 K to 376 K and compared with the experimental equilibrium adsorption isotherms.The effects of temperature and pressure on coverage are also analyzed.

  19. 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

  20. Monte Carlo techniques

    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.)

  1. 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

  2. Linking Atomistic and Mesoscale Simulations of Water Soluble Polymers

    Science.gov (United States)

    Jones, J. L.

    2003-03-01

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

  3. Atomistic study of the buckling of gold nanowires

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-06-15

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

  4. MCMini: Monte Carlo on GPGPU

    Energy Technology Data Exchange (ETDEWEB)

    Marcus, Ryan C. [Los Alamos National Laboratory

    2012-07-25

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

  5. An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

    Science.gov (United States)

    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

  6. Monte Carlo methods for electromagnetics

    CERN Document Server

    Sadiku, Matthew NO

    2009-01-01

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

  7. Monte Carlo Exploration of Warped Higgsless Models

    CERN Document Server

    Hewett, J L; Rizzo, T G

    2004-01-01

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

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

    Science.gov (United States)

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

    2010-03-01

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

  9. Limitations of reactive atomistic potentials in describing defect structures in oxides

    Science.gov (United States)

    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.

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

    CERN Document Server

    Stephenson, David; Lockerby, Duncan A

    2016-01-01

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

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

    Science.gov (United States)

    Chen, Youping

    2006-02-01

    Local densities of fundamental physical quantities, including stress and heat flux fields, are formulated for atomistic systems involving three-body forces. The obtained formulas are calculable within an atomistic simulation, in consistent with the conservation equations of thermodynamics of continuum, and can be applied to systems with general two- and three-body interaction forces. It is hoped that this work may correct some misuse of inappropriate formulas of stress and heat flux in the literature, may clarify the definition of site energy of many-body potentials, and may serve as an analytical link between an atomistic model and a continuum theory. Physical meanings of the obtained formulas, their relation with virial theorem and heat theorem, and the applicability are discussed. PMID:16468857

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

    Science.gov (United States)

    Chen, Youping

    2006-02-01

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

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

    Science.gov (United States)

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

    2010-02-25

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

  14. 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.

  15. Real-Time Examination of Atomistic Mechanisms during Shock-Induced Structural Transformation in Silicon.

    Science.gov (United States)

    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

  16. Atomistic modeling of BN nanofillers for mechanical and thermal properties: a review

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-07

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  19. Real-Time Examination of Atomistic Mechanisms during Shock-Induced Structural Transformation in Silicon

    Science.gov (United States)

    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.

  20. 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

  1. Scalable and portable visualization of large atomistic datasets

    Science.gov (United States)

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

    2004-10-01

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

  2. Kinetic activation-relaxation technique.

    Science.gov (United States)

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

    2011-10-01

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

  3. Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments.

    Science.gov (United States)

    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

  4. Monte Carlo simulation algorithm for B-DNA.

    Science.gov (United States)

    Howell, Steven C; Qiu, Xiangyun; Curtis, Joseph E

    2016-11-01

    Understanding the structure-function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small-angle X-ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all-atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub-ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B-DNA is represented using a wormlike bead-rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse-grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. © 2016 Wiley Periodicals, Inc. PMID:27671358

  5. Fundamental aspects of plasma chemical physics kinetics

    CERN Document Server

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

    2016-01-01

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

  6. Monte Carlo Simulation of Linear Polymer Thermal Depolymerization under Isothermal and Dynamic Modes

    OpenAIRE

    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...

  7. Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

    NARCIS (Netherlands)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-23

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

  9. Physisorption kinetics

    CERN Document Server

    Kreuzer, Hans Jürgen

    1986-01-01

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

  10. Molecular cooperativity and compatibility via full atomistic simulation

    Science.gov (United States)

    Kwan Yang, Kenny

    Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules

  11. Simulations of kinetically irreversible protein aggregate structure.

    OpenAIRE

    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-...

  12. Frequency-domain deviational Monte Carlo method for linear oscillatory gas flows

    Science.gov (United States)

    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.

  13. 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

  14. Kinetic divertor modeling

    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.

  15. Proton Upset Monte Carlo Simulation

    Science.gov (United States)

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

    2009-01-01

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

  16. Mineralogy of Libya Montes, Mars

    Science.gov (United States)

    Perry, K. A.; Bishop, J. L.; McKeown, N. K.

    2009-12-01

    Observations by CRISM (Compact Reconnaissance Imaging Spectrometer for Mars) have revealed a range of minerals in Libya Montes including olivine, pyroxene, and phyllosilicate [1]. Here we extend our spectral analyses of CRISM images in Libya Montes to identify carbonates. We have also performed detailed characterization of the spectral signature of the phyllosilicate- and carbonate-bearing outcrops in order to constrain the types of phyllosilicates and carbonates present. Phyllosilicate-bearing rocks in Libya Montes have spectral bands at 1.42, 2.30 and 2.39 µm, consistent with Fe- and Mg- bearing smectites. The mixture of Fe and Mg in Libya Montes may be within the clay mineral structure or within the CRISM pixel. Because the pixels have 18 meter/pixel spatial resolution, it is possible that the bands observed are due to the mixing of nontronite and saponite rather than a smectite with both Fe and Mg. Carbonates found in Libya Montes are similar to those found in Nili Fossae [2]. The carbonates have bands centered at 2.30 and 2.52 µm. Libya Montes carbonates most closely resemble the Mg-carbonate, magnesite. Olivine spectra are seen throughout Libya Montes, characterized by a positive slope from 1.2-1.8 µm. Large outcrops of olivine are relatively rare on Mars [3]. This implies that fresh bedrock has been recently exposed because olivine weathers readily compared to pyroxene and feldspar. Pyroxene in Libya Montes resembles an Fe-bearing orthopyroxene with a broad band centered at 1.82 µm. The lowermost unit identified in Libya Montes is a clay-bearing unit. Overlying this is a carbonate-bearing unit with a clear unit division visible in at least one CRISM image. An olivine-bearing unit unconformably overlies these two units and may represent a drape related to the Isidis impact, as suggested for Nili Fossae [2]. However, it appears that the carbonate in Libya Montes is an integral portion of the rock underlying the olivine-bearing unit rather than an

  17. Platelet kinetics

    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

  18. 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.

  19. Kinetic theory for dilute cohesive granular gases with a square well potential.

    Science.gov (United States)

    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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  1. Monte Carlo Particle Lists: MCPL

    CERN Document Server

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

    2016-01-01

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

  2. Electronic states in an atomistic carbon quantum dot patterned in graphene

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-08-01

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

  4. Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

    Energy Technology Data Exchange (ETDEWEB)

    Pourali, Meisam; Maghari, Ali [Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran (Iran, Islamic Republic of); Meloni, Simone, E-mail: simone.meloni@epfl.ch [Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland); Magaletti, Francesco; Casciola, Carlo Massimo [Dipartimento di Ingegneria Meccanica e Aerospaziale, Università La Sapienza, Via Eudossiana 18, 00184 Rome (Italy); Ciccotti, Giovanni [Dipartimento di Fisica and CNISM, Università La Sapienza, P.le A. Moro 5, 00185 Rome (Italy)

    2014-10-21

    We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example.

  5. Fatigue mechanisms in an austenitic steel under cyclic loading: Experiments and atomistic simulations

    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

  6. 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

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

    Science.gov (United States)

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

    2015-11-10

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

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

    Science.gov (United States)

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

    2016-01-01

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

  9. Fatigue mechanisms in an austenitic steel under cyclic loading: Experiments and atomistic simulations

    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.

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

    Institute of Scientific and Technical Information of China (English)

    R ANSARI; S ROUHI; M ARYAYI

    2013-01-01

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

  11. Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2015-01-01

    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

  13. 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.

  14. Permittivity of oxidized ultra-thin silicon films from atomistic simulations

    OpenAIRE

    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...

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

    Science.gov (United States)

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

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

  16. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.

    Science.gov (United States)

    Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F J; Javanainen, Matti; Kanduč, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S; Monticelli, Luca; Määttä, Jukka; Ollila, O H Samuli; Retegan, Marius; Róg, Tomasz; Santuz, Hubert; Tynkkynen, Joona

    2015-12-10

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https

  17. 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.

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

    Science.gov (United States)

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26809025

  19. Determining anaerobic degradation kinetics from batch tests.

    Science.gov (United States)

    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

  20. 3D 'atomistic' simulations of dopant induced variability in nanoscale implant free In0.75Ga0.25As MOSFETs

    Science.gov (United States)

    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.

  1. 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

  2. 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

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

    Science.gov (United States)

    Zhang, W.; Mi, J.

    2016-03-01

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

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

    Science.gov (United States)

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

    2015-02-01

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

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

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 詹晓力; 等

    2003-01-01

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

  6. 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.)

  7. 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

  8. Neural Adaptive Sequential Monte Carlo

    OpenAIRE

    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...

  9. Adaptive Multilevel Monte Carlo Simulation

    KAUST Repository

    Hoel, H

    2011-08-23

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

  10. Monomial Gamma Monte Carlo Sampling

    OpenAIRE

    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...

  11. 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.

  12. Applications of Atomistic Simulation to Radioactive and Hazardous Waste Glass Formulation Development

    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.

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

    Science.gov (United States)

    Molugu, Trivikram R; Brown, Michael F

    2016-09-01

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

  14. SpecSwap RMC: A novel reverse Monte Carlo approach using a discrete configuration space and pre-computed properties

    CERN Document Server

    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.

  15. Coupled structural and magnetic properties of ferric fluoride nanostructures: Part II, a Monte Carlo-Heisenberg study

    Energy Technology Data Exchange (ETDEWEB)

    Fongang, Bernard [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France); Laboratoire de Sciences des Materiaux, Departement de Physique, Universite de Yaounde i, BP 812 Yaounde (Cameroon); Labaye, Yvan [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France); Calvayrac, Florent, E-mail: Florent.Calvayrac@univ-lemans.fr [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France); Zekeng, Serge [Laboratoire de Sciences des Materiaux, Departement de Physique, Universite de Yaounde i, BP 812 Yaounde (Cameroon); Greneche, Jean-Marc [Departement PEC, Institut des Molecules et Materiaux du Mans, UMR CNRS 6283, LUNAM Universite du Maine, 72085 Le Mans, Cedex 9 (France)

    2012-11-15

    We present a numerical study of the magnetic structure of nanostructured iron fluoride, using the Monte Carlo Metropolis simulated annealing technique and a classical Heisenberg Hamiltonian with superexchange angle dependent interactions. The parameters are adjusted on experimental results, and the atomic structure and topology taken from a previous atomistic model of grain boundaries in the same system. We find perfect antiferromagnetic crystalline grains and a disordered magnetic configuration (speromagnetic) at the grain boundary, in agreement with experimental features. Both the lowest magnetic energy and the rate of magnetic frustration are found to be dependent on the relative disorientation of crystalline grains, i.e. on the cationic topology. We conclude on possible extensions of the model.

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

    Indian Academy of Sciences (India)

    Mohsen Lashgari; Davood Matloubi

    2015-03-01

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

  17. 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.

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

    Science.gov (United States)

    Noronha, S. J.; Farkas, D.

    2002-10-01

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

  19. 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.

  20. 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.

  1. 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...

  2. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-10

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

  4. Monte Carlo techniques in radiation therapy

    CERN Document Server

    Verhaegen, Frank

    2013-01-01

    Modern cancer treatment relies on Monte Carlo simulations to help radiotherapists and clinical physicists better understand and compute radiation dose from imaging devices as well as exploit four-dimensional imaging data. With Monte Carlo-based treatment planning tools now available from commercial vendors, a complete transition to Monte Carlo-based dose calculation methods in radiotherapy could likely take place in the next decade. Monte Carlo Techniques in Radiation Therapy explores the use of Monte Carlo methods for modeling various features of internal and external radiation sources, including light ion beams. The book-the first of its kind-addresses applications of the Monte Carlo particle transport simulation technique in radiation therapy, mainly focusing on external beam radiotherapy and brachytherapy. It presents the mathematical and technical aspects of the methods in particle transport simulations. The book also discusses the modeling of medical linacs and other irradiation devices; issues specific...

  5. 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

  6. Monte Carlo Treatment Planning for Advanced Radiotherapy

    DEFF Research Database (Denmark)

    Cronholm, Rickard

    for commissioning of a Monte Carlo model of a medical linear accelerator, ensuring agreement with measurements within 1% for a range of situations, is presented. The resulting Monte Carlo model was validated against measurements for a wider range of situations, including small field output factors, and agreement...... modulating the intensity of the field during the irradiation. The workflow described has the potential to fully model the dynamic delivery, including gantry rotation during irradiation, of modern radiotherapy. Three corner stones of Monte Carlo Treatment Planning are identified: Building, commissioning...... and validation of a Monte Carlo model of a medical linear accelerator (i), converting a CT scan of a patient to a Monte Carlo compliant phantom (ii) and translating the treatment plan parameters (including beam energy, angles of incidence, collimator settings etc) to a Monte Carlo input file (iii). A protocol...

  7. Solid solution hardening in face centered binary alloys: Gliding statistics of a dislocation in random solid solution by atomistic simulation

    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)

  8. 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.

  9. Mean field simulation for Monte Carlo integration

    CERN Document Server

    Del Moral, Pierre

    2013-01-01

    In the last three decades, there has been a dramatic increase in the use of interacting particle methods as a powerful tool in real-world applications of Monte Carlo simulation in computational physics, population biology, computer sciences, and statistical machine learning. Ideally suited to parallel and distributed computation, these advanced particle algorithms include nonlinear interacting jump diffusions; quantum, diffusion, and resampled Monte Carlo methods; Feynman-Kac particle models; genetic and evolutionary algorithms; sequential Monte Carlo methods; adaptive and interacting Marko

  10. 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)

  11. Extension of the Johnson-Mehl-Avrami-Kolmogorov theory incorporating anisotropic growth studied by Monte Carlo simulations

    NARCIS (Netherlands)

    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

  12. Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies.

    Science.gov (United States)

    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

  13. Monte Carlo calculation of neutron generation time in critical reactor and subcritical reactor with an external source

    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)

  14. 1-D EQUILIBRIUM DISCRETE DIFFUSION MONTE CARLO

    Energy Technology Data Exchange (ETDEWEB)

    T. EVANS; ET AL

    2000-08-01

    We present a new hybrid Monte Carlo method for 1-D equilibrium diffusion problems in which the radiation field coexists with matter in local thermodynamic equilibrium. This method, the Equilibrium Discrete Diffusion Monte Carlo (EqDDMC) method, combines Monte Carlo particles with spatially discrete diffusion solutions. We verify the EqDDMC method with computational results from three slab problems. The EqDDMC method represents an incremental step toward applying this hybrid methodology to non-equilibrium diffusion, where it could be simultaneously coupled to Monte Carlo transport.

  15. Multidimensional stochastic approximation Monte Carlo.

    Science.gov (United States)

    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

  16. Chemical and Biological Kinetics

    Science.gov (United States)

    Emanuel', N. M.

    1981-10-01

    Examples of the application of the methods and ideas of chemical kinetics in various branches of chemistry and biology are considered and the results of studies on the kinetics and mechanisms of autoxidation and inhibited and catalysed oxidation of organic substances in the liquid phase are surveyed. Problems of the kinetics of the ageing of polymers and the principles of their stabilisation are discussed and certain trends in biological kinetics (kinetics of tumour growth, kinetic criteria of the effectiveness of chemotherapy, problems of gerontology, etc.) are considered. The bibliography includes 281 references.

  17. Efficient implementation of the Hellmann-Feynman theorem in a diffusion Monte Carlo calculation.

    Science.gov (United States)

    Vitiello, S A

    2011-02-01

    Kinetic and potential energies of systems of (4)He atoms in the solid phase are computed at T = 0. Results at two densities of the liquid phase are presented as well. Calculations are performed by the multiweight extension to the diffusion Monte Carlo method that allows the application of the Hellmann-Feynman theorem in a robust and efficient way. This is a general method that can be applied in other situations of interest as well.

  18. Atomistic Conversion Reaction Mechanism of WO3 in Secondary Ion Batteries of Li, Na, and Ca

    Energy Technology Data Exchange (ETDEWEB)

    He, Yang; Gu, Meng; Xiao, Hai Yan; Luo, Langli; Shao, Yuyan; Gao, Fei; Du, Yingge; Mao, Scott X.; Wang, Chong M.

    2016-05-13

    Reversible insertion and extraction of ionic species into a host lattice governs the basic operating principle for both rechargeable battery (such as lithium batteries) and electrochromic devices (such as ANA Boeing 787-8 Dreamliner electrochromic window). Intercalation and/or conversion are two fundamental chemical processes for some materials in response to the ion insertion. The interplay between these two chemical processes has never been established. It is speculated that the conversion reaction is initiated by ion intercalation. However, experimental evidence of intercalation and subsequent conversion remains unexplored. Here, using in situ HRTEM and spectroscopy, we captured the atomistic conversion reaction processes during lithium, sodium and calcium ion insertion into tungsten trioxide (WO3) single crystal model electrodes. An intercalation step right prior to conversion is explicitly revealed at atomic scale for the first time for these three ion species. Combining nanoscale diffraction and ab initio molecular dynamics simulations, it is found that, beyond intercalation, the inserted ion-oxygen bonding formation destabilized the transition-metal framework which gradually shrunk, distorted and finally collapsed to a pseudo-amorphous structure. This study provides a full atomistic picture on the transition from intercalation to conversion, which is of essential for material applications in both secondary ion batteries and electrochromic devices.

  19. Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.

    Science.gov (United States)

    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

  20. 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)

  1. Fracture toughness from atomistic simulations: Brittleness induced by emission of sessile dislocations

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-08-04

    Using atomistic simulations of crack response for intermetallic materials the author shows that when the emitted dislocations are sessile and stay in the immediate vicinity of the crack tip the emitted dislocations can actually lead to brittle failure. She present the results of an atomistic simulation study of the simultaneous dislocation emission and crack propagation process in this class of materials. She used a molecular statics technique with embedded atom (EAM) potentials developed for NiAl. The crystal structure of NiAl is the CsCl type (B2) with a lattice parameter of 0.287 nm, which is reproduced by the potential together with the cohesive energy and elastic constants. The compound stays ordered up to the melting point, indicating a strong tendency towards chemical ordering with a relatively high energy of the antiphase boundary (APB). As a result of this relatively large energy the dislocations of 1/2<111> type Burgers vectors imply a high energy and the deformation process occurs via the larger <100> type dislocations.

  2. Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

    Science.gov (United States)

    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.

  3. Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation.

    Science.gov (United States)

    Zahariev, Tsvetan K; Slavchov, Radomir I; Tadjer, Alia V; Ivanova, Anela N

    2014-04-15

    Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems.

  4. Atomistic nature in band-to-band tunneling in two-dimensional silicon pn tunnel diodes

    Science.gov (United States)

    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.

  5. 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.

  6. 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.

  7. Monte Carlo lattice program KIM

    International Nuclear Information System (INIS)

    The Monte Carlo program KIM solves the steady-state linear neutron transport equation for a fixed-source problem or, by successive fixed-source runs, for the eigenvalue problem, in a two-dimensional thermal reactor lattice. Fluxes and reaction rates are the main quantities computed by the program, from which power distribution and few-group averaged cross sections are derived. The simulation ranges from 10 MeV to zero and includes anisotropic and inelastic scattering in the fast energy region, the epithermal Doppler broadening of the resonances of some nuclides, and the thermalization phenomenon by taking into account the thermal velocity distribution of some molecules. Besides the well known combinatorial geometry, the program allows complex configurations to be represented by a discrete set of points, an approach greatly improving calculation speed

  8. General Monte Carlo code MONK

    International Nuclear Information System (INIS)

    The Monte Carlo code MONK is a general program written to provide a high degree of flexibility to the user. MONK is distinguished by its detailed representation of nuclear data in point form i.e., the cross-section is tabulated at specific energies instead of the more usual group representation. The nuclear data are unadjusted in the point form but recently the code has been modified to accept adjusted group data as used in fast and thermal reactor applications. The various geometrical handling capabilities and importance sampling techniques are described. In addition to the nuclear data aspects, the following features are also described; geometrical handling routines, tracking cycles, neutron source and output facilities. 12 references. (U.S.)

  9. Atomistic analyses of competition between site-selective segregation and association of point defects at grain boundary in Y2O3-doped ZrO2

    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)

  10. Methods of nonlinear kinetics

    OpenAIRE

    Gorban, A. N.; Karlin, I. V.

    2003-01-01

    Nonlinear kinetic equations are reviewed for a wide audience of specialists and postgraduate students in physics, mathematical physics, material science, chemical engineering and interdisciplinary research. Contents: The Boltzmann equation, Phenomenology and Quasi-chemical representation of the Boltzmann equation, Kinetic models, Discrete velocity models, Direct simulation, Lattice Gas and Lattice Boltzmann models, Minimal Boltzmann models for flows at low Knudsen number, Other kinetic equati...

  11. Challenges of Monte Carlo Transport

    Energy Technology Data Exchange (ETDEWEB)

    Long, Alex Roberts [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Computational Physics and Methods (CCS-2)

    2016-06-10

    These are slides from a presentation for Parallel Summer School at Los Alamos National Laboratory. Solving discretized partial differential equations (PDEs) of interest can require a large number of computations. We can identify concurrency to allow parallel solution of discrete PDEs. Simulated particles histories can be used to solve the Boltzmann transport equation. Particle histories are independent in neutral particle transport, making them amenable to parallel computation. Physical parameters and method type determine the data dependencies of particle histories. Data requirements shape parallel algorithms for Monte Carlo. Then, Parallel Computational Physics and Parallel Monte Carlo are discussed and, finally, the results are given. The mesh passing method greatly simplifies the IMC implementation and allows simple load-balancing. Using MPI windows and passive, one-sided RMA further simplifies the implementation by removing target synchronization. The author is very interested in implementations of PGAS that may allow further optimization for one-sided, read-only memory access (e.g. Open SHMEM). The MPICH_RMA_OVER_DMAPP option and library is required to make one-sided messaging scale on Trinitite - Moonlight scales poorly. Interconnect specific libraries or functions are likely necessary to ensure performance. BRANSON has been used to directly compare the current standard method to a proposed method on idealized problems. The mesh passing algorithm performs well on problems that are designed to show the scalability of the particle passing method. BRANSON can now run load-imbalanced, dynamic problems. Potential avenues of improvement in the mesh passing algorithm will be implemented and explored. A suite of test problems that stress DD methods will elucidate a possible path forward for production codes.

  12. Challenges of Monte Carlo Transport

    Energy Technology Data Exchange (ETDEWEB)

    Long, Alex Roberts [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Computational Physics and Methods (CCS-2)

    2016-06-10

    These are slides from a presentation for Parallel Summer School at Los Alamos National Laboratory. Solving discretized partial differential equations (PDEs) of interest can require a large number of computations. We can identify concurrency to allow parallel solution of discrete PDEs. Simulated particles histories can be used to solve the Boltzmann transport equation. Particle histories are independent in neutral particle transport, making them amenable to parallel computation. Physical parameters and method type determine the data dependencies of particle histories. Data requirements shape parallel algorithms for Monte Carlo. Then, Parallel Computational Physics and Parallel Monte Carlo are discussed and finally the results are given. The mesh passing method greatly simplifies the IMC implementation and allows simple load-balancing. Using MPI windows and passive, one-sided RMA further simplifies the implementation by removing target synchronization. The author is very interested in implementations of PGAS that may allow further optimization for one-sided, read-only memory access (e.g. Open SHMEM). The MPICH_RMA_OVER_DMAPP option and library is required to make one-sided messaging scale on Trinitite - Moonlight scales poorly. Interconnect specific libraries or functions are likely necessary to ensure performance. BRANSON has been used to directly compare the current standard method to a proposed method on idealized problems. The mesh passing algorithm performs well on problems that are designed to show the scalability of the particle passing method. BRANSON can now run load-imbalanced, dynamic problems. Potential avenues of improvement in the mesh passing algorithm will be implemented and explored. A suite of test problems that stress DD methods will elucidate a possible path forward for production codes.

  13. The Specific Bias in Dynamic Monte Carlo Simulations of Nuclear Reactor

    Science.gov (United States)

    Yamamoto, Toshihisa; Endo, Hiroshi; Ishizu, Tomoko; Tatewaki, Isao

    2014-06-01

    During the development of Monte-Carlo-based dynamic code system, we have encountered two major Monte-Carlo-specific problems. One is the break down due to "false super-criticality" which is caused by an accidentally large eigenvalue due to statistical error in spite of the fact that the reactor is actually not. The other problem, which is the main topic in this paper, is that the statistical error in power level using the reactivity calculated with Monte Carlo code is not symmetric about its mean but always positively biased. This signifies that the bias is accumulated as the calculation proceeds and consequently results in over-estimation of the final power level. It should be noted that the bias will not eliminated by refining time step as long as the variance is not zero. A preliminary investigation on this matter using the one-group-precursor point kinetic equations was made and it was concluded that the bias in power level is approximately proportional to the product of variance in Monte Carlo calculation and elapsed time. This conclusion was verified with some numerical experiments. This outcome is important in quantifying the required precision of the Monte-Carlo-based reactivity calculations.

  14. Atomistic simulation of the premelting of iron and aluminum : Implications for high-pressure melting-curve measurements

    NARCIS (Netherlands)

    Starikov, Sergey V.; Stegailov, Vladimir V.

    2009-01-01

    Using atomistic simulations we show the importance of the surface premelting phenomenon for the melting-curve measurements at high pressures. The model under consideration mimics the experimental conditions deployed for melting studies with diamond-anvil cells. The iron is considered in this work be

  15. A hybrid atomistic electrodynamics-quantum mechanical approach for simulating surface-enhanced Raman scattering.

    Science.gov (United States)

    Payton, John L; Morton, Seth M; Moore, Justin E; Jensen, Lasse

    2014-01-21

    Surface-enhanced Raman scattering (SERS) is a technique that has broad implications for biological and chemical sensing applications by providing the ability to simultaneously detect and identify a single molecule. The Raman scattering of molecules adsorbed on metal nanoparticles can be enhanced by many orders of magnitude. These enhancements stem from a twofold mechanism: an electromagnetic mechanism (EM), which is due to the enhanced local field near the metal surface, and a chemical mechanism (CM), which is due to the adsorbate specific interactions between the metal surface and the molecules. The local field near the metal surface can be significantly enhanced due to the plasmon excitation, and therefore chemists generally accept that the EM provides the majority of the enhancements. While classical electrodynamics simulations can accurately simulate the local electric field around metal nanoparticles, they offer few insights into the spectral changes that occur in SERS. First-principles simulations can directly predict the Raman spectrum but are limited to small metal clusters and therefore are often used for understanding the CM. Thus, there is a need for developing new methods that bridge the electrodynamics simulations of the metal nanoparticle and the first-principles simulations of the molecule to facilitate direct simulations of SERS spectra. In this Account, we discuss our recent work on developing a hybrid atomistic electrodynamics-quantum mechanical approach to simulate SERS. This hybrid method is called the discrete interaction model/quantum mechanics (DIM/QM) method and consists of an atomistic electrodynamics model of the metal nanoparticle and a time-dependent density functional theory (TDDFT) description of the molecule. In contrast to most previous work, the DIM/QM method enables us to retain a detailed atomistic structure of the nanoparticle and provides a natural bridge between the electronic structure methods and the macroscopic

  16. Kinetic approach to the cluster liquid-gas transition

    CERN Document Server

    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.

  17. The Kinetics of Phase Separation in Asymmetric Membranes

    OpenAIRE

    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...

  18. Kinetic process of nitridation on the α-sapphire surface

    Institute of Scientific and Technical Information of China (English)

    Tang Xingzhou; Li Shuping; Kang Junyong; Chen Jiaqi

    2014-01-01

    We established a model to simulate the growth process of nitridation and clarified the inner mechanisms of nitridation and over-nitridation by combining the kinetic Monte Carlo and molecular dynamics methods.Supported by reflection high-energy electron diffraction results with growth in an MBE system,the tendency of nitridation on α-sapphire in different conditions was observed and analyzed.The best conditions for nitridation on the α-sapphire surface are found by our simulation.

  19. Difference in aggregation between functional and toxic amyloids studied by atomistic simulations

    Science.gov (United States)

    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.

  20. Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers.

    Science.gov (United States)

    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

  1. Mapping between atomistic simulations and Eshelby inclusions in the shear deformation of an amorphous silicon model

    Science.gov (United States)

    Albaret, T.; Tanguy, A.; Boioli, F.; Rodney, D.

    2016-05-01

    In this paper we perform quasistatic shear simulations of model amorphous silicon bulk samples with Stillinger-Weber-type potentials. Local plastic rearrangements identified based on local energy variations are fitted through their displacement fields on collections of Eshelby spherical inclusions, allowing determination of their transformation strain tensors. The latter are then used to quantitatively reproduce atomistic stress-strain curves, in terms of both shear and pressure components. We demonstrate that our methodology is able to capture the plastic behavior predicted by different Stillinger-Weber potentials, in particular, their different shear tension coupling. These calculations justify the decomposition of plasticity into shear transformations used so far in mesoscale models and provide atomic-scale parameters that can be used to limit the empiricism needed in such models up to now.

  2. Frozen-density embedding theory with average solvent charge densities from explicit atomistic simulations.

    Science.gov (United States)

    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

  3. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    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.

  4. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

    Science.gov (United States)

    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

  5. Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows

    CERN Document Server

    Fyta, Maria; Kaxiras, Efthimios; Succi, Sauro

    2007-01-01

    We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and mesoscopic scales and is capable of describing self-consistent hydrodynamic effects on molecular motion at a computational cost which scales linearly with both solute size and solvent volume. For an application of our multiscale method, we consider the much studied problem of biopolymer translocation through nanopores: we find that the method reproduces with remarkable accuracy the statistical scaling behavior of the translocation process and provides valuable insight into the cooperative aspects of biopolymer and hydrodynamic motion.

  6. Atomistic mechanisms of amorphization during nanoindentation of SiC: A molecular dynamics study

    Science.gov (United States)

    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.

  7. Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia.

    Directory of Open Access Journals (Sweden)

    Ramon Reigada

    Full Text Available The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic and carbon tetrachloride (non-anesthetic. Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.

  8. 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.

  9. Thermochemistry of organic reactions in microporous oxides by atomistic simulations: benchmarking against periodic B3LYP.

    Science.gov (United States)

    Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole

    2010-07-15

    The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol. PMID:20557090

  10. Mechanism of the Cassie-Wenzel transition via the atomistic and continuum string methods

    Energy Technology Data Exchange (ETDEWEB)

    Giacomello, Alberto, E-mail: alberto.giacomello@uniroma1.it; Casciola, Carlo Massimo [Dipartimento di Ingegneria Meccanica e Aerospaziale, Università di Roma “La Sapienza,” 00184 Rome (Italy); Meloni, Simone, E-mail: simone.meloni@epfl.ch [Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland); Müller, Marcus [Institut für Theoretische Physik, Georg-August-Universität Göttingen, 37077 Göttingen (Germany)

    2015-03-14

    The string method is a general and flexible strategy to compute the most probable transition path for an activated process (rare event). We apply here the atomistic string method in the density field to the Cassie-Wenzel transition, a central problem in the field of superhydrophobicity. We discuss in detail the mechanism of wetting of a submerged hydrophobic cavity of nanometer size and its dependence on the geometry of the cavity. Furthermore, we analyze the algorithmic analogies between the continuum “interface” string method and CREaM [Giacomello et al., Phys. Rev. Lett. 109, 226102 (2012)], a method inspired by the string that allows for a faster and simpler computation of the mechanism and of the free-energy profiles of the wetting process.

  11. Atomistic simulations of surface coverage effects in anisotropic wet chemical etching of crystalline silicon

    Energy Technology Data Exchange (ETDEWEB)

    Gosalvez, M.A.; Foster, A.S.; Nieminen, R.M

    2002-12-30

    Atomistic simulations of anisotropic wet chemical etching of crystalline silicon have been performed in order to determine the dependence of the etch rates of different crystallographic orientations on surface coverage and clustering of OH radicals. We show that the etch rate is a non-monotonic function of OH coverage and that there always exists a coverage value at which the etch rate reaches a maximum. The dependence of the anisotropy of the etching process on coverage, including the dependence of the fastest-etched plane orientation, is implicitly contained in the model and predictions of convex corner under-etching structures are made. We show that the whole etching process is controlled by only a few surface configurations involving a particular type of next-nearest neighbours. The relative value of the removal probabilities of these confitions determines the balance in the occurrence of step propagation and etch pitting for all surface orientations.

  12. Atomistic study of energy funneling in the light-harvesting complex of green sulfur bacteria

    CERN Document Server

    Huh, Joonsuk; Brookes, Jennifer C; Valleau, Stéphanie; Fujita, Takatoshi; Aspuru-Guzik, Alán

    2013-01-01

    Phototrophic organisms such as plants, photosynthetic bacteria and algae use microscopic complexes of pigment molecules to absorb sunlight. Within the light-harvesting complexes, which frequently have multiple functional and structural subunits, the energy is transferred in the form of molecular excitations with very high efficiency. Green sulfur bacteria are considered to be amongst the most efficient light-harvesting organisms. Despite multiple experimental and theoretical studies of these bacteria the physical origin of the efficient and robust energy transfer in their light-harvesting complexes is not well understood. To study excitation dynamics at the systems level we introduce an atomistic model that mimic a complete light-harvesting apparatus of green sulfur bacteria. The model contains about 4000 pigment molecules and comprises a double wall roll for the chlorosome, a baseplate and six Fenna-Matthews-Olson trimer complexes. We show that the fast relaxation within functional subunits combined with the...

  13. Atomistic-Continuum Hybrid Simulation of Heat Transfer between Argon Flow and Copper Plates

    CERN Document Server

    Mao, Yijin; Chen, C L

    2016-01-01

    A simulation work aiming to study heat transfer coefficient between argon fluid flow and copper plate is carried out based on atomistic-continuum hybrid method. Navier-Stokes equations for continuum domain are solved through the Pressure Implicit with Splitting of Operators (PISO) algorithm, and the atom evolution in molecular domain is solved through the Verlet algorithm. The solver is validated by solving Couette flow and heat conduction problems. With both momentum and energy coupling method applied, simulations on convection of argon flows between two parallel plates are performed. The top plate is kept as a constant velocity and has higher temperature, while the lower one, which is modeled with FCC copper lattices, is also fixed but has lower temperature. It is found that, heat transfer between argon fluid flow and copper plate in this situation is much higher than that at macroscopic when the flow is fully developed.

  14. NATO Advanced Study Institute on Surface Diffusion : Atomistic and Collective Processes

    CERN Document Server

    1997-01-01

    The interest in the problem of surface diffusion has been steadily growing over the last fifteen years. This is clearly evident from the increase in the number of papers dealing with the problem, the development of new experimental techniques, and the specialized sessions focusing on diffusion in national and international meetings. Part of the driving force behind this increasing activity is our recently acquired ability to observe and possibly control atomic scale phenomena. It is now possible to look selectively at individual atomistic processes and to determine their relative importance during growth and reactions at surfaces. The number of researchers interested in this problem also has been growing steadily which generates the need for a good reference source to farniliarize newcomers to the problem. While the recent emphasis is on the role of diffusion during growth, there is also continuing progress on the more traditional aspects of the problem describing mass transport in an ensemble of particles. S...

  15. 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.

  16. 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.

  17. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    Science.gov (United States)

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Summary Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  18. Atomistic studies of nucleation of He clusters and bubbles in bcc iron

    Science.gov (United States)

    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.

  19. Filler reinforcement in cross-linked elastomer nanocomposites: insights from fully atomistic molecular dynamics simulation.

    Science.gov (United States)

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

    Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more

  20. Filler reinforcement in cross-linked elastomer nanocomposites: insights from fully atomistic molecular dynamics simulation.

    Science.gov (United States)

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

    Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more

  1. Monte carlo simulation for soot dynamics

    KAUST Repository

    Zhou, Kun

    2012-01-01

    A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.

  2. Fast quantum Monte Carlo on a GPU

    CERN Document Server

    Lutsyshyn, Y

    2013-01-01

    We present a scheme for the parallelization of quantum Monte Carlo on graphical processing units, focusing on bosonic systems and variational Monte Carlo. We use asynchronous execution schemes with shared memory persistence, and obtain an excellent acceleration. Comparing with single core execution, GPU-accelerated code runs over x100 faster. The CUDA code is provided along with the package that is necessary to execute variational Monte Carlo for a system representing liquid helium-4. The program was benchmarked on several models of Nvidia GPU, including Fermi GTX560 and M2090, and the latest Kepler architecture K20 GPU. Kepler-specific optimization is discussed.

  3. Advanced computers and Monte Carlo

    International Nuclear Information System (INIS)

    High-performance parallelism that is currently available is synchronous in nature. It is manifested in such architectures as Burroughs ILLIAC-IV, CDC STAR-100, TI ASC, CRI CRAY-1, ICL DAP, and many special-purpose array processors designed for signal processing. This form of parallelism has apparently not been of significant value to many important Monte Carlo calculations. Nevertheless, there is much asynchronous parallelism in many of these calculations. A model of a production code that requires up to 20 hours per problem on a CDC 7600 is studied for suitability on some asynchronous architectures that are on the drawing board. The code is described and some of its properties and resource requirements ae identified to compare with corresponding properties and resource requirements are identified to compare with corresponding properties and resource requirements are identified to compare with corresponding properties and resources of some asynchronous multiprocessor architectures. Arguments are made for programer aids and special syntax to identify and support important asynchronous parallelism. 2 figures, 5 tables

  4. 11th International Conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing

    CERN Document Server

    Nuyens, Dirk

    2016-01-01

    This book presents the refereed proceedings of the Eleventh International Conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing that was held at the University of Leuven (Belgium) in April 2014. These biennial conferences are major events for Monte Carlo and quasi-Monte Carlo researchers. The proceedings include articles based on invited lectures as well as carefully selected contributed papers on all theoretical aspects and applications of Monte Carlo and quasi-Monte Carlo methods. Offering information on the latest developments in these very active areas, this book is an excellent reference resource for theoreticians and practitioners interested in solving high-dimensional computational problems, arising, in particular, in finance, statistics and computer graphics.

  5. Avariide kiuste Monte Carlosse / Aare Arula

    Index Scriptorium Estoniae

    Arula, Aare

    2007-01-01

    Vt. ka Tehnika dlja Vsehh nr. 3, lk. 26-27. 26. jaanuaril 1937 Tallinnast Monte Carlo tähesõidule startinud Karl Siitanit ja tema meeskonda ootasid ees seiklused, mis oleksid neile peaaegu elu maksnud

  6. Aasta film - joonisfilm "Mont Blanc" / Verni Leivak

    Index Scriptorium Estoniae

    Leivak, Verni, 1966-

    2002-01-01

    Eesti Filmiajakirjanike Ühing andis aasta 2001 parima filmi tiitli Priit Tenderi joonisfilmile "Mont Blanc" : Eesti Joonisfilm 2001.Ka filmikriitikute eelistused kinodes ja televisioonis 2001. aastal näidatud filmide osas

  7. Monte Carlo methods for particle transport

    CERN Document Server

    Haghighat, Alireza

    2015-01-01

    The Monte Carlo method has become the de facto standard in radiation transport. Although powerful, if not understood and used appropriately, the method can give misleading results. Monte Carlo Methods for Particle Transport teaches appropriate use of the Monte Carlo method, explaining the method's fundamental concepts as well as its limitations. Concise yet comprehensive, this well-organized text: * Introduces the particle importance equation and its use for variance reduction * Describes general and particle-transport-specific variance reduction techniques * Presents particle transport eigenvalue issues and methodologies to address these issues * Explores advanced formulations based on the author's research activities * Discusses parallel processing concepts and factors affecting parallel performance Featuring illustrative examples, mathematical derivations, computer algorithms, and homework problems, Monte Carlo Methods for Particle Transport provides nuclear engineers and scientists with a practical guide ...

  8. Frontiers of quantum Monte Carlo workshop: preface

    International Nuclear Information System (INIS)

    The introductory remarks, table of contents, and list of attendees are presented from the proceedings of the conference, Frontiers of Quantum Monte Carlo, which appeared in the Journal of Statistical Physics

  9. Simulation and the Monte Carlo method

    CERN Document Server

    Rubinstein, Reuven Y

    2016-01-01

    Simulation and the Monte Carlo Method, Third Edition reflects the latest developments in the field and presents a fully updated and comprehensive account of the major topics that have emerged in Monte Carlo simulation since the publication of the classic First Edition over more than a quarter of a century ago. While maintaining its accessible and intuitive approach, this revised edition features a wealth of up-to-date information that facilitates a deeper understanding of problem solving across a wide array of subject areas, such as engineering, statistics, computer science, mathematics, and the physical and life sciences. The book begins with a modernized introduction that addresses the basic concepts of probability, Markov processes, and convex optimization. Subsequent chapters discuss the dramatic changes that have occurred in the field of the Monte Carlo method, with coverage of many modern topics including: Markov Chain Monte Carlo, variance reduction techniques such as the transform likelihood ratio...

  10. Smart detectors for Monte Carlo radiative transfer

    CERN Document Server

    Baes, Maarten

    2008-01-01

    Many optimization techniques have been invented to reduce the noise that is inherent in Monte Carlo radiative transfer simulations. As the typical detectors used in Monte Carlo simulations do not take into account all the information contained in the impacting photon packages, there is still room to optimize this detection process and the corresponding estimate of the surface brightness distributions. We want to investigate how all the information contained in the distribution of impacting photon packages can be optimally used to decrease the noise in the surface brightness distributions and hence to increase the efficiency of Monte Carlo radiative transfer simulations. We demonstrate that the estimate of the surface brightness distribution in a Monte Carlo radiative transfer simulation is similar to the estimate of the density distribution in an SPH simulation. Based on this similarity, a recipe is constructed for smart detectors that take full advantage of the exact location of the impact of the photon pack...

  11. Introduction to chemical kinetics

    CERN Document Server

    Soustelle, Michel

    2013-01-01

    This book is a progressive presentation of kinetics of the chemical reactions. It provides complete coverage of the domain of chemical kinetics, which is necessary for the various future users in the fields of Chemistry, Physical Chemistry, Materials Science, Chemical Engineering, Macromolecular Chemistry and Combustion. It will help them to understand the most sophisticated knowledge of their future job area. Over 15 chapters, this book present the fundamentals of chemical kinetics, its relations with reaction mechanisms and kinetic properties. Two chapters are then devoted to experimental re

  12. Principles of chemical kinetics

    CERN Document Server

    House, James E

    2007-01-01

    James House's revised Principles of Chemical Kinetics provides a clear and logical description of chemical kinetics in a manner unlike any other book of its kind. Clearly written with detailed derivations, the text allows students to move rapidly from theoretical concepts of rates of reaction to concrete applications. Unlike other texts, House presents a balanced treatment of kinetic reactions in gas, solution, and solid states. The entire text has been revised and includes many new sections and an additional chapter on applications of kinetics. The topics covered include quantitative rela

  13. Monte Carlo simulation of granular fluids

    OpenAIRE

    Montanero, J. M.

    2003-01-01

    An overview of recent work on Monte Carlo simulations of a granular binary mixture is presented. The results are obtained numerically solving the Enskog equation for inelastic hard-spheres by means of an extension of the well-known direct Monte Carlo simulation (DSMC) method. The homogeneous cooling state and the stationary state reached using the Gaussian thermostat are considered. The temperature ratio, the fourth velocity moments and the velocity distribution functions are obtained for bot...

  14. Systematic hierarchical coarse-graining with the inverse Monte Carlo method

    Energy Technology Data Exchange (ETDEWEB)

    Lyubartsev, Alexander P., E-mail: alexander.lyubartsev@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Naômé, Aymeric, E-mail: aymeric.naome@unamur.be [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Vercauteren, Daniel P., E-mail: daniel.vercauteren@unamur.be [UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Laaksonen, Aatto, E-mail: aatto@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Science for Life Laboratory, 17121 Solna (Sweden)

    2015-12-28

    We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730–3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.

  15. Systematic hierarchical coarse-graining with the inverse Monte Carlo method

    Science.gov (United States)

    Lyubartsev, Alexander P.; Naômé, Aymeric; Vercauteren, Daniel P.; Laaksonen, Aatto

    2015-12-01

    We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730-3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.

  16. Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

    CERN Document Server

    Beauchamp, Kyle A; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

    2015-01-01

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using t...

  17. Continuum Plate Theory and Atomistic Modeling to Find the Flexural Rigidity of a Graphene Sheet Interacting with a Substrate

    Directory of Open Access Journals (Sweden)

    M. W. Roberts

    2010-01-01

    Full Text Available Using a combination of continuum modeling, atomistic simulations, and numerical optimization, we estimate the flexural rigidity of a graphene sheet. We consider a rectangular sheet that is initially parallel to a rigid substrate. The sheet interacts with the substrate by van der Waals forces and deflects in response to loading on a pair of opposite edges. To estimate the flexural rigidity, we model the graphene sheet as a continuum and numerically solve an appropriate differential equation for the transverse deflection. This solution depends on the flexural rigidity. We then use an optimization procedure to find the value of the flexural rigidity that minimizes the difference between the numerical solutions and the deflections predicted by atomistic simulations. This procedure predicts a flexural rigidity of 0.26 nN nm=1.62 eV.

  18. Plasma kinetic theory

    CERN Document Server

    Swanson, Donald Gary

    2008-01-01

    Developed from the lectures of a leading expert in plasma wave research, Plasma Kinetic Theory provides the essential material for an introductory course on plasma physics as well as the basis for a more advanced course on kinetic theory. Exploring various wave phenomena in plasmas, it offers wide-ranging coverage of the field. After introducing basic kinetic equations and the Lenard–Balescu equation, the book covers the important Vlasov–Maxwell equations. The solutions of these equations in linear and quasilinear approximations comprise the majority of kinetic theory. Another main topic in kinetic theory is to assess the effects of collisions or correlations in waves. The author discusses the effects of collisions in magnetized plasma and calculates the different transport coefficients, such as pressure tensor, viscosity, and thermal diffusion, that depend on collisions. With worked examples and problem sets that enable sound comprehension, this text presents a detailed, mathematical approach to app...

  19. The continuum elastic and atomistic viewpoints on the formation volume and strain energy of a point defect

    OpenAIRE

    Garikipati, K.; Falk, M. L.; Bouville, M.; Puchala, B.; Narayanan, H.

    2005-01-01

    We discuss the roles of continuum linear elasticity and atomistic calculations in determining the formation volume and the strain energy of formation of a point defect in a crystal. Our considerations bear special relevance to defect formation under stress. The elasticity treatment is based on the Green's function solution for a center of contraction or expansion in an anisotropic solid. It makes possible the precise definition of a formation volume tensor and leads to an extension of Eshelby...

  20. Atomistic simulations to micro-mechanisms of adhesion in automotive applications

    Science.gov (United States)

    Sen, Fatih Gurcag

    This study aimed at depicting atomistic and microstructural aspects of adhesion and friction that appear in different automotive applications and manufacturing processes using atomistic simulations coupled with tribological tests and surface characterization experiments. Thin films that form at the contact interfaces due to chemical reactions and coatings that are developed to mitigate or enhance adhesion were studied in detail. The adhesion and friction experiments conducted on diamond-like carbon (DLC) coatings against Al indicated that F incorporation into DLC decreased the coefficient of friction (COF) by 30% -with respect to H-DLC that is known to have low COF and anti-adhesion properties against Al- to 0.14 owing to formation of repulsive F-F interactions at the sliding interface as shown by density functional theory (DFT) calculations. F atoms transferred to the Al surface with an increase in the contact pressure, and this F transfer led to the formation of a stable AlF3 compound at the Al surface as confirmed by XPS and cross-sectional FIB-TEM. The incorporation of Si and O in a F-containing DLC resulted in humidity independent low COF of 0.08 due to the hydration effect of the Si-O-Si chains in the carbonaceous tribolayers that resulted in repulsive OH-OH interactions at the contact interface. At high temperatures, adhesion of Al was found to be enhanced as a result of superplastic oxide fibers on the Al surface. Molecular dynamics (MD) simulations of tensile deformation of Al nanowires in oxygen carried out with ReaxFF showed that native oxide of Al has an oxygen deficient, low density structure and in O2, the oxygen diffusion in amorphous oxide healed the broken Al-O bonds during applied strain and resulted in the superplasticity. The oxide shell also provided nucleation sites for dislocations in Al crystal. In fuel cell applications, where low Pt/carbon adhesion is causing durability problems, spin-polarized DFT showed that metals with unfilled d

  1. Atomistic modeling of nanowires, small-scale fatigue damage in cast magnesium, and materials for MEMS

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Martin L. [Univ. of Colorado, Boulder, CO (United States); Talmage, Mellisa J. [Univ. of Colorado, Boulder, CO (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); West, Neil [Univ. of Colorado, Boulder, CO (United States); Gullett, Philip Michael [Mississippi State Univ., Mississippi State, MS (United States); Miller, David C. [Univ. of Colorado, Boulder, CO (United States); Spark, Kevin [Univ. of Colorado, Boulder, CO (United States); Diao, Jiankuai [Univ. of Colorado, Boulder, CO (United States); Horstemeyer, Mark F. [Mississippi State Univ., Mississippi State, MS (United States); Zimmerman, Jonathan A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gall, K. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2006-10-01

    Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project

  2. Ultrathin Molecular-Layer-by-Layer Polyamide Membranes: Insights from Atomistic Molecular Simulations.

    Science.gov (United States)

    Liyana-Arachchi, Thilanga P; Sturnfield, James F; Colina, Coray M

    2016-09-01

    In this study, we present an atomistic simulation study of several physicochemical properties of polyamide (PA) membranes formed from interfacial polymerization or from a molecular-layer-by-layer (mLbL) on a silicon wafer. These membranes are composed of meta-phenylenediamine (MPD) and benzene-1,3,5-tricarboxylic acid chloride (TMC) for potential reverse osmosis (RO) applications. The mLbL membrane generation procedure and the force field models were validated, by comparison with available experimental data, for hydrated density, membrane swelling, and pore size distributions of PA membranes formed by interfacial polymerization. Physicochemical properties such as density, free volume, thickness, the degree of cross-linking, atomic compositions, and average molecular orientation (which is relevant for the mLbL membranes) are compared for these different processes. The mLbL membranes are investigated systematically with respect to TMC monomer growth rate per substrate surface area, MPD/TMC ratio, and the number of mLbL deposition cycles. Atomistic simulations show that the mLbL deposition generates membranes with a constant film growth if both the TMC monomer growth rate and MPD/TMC monomer ratio are kept constant. The film growth rate increases with TMC monomer growth rate or MPD/TMC ratio. Furthermore, it was found on one hand that the mLbL membrane density and free volume varies significantly with respect to the TMC monomer growth rate, while on the other hand the degree of cross-linking and the atomic composition varies considerably with the MPD/TMC ratio. Additionally, it was found that both TMC and MPD orient at a tilted angle with respect to the substrate surface, where their angular distribution and average angle orientation depend on both the TMC growth rate and the number of deposition cycles. This study illustrates that molecular simulations can play a crucial role in the understanding of structural properties that can empower the design of the next

  3. Reactive molecular dynamics simulation and chemical kinetic modeling of pyrolysis and combustion of n-dodecane

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Quan-De [College of Chemistry, Sichuan University, Chengdu (China); Wang, Jing-Bo; Li, Juan-Qin; Tan, Ning-Xin; Li, Xiang-Yuan [College of Chemical Engineering, Sichuan University, Chengdu (China)

    2011-02-15

    The initiation mechanisms and kinetics of pyrolysis and combustion of n-dodecane are investigated by using the reactive molecular dynamics (ReaxFF MD) simulation and chemical kinetic modeling. From ReaxFF MD simulations, we find the initiation mechanisms of pyrolysis of n-dodecane are mainly through two pathways, (1) the cleavage of C-C bond to form smaller hydrocarbon radicals, and (2) the dehydrogenation reaction to form an H radical and the corresponding n-C{sub 12}H{sub 25} radical. Another pathway is the H-abstraction reactions by small radicals including H, CH{sub 3}, and C{sub 2}H{sub 5}, which are the products after the initiation reaction of n-dodecane pyrolysis. ReaxFF MD simulations lead to reasonable Arrhenius parameters compared with experimental results based on first-order kinetic analysis of n-dodecane pyrolysis. The density/pressure effects on the pyrolysis of n-dodecane are also analyzed. By appropriate mapping of the length and time from macroscopic kinetic modeling to ReaxFF MD, a simple comparison of the conversion of n-dodecane from ReaxFF MD simulations and that from kinetic modeling is performed. In addition, the oxidation of n-dodecane is studied by ReaxFF MD simulations. We find that formaldehyde molecule is an important intermediate in the oxidation of n-dodecane, which has been confirmed by kinetic modeling, and ReaxFF leads to reasonable reaction pathways for the oxidation of n-dodecane. These results indicate that ReaxFF MD simulations can give an atomistic description of the initiation mechanism and product distributions of pyrolysis and combustion for hydrocarbon fuels, and can be further used to provide molecular based robust kinetic reaction mechanism for chemical kinetic modeling of hydrocarbon fuels. (author)

  4. Development of Monte Carlo depletion code MCDEP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, K. S.; Kim, K. Y.; Lee, J. C.; Ji, S. K. [KAERI, Taejon (Korea, Republic of)

    2003-07-01

    Monte Carlo neutron transport calculation has been used to obtain a reference solution in reactor physics analysis. The typical and widely-used Monte Carlo transport code is MCNP (Monte Carlo N-Particle Transport Code) developed in Los Alamos National Laboratory. The drawbacks of Monte-Carlo transport codes are the lacks of the capacities for the depletion and temperature dependent calculations. In this research we developed MCDEP (Monte Carlo Depletion Code Package) using MCNP with the capacity of the depletion calculation. This code package is the integration of MCNP and depletion module of ORIGEN-2 using the matrix exponential method. This code package enables the automatic MCNP and depletion calculations only with the initial MCNP and MCDEP inputs prepared by users. Depletion chains were simplified for the efficiency of computing time and the treatment of short-lived nuclides without cross section data. The results of MCDEP showed that the reactivity and pin power distributions for the PWR fuel pins and assemblies are consistent with those of CASMO-3 and HELIOS.

  5. Approaching Chemical Accuracy with Quantum Monte Carlo

    CERN Document Server

    Petruzielo, F R; Umrigar, C J

    2012-01-01

    A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space.

  6. Monte Carlo wave packet approach to dissociative multiple ionization in diatomic molecules

    DEFF Research Database (Denmark)

    Leth, Henriette Astrup; Madsen, Lars Bojer; Mølmer, Klaus

    2010-01-01

    A detailed description of the Monte Carlo wave packet technique applied to dissociative multiple ionization of diatomic molecules in short intense laser pulses is presented. The Monte Carlo wave packet technique relies on the Born-Oppenheimer separation of electronic and nuclear dynamics...... separately for each molecular charge state. Our model circumvents the solution of a multiparticle Schrödinger equation and makes it possible to extract the kinetic energy release spectrum via the Coulomb explosion channel as well as the physical origin of the different structures in the spectrum....... The computational effort is restricted and the model is applicable to any molecular system where electronic Born-Oppenheimer curves, dipole moment functions, and ionization rates as a function of nuclear coordinates can be determined....

  7. Three Dimension Monte Carlo Simulation of Austenite Grain Growth in CGHAZ of an Ultrafine Grain Steel

    Institute of Scientific and Technical Information of China (English)

    Dong CHEN; Yongping LEI; Xiaoyan LI; Yaowu SHI; Zhiling TIAN

    2003-01-01

    In the present research Monte Carlo technique was used to simulate the grain growth in heat-affected zone(HAZ) of an ultrafine grain steel. An experimental data based (EBD) model proposed by Gao was used to establish the relation between tMCS and real time temperature kinetics in our simulation. The simulations give out the evolution of grain structure and grain size distribution in HAZ of the ultrafine grain steel. A Microsoft Window based on computer program for the simulation of grain growth in the HAZ of weldment in three dimensions has been developed using Monte Carlo technique. For the system, inputting the temperature field data and material properties, the evolution of grain structure, both image of simulated grain structure and numerical datum reflecting grain size distribution can be produced by the program. The system was applied to the ultrafine grain steel welding, and the simulated results show that the ultrafine grain steel has large tendency of grain growth.

  8. A particle-in-cell plus Monte Carlo study of plasma-induced damage of normal incidence collector optics used in extreme ultraviolet lithography

    NARCIS (Netherlands)

    Wieggers, R. C.; W. J. Goedheer,; M.R. Akdim,; F. Bijkerk,; Zegeling, P. A.

    2008-01-01

    We present a kinetic simulation of the plasma formed by photoionization in the intense flux of an extreme ultraviolet lithography (EUVL) light source. The model is based on the particle-in-cell plus Monte Carlo approach. The photoelectric effect and ionization by electron collisions are included. Th

  9. Kinetics of phase transformations

    International Nuclear Information System (INIS)

    This volume contains papers presented at the Materials Research Society symposium on Kinetics of Phase Transformations held in Boston, Massachusetts from November 26-29, 1990. The symposium provided a forum for research results in an exceptionally broad and interdisciplinary field. Presentations covered nearly every major class of transformations including solid-solid, liquid-solid, transport phenomena and kinetics modeling. Papers involving amorphous Si, a dominant topic at the symposium, are collected in the first section followed by sections on four major areas of transformation kinetics. The symposium opened with joint sessions on ion and electron beam induced transformations in conjunction with the Surface Chemistry and Beam-Solid Interactions: symposium. Subsequent sessions focused on the areas of ordering and nonlinear diffusion kinetics, solid state reactions and amorphization, kinetics and defects of amorphous silicon, and kinetics of melting and solidification. Seven internationally recognized invited speakers reviewed many of the important problems and recent results in these areas, including defects in amorphous Si, crystal to glass transformations, ordering kinetics, solid-state amorphization, computer modeling, and liquid/solid transformations

  10. Irreversible processes kinetic theory

    CERN Document Server

    Brush, Stephen G

    2013-01-01

    Kinetic Theory, Volume 2: Irreversible Processes deals with the kinetic theory of gases and the irreversible processes they undergo. It includes the two papers by James Clerk Maxwell and Ludwig Boltzmann in which the basic equations for transport processes in gases are formulated, together with the first derivation of Boltzmann's ""H-theorem"" and a discussion of this theorem, along with the problem of irreversibility.Comprised of 10 chapters, this volume begins with an introduction to the fundamental nature of heat and of gases, along with Boltzmann's work on the kinetic theory of gases and s

  11. A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nomura, K; Seymour, R; Wang, W; Kalia, R; Nakano, A; Vashishta, P; Shimojo, F; Yang, L H

    2009-02-17

    A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based on hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).

  12. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    Science.gov (United States)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  13. Analytical potential for atomistic simulations of silicon, carbon, and silicon carbide

    Science.gov (United States)

    Erhart, Paul; Albe, Karsten

    2005-01-01

    We present an analytical bond-order potential for silicon, carbon, and silicon carbide that has been optimized by a systematic fitting scheme. The functional form is adopted from a preceding work [Phys. Rev. B 65, 195124 (2002)] and is built on three independently fitted potentials for SiSi , CC , and SiC interaction. For elemental silicon and carbon, the potential perfectly reproduces elastic properties and agrees very well with first-principles results for high-pressure phases. The formation enthalpies of point defects are reasonably reproduced. In the case of silicon stuctural features of the melt agree nicely with data taken from literature. For silicon carbide the dimer as well as the solid phases B1, B2, and B3 were considered. Again, elastic properties are very well reproduced including internal relaxations under shear. Comparison with first-principles data on point defect formation enthalpies shows fair agreement. The successful validation of the potentials for configurations ranging from the molecular to the bulk regime indicates the transferability of the potential model and makes it a good choice for atomistic simulations that sample a large configuration space.

  14. Diffraction Anomalous Fine Structure study and atomistic simulation of Ge/Si nanoislands

    Energy Technology Data Exchange (ETDEWEB)

    Katcho, N.A. [Instituto de Quimica Fisica Rocasolano, IQFR-CSIC, c. Serrano 119, 28006 Madrid (Spain); ICMA, Dep. Fisica de la Materia Condensada, CSIC-Universidad de Zaragoza (Spain); Richard, M.-I. [Aix-Marseille Universite, IM2NP-CNRS, Faculte des Sciences et Techniques, F-13397 Marseille Cedex (France); Proietti, M.G., E-mail: proietti@unizar.es [ICMA, Dep. Fisica de la Materia Condensada, CSIC-Universidad de Zaragoza (Spain); Renevier, H., E-mail: hubert.renevier@grenoble-inp.fr [LMGP, Grenoble INP - Minatec, Grenoble (France); Leclere, C. [LMGP, Grenoble INP - Minatec, Grenoble (France); Favre-Nicolin, V. [CEA-UJF, INAC, SP2M, Grenoble (France); Zhang, J.J.; Bauer, G. [Institut fuer Halbleiter - und Festkoerperphysik, Johannes Kepler Universitaet Linz (Austria)

    2012-08-01

    We applied Grazing Incidence Diffraction Anomalous Fine Structure to the study of the structure of Ge dome-shaped nanoislands, grown by Molecular Beam Epitaxy on Si (0 0 1) substrates at a temperature of 650 Degree-Sign C. We determined the vertical composition of the islands showing the presence of a strong Ge/Si intermixing that is nearly constant from bottom to top. In particular, an abrupt change is found at the substrate interface where the composition switches from pure Si to Ge{sub 0.6}Si{sub 0.4}. The analysis of the Diffraction Anomalous Fine Structure oscillations of the spectra is crucial to obtain the true composition profile. We performed atomistic simulations to investigate the role of the strained substrate underneath the dome on the diffraction results and to quantify the resolution of our method. Anomalous Diffraction spectra and Diffraction Anomalous Fine Structure oscillations have been simulated for a real size and real shape cluster including faceting, giving a more detailed data interpretation and understanding of the Ge-Si intermixing mechanism.

  15. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Directory of Open Access Journals (Sweden)

    Thomas M. Vlasic

    2016-08-01

    Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  16. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations.

    Science.gov (United States)

    Oakes, V; Furini, S; Domene, C

    2016-01-01

    The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs. PMID:27586285

  17. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Science.gov (United States)

    Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

    2016-08-01

    This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  18. Atomistic simulations of fracture in the B2 phase of the Nb-Ti-Al system

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Computer Simulation Lab.

    1998-06-30

    Atomistic simulations of the crack tip configuration in the B2 phase of Nb-rich alloys in the Nb-Ti-Al are presented. The alloy compositions studied are Nb-16Al-16Ti and Nb-16Al-33Ti. The simulations were carried out using molecular statics and empirical embedded atom method (EAM) potentials for the ternary system developed in previous work. The behavior of a semi-infinite crack was studied under mode I loading for different crack tip geometries. The crack was embedded in a simulation cell with periodic boundary conditions along the direction parallel to the crack front and fixed boundary conditions along the periphery of the simulation cell. The quasi-static simulations were carried out using a molecular statics relaxation technique to obtain the minimum energy configuration of the atoms starting from their initial elastic positions, under increasingly higher stress intensities. The competition between dislocation emission and cleavage was studied in these alloys as a function of Ti content. Cracks along {l_brace}110{r_brace}-type planes with crack fronts oriented along different directions were studied. The alloys showed increased ductility with increased Ti content. The simulations show more ductile behavior than other intermetallics, due to easier dislocation emission processes at the crack tip. (orig.) 30 refs.

  19. Atomistic structure of the coherent Ni/Ni[sub 3]Al interface

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. (Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering); Campos, M.F. de; Souze, R.M. de; Goldenstein, H. (Escola Politecnica USP, Sao Paulo (Brazil). Dept. de Metalurgia)

    1994-02-01

    Most Ni-based superalloys are strengthened by the presence of coherent precipitates of an ordered fcc bases phase, known as [gamma][prime]. This phase is basically Ni[sub 3]Al. The precipitates are coherent up to a certain size and they present a cubic shape with faces oriented in the (100) planes of both matrix and precipitate. The detailed atomistic structure of this interface has not been studied. Interest in the use of ordered intermetallic compounds as possible structural materials has resulted in a large amount of work in Ni[sub 3]Al and in particular, the development of interatomic potentials for the Ni-Al system using the embedded atom technique. These potentials have been employed in the simulation of a variety of defects in Ni[sub 3]Al, including dislocation cores, grain boundaries and free surfaces. However, there is no simulation of the Ni/Ni[sub 3]Al interface structure using the embedded atom method. The objective of the present work is to carry out such a simulation. Besides the practical importance of the interface in superalloys, it is the simplest type of interface that can be modeled and it is a good starting point for interface work using the embedded atom technique.

  20. Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

    KAUST Repository

    Hong, Bingbing

    2013-10-02

    We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH 2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henrys constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henrys constant. Dependence of the calculated Henrys constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. © 2013 Taylor & Francis.

  1. Prediction of TF target sites based on atomistic models of protein-DNA complexes

    Directory of Open Access Journals (Sweden)

    Collado-Vides Julio

    2008-10-01

    Full Text Available Abstract Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.

  2. Ash'arite's atomistic conception of the physical world: A restatement

    Energy Technology Data Exchange (ETDEWEB)

    Pozi, Firdaus; Othman, Mohd Yusof [School of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia and Institute of Islam Hadhari, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan (Malaysia); Mohamed, Faizal [School of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan (Malaysia)

    2013-11-27

    Atomism plays an important role in the history of human thought. It can be traced back from Democritus atomos in the 500 BC to particle physics and quantum theory in the 21{sup st} century. However, as it being rejected and developed in the course of history of science, it still brings the fundamental question that perplexes physicists. It gives the views that the world is eternal; that the laws of nature is immutable and eternal therefore all phenomena can be determined through the laws and that there is no reality behind the quantum world. In this paper, we shall briefly describe all these three views on the nature of the physical world or universe and this include on the nature of matter. Then, we shall explain our stand on those conceptions based on the Ash'arites atomistic conception of the physical world. We hope this paper can shed a light on several fundamental issues in the conception of the universe and gives the proper response to them.

  3. Unfolding proteins with mechanical forces: From toy models to atomistic simulations

    Science.gov (United States)

    Makarov, Dmitrii

    2011-03-01

    The remarkable combination of strength and toughness, displayed by certain biological materials (e.g. spider silk) and often unmatched by artificial materials, is believed to originate from the mechanical response of individual load-bearing protein domains. Single-molecule pulling experiments carried out during the last decade showed that those proteins, when loaded, respond in a non-equilibrium fashion and can dissipate large amounts of energy though the breaking of sacrificial bonds. In my talk, I will discuss what structural properties correlate with mechanical strength and toughness at the single-molecule level, how thermodynamic stability is related to the mechanical stability, and why both atomistic simulations and simple models seem to fail to reconcile the mechanical responses of the same proteins measured under varied loading regimes. I will further discuss whether it is easier to unfold a protein mechanically by pulling at its ends or by threading it through a narrow pore. The latter process is believed to commonly occur in living organisms as an intermediate step in protein degradation. Supported by the NSF and the Robert A. Welch Foundation.

  4. Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis.

    Science.gov (United States)

    Sutthibutpong, Thana; Noy, Agnes; Harris, Sarah

    2016-01-01

    While DNA supercoiling is ubiquitous in vivo, the structure of supercoiled DNA is more challenging to study experimentally than simple linear sequences because the DNA must have a closed topology in order to sustain superhelical stress. DNA minicircles, which are closed circular double-stranded DNA sequences typically containing between 60 and 500 base pairs, have proven to be useful biochemical tools for the study of supercoiled DNA mechanics. We present detailed protocols for constructing models of DNA minicircles in silico, for performing atomistic molecular dynamics (MD) simulations of supercoiled minicircle DNA, and for analyzing the results of the calculations. These simulations are computationally challenging due to the large system sizes. However, improvements in parallel computing software and hardware promise access to improve conformational sampling and simulation timescales. Given the concurrent improvements in the resolution of experimental techniques such as atomic force microscopy (AFM) and cryo-electron microscopy, the study of DNA minicircles will provide a more complete understanding of both the structure and the mechanics of supercoiled DNA. PMID:27283311

  5. Development and assessment of atomistic models for predicting static friction coefficients

    Science.gov (United States)

    Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

    2016-08-01

    The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

  6. Atomistic insights into dislocation-based mechanisms of void growth and coalescence

    Science.gov (United States)

    Mi, Changwen; Buttry, Daniel A.; Sharma, Pradeep; Kouris, Demitris A.

    2011-09-01

    One of the low-temperature failure mechanisms in ductile metallic alloys is the growth of voids and their coalescence. In the present work we attempt to obtain atomistic insights into the mechanisms underpinning cavitation in a representative metal, namely Aluminum. Often the pre-existing voids in metallic alloys such as Al have complex shapes (e.g. corrosion pits) and the defromation/damage mechanisms exhibit a rich size-dependent behavior across various material length scales. We focus on these two issues in this paper through large-scale calculations on specimens of sizes ranging from 18 thousand to 1.08 million atoms. In addition to the elucidation of the dislocation propagation based void growth mechanism we highlight the observed length scale effect reflected in the effective stress-strain response, stress triaxiality and void fraction evolution. Furthermore, as expected, the conventionally used Gurson's model fails to capture the observed size-effects calling for a mechanistic modification that incorporates the mechanisms observed in our (and other researchers') simulation. Finally, in our multi-void simulations, we find that, the splitting of a big void into a distribution of small ones increases the load-carrying capacity of specimens. However, no obvious dependence of the void fraction evolution on void coalescence is observed.

  7. Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

    KAUST Repository

    French, William R.

    2013-01-01

    We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

  8. Calculation of phonon dispersion in carbon nanotubes using a continuum-atomistic finite element approach

    Directory of Open Access Journals (Sweden)

    Michael J. Leamy

    2011-12-01

    Full Text Available Dispersion calculations are presented for cylindrical carbon nanotubes using a manifold-based continuum-atomistic finite element formulation combined with Bloch analysis. The formulated finite elements allow any (n,m chiral nanotube, or mixed tubes formed by periodically-repeating heterojunctions, to be examined quickly and accurately using only three input parameters (radius, chiral angle, and unit cell length and a trivial structured mesh, thus avoiding the tedious geometry generation and energy minimization tasks associated with ab initio and lattice dynamics-based techniques. A critical assessment of the technique is pursued to determine the validity range of the resulting dispersion calculations, and to identify any dispersion anomalies. Two small anomalies in the dispersion curves are documented, which can be easily identified and therefore rectified. They include difficulty in achieving a zero energy point for the acoustic twisting phonon, and a branch veering in nanotubes with nonzero chiral angle. The twisting mode quickly restores its correct group velocity as wavenumber increases, while the branch veering is associated with a rapid exchange of eigenvectors at the veering point, which also lessens its impact. By taking into account the two noted anomalies, accurate predictions of acoustic and low-frequency optical branches can be achieved out to the midpoint of the first Brillouin zone.

  9. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    Science.gov (United States)

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

  10. A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

    International Nuclear Information System (INIS)

    A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based on hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops · day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).

  11. Molecular Simulations of Cyclic Loading Behavior of Carbon Nanotubes Using the Atomistic Finite Element Method

    Directory of Open Access Journals (Sweden)

    Jianfeng Wang

    2009-01-01

    Full Text Available The potential applications of carbon nanotubes (CNT in many engineered bionanomaterials and electromechanical devices have imposed an urgent need on the understanding of the fatigue behavior and mechanism of CNT under cyclic loading conditions. To date, however, very little work has been done in this field. This paper presents the results of a theoretical study on the behavior of CNT subject to cyclic tensile and compressive loads using quasi-static molecular simulations. The Atomistic Finite Element Method (AFEM has been applied in the study. It is shown that CNT exhibited extreme cyclic loading resistance with yielding strain and strength becoming constant within limited number of loading cycles. Viscoelastic behavior including nonlinear elasticity, hysteresis, preconditioning (stress softening, and large strain have been observed. Chiral symmetry was found to have appreciable effects on the cyclic loading behavior of CNT. Mechanisms of the observed behavior have been revealed by close examination of the intrinsic geometric and mechanical features of tube structure. It was shown that the accumulated residual defect-free morphological deformation was the primary mechanism responsible for the cyclic failure of CNT, while the bond rotating and stretching experienced during loading/unloading played a dominant role on the strength, strain and modulus behavior of CNT.

  12. Continuum and atomistic description of excess electrons in TiO2

    International Nuclear Information System (INIS)

    The modelling of an excess electron in a semiconductor in a prototypical dye sensitised solar cell is carried out using two complementary approaches: atomistic simulation of the TiO2 nanoparticle surface is complemented by a dielectric continuum model of the solvent–semiconductor interface. The two methods are employed to characterise the bound (excitonic) states formed by the interaction of the electron in the semiconductor with a positive charge opposite the interface. Density-functional theory (DFT) calculations show that the excess electron in TiO2 in the presence of a counterion is not fully localised but extends laterally over a large region, larger than system sizes accessible to DFT calculations. The numerical description of the excess electron at the semiconductor–electrolyte interface based on the continuum model shows that the exciton is also delocalised over a large area: the exciton radius can have values from tens to hundreds of Ångströms, depending on the nature of the semiconductor (characterised by the dielectric constant and the electron effective mass in our model). (paper)

  13. Atomistic Insights Into the Oriented Attachment of Tunnel-Based Oxide Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Yifei; Wood, Stephen M; He, Kun; Yao, Wentao; Tompsett, David; Lu, Jun; Nie, Anmin; Islam, M. Saiful; Shahbazian-Yassar, Reza

    2016-01-01

    Controlled synthesis of nanomaterials is one of the grand challenges facing materials scientists. In particular, how tunnel-based nanomaterials aggregate during synthesis while maintaining their well-aligned tunneled structure is not fully understood. Here, we describe the atomistic mechanism of oriented attachment (OA) during solution synthesis of tunneled α-MnO2 nanowires based on a combination of in situ liquid cell transmission electron microscopy (TEM), aberration-corrected scanning TEM with subangstrom spatial resolution, and first-principles calculations. It is found that primary tunnels (1 × 1 and 2 × 2) attach along their common {110} lateral surfaces to form interfaces corresponding to 2 × 3 tunnels that facilitate their short-range ordering. The OA growth of α-MnO2 nanowires is driven by the stability gained from elimination of {110} surfaces and saturation of Mn atoms at {110}-edges. During this process, extra [MnOx] radicals in solution link the two adjacent {110} surfaces and bond with the unsaturated Mn atoms from both surface edges to produce stable nanowire interfaces. Our results provide insights into the controlled synthesis and design of nanomaterials in which tunneled structures can be tailored for use in catalysis, ion exchange, and energy storage applications.

  14. Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

    Directory of Open Access Journals (Sweden)

    Helgi Adalsteinsson

    2008-01-01

    Full Text Available Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-level dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.

  15. Large-scale atomistic simulations of helium-3 bubble growth in complex palladium alloys.

    Science.gov (United States)

    Hale, Lucas M; Zimmerman, Jonathan A; Wong, Bryan M

    2016-05-21

    Palladium is an attractive material for hydrogen and hydrogen-isotope storage applications due to its properties of large storage density and high diffusion of lattice hydrogen. When considering tritium storage, the material's structural and mechanical integrity is threatened by both the embrittlement effect of hydrogen and the creation and evolution of additional crystal defects (e.g., dislocations, stacking faults) caused by the formation and growth of helium-3 bubbles. Using recently developed inter-atomic potentials for the palladium-silver-hydrogen system, we perform large-scale atomistic simulations to examine the defect-mediated mechanisms that govern helium bubble growth. Our simulations show the evolution of a distribution of material defects, and we compare the material behavior displayed with expectations from experiment and theory. We also present density functional theory calculations to characterize ideal tensile and shear strengths for these materials, which enable the understanding of how and why our developed potentials either meet or confound these expectations. PMID:27208963

  16. Hierarchical Statistical 3D ' Atomistic' Simulation of Decanano MOSFETs: Drift-Diffusion, Hydrodynamic and Quantum Mechanical Approaches

    Science.gov (United States)

    Asenov, Asen; Brown, A. R.; Slavcheva, G.; Davies, J. H.

    2000-01-01

    When MOSFETs are scaled to deep submicron dimensions the discreteness and randomness of the dopant charges in the channel region introduces significant fluctuations in the device characteristics. This effect, predicted 20 year ago, has been confirmed experimentally and in simulation studies. The impact of the fluctuations on the functionality, yield, and reliability of the corresponding systems shifts the paradigm of the numerical device simulation. It becomes insufficient to simulate only one device representing one macroscopical design in a continuous charge approximation. An ensemble of macroscopically identical but microscopically different devices has to be characterized by simulation of statistically significant samples. The aims of the numerical simulations shift from predicting the characteristics of a single device with continuous doping towards estimating the mean values and the standard deviations of basic design parameters such as threshold voltage, subthreshold slope, transconductance, drive current, etc. for the whole ensemble of 'atomistically' different devices in the system. It has to be pointed out that even the mean values obtained from 'atomistic' simulations are not identical to the values obtained from continuous doping simulations. In this paper we present a hierarchical approach to the 'atomistic' simulation of aggressively scaled decanano MOSFETs. A full scale 3D drift-diffusion'atomostic' simulation approach is first described and used for verification of the more economical, but also more restricted, options. To reduce the processor time and memory requirements at high drain voltage we have developed a self-consistent option based on a thin slab solution of the current continuity equation only in the channel region. This is coupled to the Poisson's equation solution in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison with the full self-consistent solution. At low drain

  17. Quantum Monte Carlo with Variable Spins

    CERN Document Server

    Melton, Cody A; Mitas, Lubos

    2016-01-01

    We investigate the inclusion of variable spins in electronic structure quantum Monte Carlo, with a focus on diffusion Monte Carlo with Hamiltonians that include spin-orbit interactions. Following our previous introduction of fixed-phase spin-orbit diffusion Monte Carlo (FPSODMC), we thoroughly discuss the details of the method and elaborate upon its technicalities. We present a proof for an upper-bound property for complex nonlocal operators, which allows for the implementation of T-moves to ensure the variational property. We discuss the time step biases associated with our particular choice of spin representation. Applications of the method are also presented for atomic and molecular systems. We calculate the binding energies and geometry of the PbH and Sn$_2$ molecules, as well as the electron affinities of the 6$p$ row elements in close agreement with experiments.

  18. Monte Carlo strategies in scientific computing

    CERN Document Server

    Liu, Jun S

    2008-01-01

    This paperback edition is a reprint of the 2001 Springer edition This book provides a self-contained and up-to-date treatment of the Monte Carlo method and develops a common framework under which various Monte Carlo techniques can be "standardized" and compared Given the interdisciplinary nature of the topics and a moderate prerequisite for the reader, this book should be of interest to a broad audience of quantitative researchers such as computational biologists, computer scientists, econometricians, engineers, probabilists, and statisticians It can also be used as the textbook for a graduate-level course on Monte Carlo methods Many problems discussed in the alter chapters can be potential thesis topics for masters’ or PhD students in statistics or computer science departments Jun Liu is Professor of Statistics at Harvard University, with a courtesy Professor appointment at Harvard Biostatistics Department Professor Liu was the recipient of the 2002 COPSS Presidents' Award, the most prestigious one for sta...

  19. CosmoPMC: Cosmology Population Monte Carlo

    CERN Document Server

    Kilbinger, Martin; Cappe, Olivier; Cardoso, Jean-Francois; Fort, Gersende; Prunet, Simon; Robert, Christian P; Wraith, Darren

    2011-01-01

    We present the public release of the Bayesian sampling algorithm for cosmology, CosmoPMC (Cosmology Population Monte Carlo). CosmoPMC explores the parameter space of various cosmological probes, and also provides a robust estimate of the Bayesian evidence. CosmoPMC is based on an adaptive importance sampling method called Population Monte Carlo (PMC). Various cosmology likelihood modules are implemented, and new modules can be added easily. The importance-sampling algorithm is written in C, and fully parallelised using the Message Passing Interface (MPI). Due to very little overhead, the wall-clock time required for sampling scales approximately with the number of CPUs. The CosmoPMC package contains post-processing and plotting programs, and in addition a Monte-Carlo Markov chain (MCMC) algorithm. The sampling engine is implemented in the library pmclib, and can be used independently. The software is available for download at http://www.cosmopmc.info.

  20. Development and Application of MCNP5 and KENO-VI Monte Carlo Models for the Atucha-2 PHWR Analysis

    OpenAIRE

    O. Mazzantini; F. D'Auria; M. Pecchia; Parisi, C

    2011-01-01

    The geometrical complexity and the peculiarities of Atucha-2 PHWR require the adoption of advanced Monte Carlo codes for performing realistic neutronic simulations. Core models of Atucha-2 PHWR were developed using both MCNP5 and KENO-VI codes. The developed models were applied for calculating reactor criticality states at beginning of life, reactor cell constants, and control rods volumes. The last two applications were relevant for performing successive three dimensional neutron kinetic ana...

  1. Extension of the Johnson-Mehl-Avrami-Kolmogorov theory incorporating anisotropic growth studied by Monte Carlo simulations

    OpenAIRE

    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 generally anisotropic, leads to hard impingement, and obtains strong deviations from the traditional Johnson-Mehl-Avrami-Kolmogorov (JMAK) theory. Within the MC simulations 1D growth can occur wit...

  2. Building a Hydrodynamics Code with Kinetic Theory

    CERN Document Server

    Sagert, Irina; Colbry, Dirk; Pickett, Rodney; Strother, Terrance

    2013-01-01

    We report on the development of a test-particle based kinetic Monte Carlo code for large systems and its application to simulate matter in the continuum regime. Our code combines advantages of the Direct Simulation Monte Carlo and the Point-of-Closest-Approach methods to solve the collision integral of the Boltzmann equation. With that, we achieve a high spatial accuracy in simulations while maintaining computational feasibility when applying a large number of test-particles. The hybrid setup of our approach allows us to study systems which move in and out of the hydrodynamic regime, with low and high particle densities. To demonstrate our code's ability to reproduce hydrodynamic behavior we perform shock wave simulations and focus here on the Sedov blast wave test. The blast wave problem describes the evolution of a spherical expanding shock front and is an important verification problem for codes which are applied in astrophysical simulation, especially for approaches which aim to study core-collapse supern...

  3. Geodesic Monte Carlo on Embedded Manifolds.

    Science.gov (United States)

    Byrne, Simon; Girolami, Mark

    2013-12-01

    Markov chain Monte Carlo methods explicitly defined on the manifold of probability distributions have recently been established. These methods are constructed from diffusions across the manifold and the solution of the equations describing geodesic flows in the Hamilton-Jacobi representation. This paper takes the differential geometric basis of Markov chain Monte Carlo further by considering methods to simulate from probability distributions that themselves are defined on a manifold, with common examples being classes of distributions describing directional statistics. Proposal mechanisms are developed based on the geodesic flows over the manifolds of support for the distributions, and illustrative examples are provided for the hypersphere and Stiefel manifold of orthonormal matrices. PMID:25309024

  4. Monte Carlo dose computation for IMRT optimization*

    Science.gov (United States)

    Laub, W.; Alber, M.; Birkner, M.; Nüsslin, F.

    2000-07-01

    A method which combines the accuracy of Monte Carlo dose calculation with a finite size pencil-beam based intensity modulation optimization is presented. The pencil-beam algorithm is employed to compute the fluence element updates for a converging sequence of Monte Carlo dose distributions. The combination is shown to improve results over the pencil-beam based optimization in a lung tumour case and a head and neck case. Inhomogeneity effects like a broader penumbra and dose build-up regions can be compensated for by intensity modulation.

  5. Monte Carlo simulation of granular fluids

    CERN Document Server

    Montanero, J M

    2003-01-01

    An overview of recent work on Monte Carlo simulations of a granular binary mixture is presented. The results are obtained numerically solving the Enskog equation for inelastic hard-spheres by means of an extension of the well-known direct Monte Carlo simulation (DSMC) method. The homogeneous cooling state and the stationary state reached using the Gaussian thermostat are considered. The temperature ratio, the fourth velocity moments and the velocity distribution functions are obtained for both cases. The shear viscosity characterizing the momentum transport in the thermostatted case is calculated as well. The simulation results are compared with analytical predictions showing an excellent agreement.

  6. Monte carlo simulations of organic photovoltaics.

    Science.gov (United States)

    Groves, Chris; Greenham, Neil C

    2014-01-01

    Monte Carlo simulations are a valuable tool to model the generation, separation, and collection of charges in organic photovoltaics where charges move by hopping in a complex nanostructure and Coulomb interactions between charge carriers are important. We review the Monte Carlo techniques that have been applied to this problem, and describe the results of simulations of the various recombination processes that limit device performance. We show how these processes are influenced by the local physical and energetic structure of the material, providing information that is useful for design of efficient photovoltaic systems.

  7. Monte Carlo dose distributions for radiosurgery

    Energy Technology Data Exchange (ETDEWEB)

    Perucha, M.; Leal, A.; Rincon, M.; Carrasco, E. [Sevilla Univ. (Spain). Dept. Fisiologia Medica y Biofisica; Sanchez-Doblado, F. [Sevilla Univ. (Spain). Dept. Fisiologia Medica y Biofisica]|[Hospital Univ. Virgen Macarena, Sevilla (Spain). Servicio de Oncologia Radioterapica; Nunez, L. [Clinica Puerta de Hierro, Madrid (Spain). Servicio de Radiofisica; Arrans, R.; Sanchez-Calzado, J.A.; Errazquin, L. [Hospital Univ. Virgen Macarena, Sevilla (Spain). Servicio de Oncologia Radioterapica; Sanchez-Nieto, B. [Royal Marsden NHS Trust (United Kingdom). Joint Dept. of Physics]|[Inst. of Cancer Research, Sutton, Surrey (United Kingdom)

    2001-07-01

    The precision of Radiosurgery Treatment planning systems is limited by the approximations of their algorithms and by their dosimetrical input data. This fact is especially important in small fields. However, the Monte Carlo methods is an accurate alternative as it considers every aspect of particle transport. In this work an acoustic neurinoma is studied by comparing the dose distribution of both a planning system and Monte Carlo. Relative shifts have been measured and furthermore, Dose-Volume Histograms have been calculated for target and adjacent organs at risk. (orig.)

  8. Monte Carlo simulation of neutron scattering instruments

    International Nuclear Information System (INIS)

    A library of Monte Carlo subroutines has been developed for the purpose of design of neutron scattering instruments. Using small-angle scattering as an example, the philosophy and structure of the library are described and the programs are used to compare instruments at continuous wave (CW) and long-pulse spallation source (LPSS) neutron facilities. The Monte Carlo results give a count-rate gain of a factor between 2 and 4 using time-of-flight analysis. This is comparable to scaling arguments based on the ratio of wavelength bandwidth to resolution width

  9. Monte Carlo dose distributions for radiosurgery

    International Nuclear Information System (INIS)

    The precision of Radiosurgery Treatment planning systems is limited by the approximations of their algorithms and by their dosimetrical input data. This fact is especially important in small fields. However, the Monte Carlo methods is an accurate alternative as it considers every aspect of particle transport. In this work an acoustic neurinoma is studied by comparing the dose distribution of both a planning system and Monte Carlo. Relative shifts have been measured and furthermore, Dose-Volume Histograms have been calculated for target and adjacent organs at risk. (orig.)

  10. Kinetic equations: computation

    CERN Document Server

    Pareschi, Lorenzo

    2013-01-01

    Kinetic equations bridge the gap between a microscopic description and a macroscopic description of the physical reality. Due to the high dimensionality the construction of numerical methods represents a challenge and requires a careful balance between accuracy and computational complexity.

  11. Chemical Kinetics Database

    Science.gov (United States)

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  12. Fast sequential Monte Carlo methods for counting and optimization

    CERN Document Server

    Rubinstein, Reuven Y; Vaisman, Radislav

    2013-01-01

    A comprehensive account of the theory and application of Monte Carlo methods Based on years of research in efficient Monte Carlo methods for estimation of rare-event probabilities, counting problems, and combinatorial optimization, Fast Sequential Monte Carlo Methods for Counting and Optimization is a complete illustration of fast sequential Monte Carlo techniques. The book provides an accessible overview of current work in the field of Monte Carlo methods, specifically sequential Monte Carlo techniques, for solving abstract counting and optimization problems. Written by authorities in the

  13. Electrochemical kinetics theoretical aspects

    CERN Document Server

    Vetter, Klaus J

    1967-01-01

    Electrochemical Kinetics: Theoretical Aspects focuses on the processes, methodologies, reactions, and transformations in electrochemical kinetics. The book first offers information on electrochemical thermodynamics and the theory of overvoltage. Topics include equilibrium potentials, concepts and definitions, electrical double layer and electrocapillarity, and charge-transfer, diffusion, and reaction overvoltage. Crystallization overvoltage, total overvoltage, and resistance polarization are also discussed. The text then examines the methods of determining electrochemical reaction mechanisms

  14. Comment on "Monte Carlo simulations for a Lotka-type model with reactant diffusion and interactions".

    Science.gov (United States)

    Zhdanov, Vladimir P

    2002-03-01

    Discussing the effect of adsorbate-adsorbate lateral interactions on the kinetics of heterogeneous catalytic reactions, Zvejnieks and Kuzovkov [Phys. Rev. E 63, 051104 (2001)] conclude that in the case of adsorbed particles the Metropolis Monte Carlo dynamics is meaningless and propose to use their own dynamics, which is equivalent to the Glauber dynamics. In this Comment, I show that these and other conclusions and prescriptions by Zvejnieks and Kuzovkov are not in line with the general principles of simulations of rate processes in adsorbed overlayers.

  15. Classical trajectory Monte Carlo investigation for Lorentz ionization of H (1s)

    Institute of Scientific and Technical Information of China (English)

    He Bin; Wang Jian-Guo; Liu Chun-Lei

    2013-01-01

    Lorentz ionization of H(1s) is investigated by classical trajectory Monte Carlo (CTMC) simulation.The effect of the transverse magnetic field on the considered process is analyzed in terms of the time evolution of interactions in the system,total electron energy,and electron trajectories.A classical mechanism for the ionization is found,where the variation of the kinetic energy of the nuclei is found to be important in the process.Compared with the results of tunneling ionization,the classical mechanism becomes more and more important with the increase of the velocity of the H-atom or the strength of the magnetic field.

  16. Linewidth of Cyclotron Absorption in Band-Gap Graphene: Relaxation Time Approximation vs. Monte Carlo Method

    Directory of Open Access Journals (Sweden)

    S.V. Kryuchkov

    2015-03-01

    Full Text Available The power of the elliptically polarized electromagnetic radiation absorbed by band-gap graphene in presence of constant magnetic field is calculated. The linewidth of cyclotron absorption is shown to be non-zero even if the scattering is absent. The calculations are performed analytically with the Boltzmann kinetic equation and confirmed numerically with the Monte Carlo method. The dependence of the linewidth of the cyclotron absorption on temperature applicable for a band-gap graphene in the absence of collisions is determined analytically.

  17. Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules

    CERN Document Server

    Lester, William A; Reynolds, PJ

    1994-01-01

    This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n

  18. Use of Monte Carlo Methods in brachytherapy; Uso del metodo de Monte Carlo en braquiterapia

    Energy Technology Data Exchange (ETDEWEB)

    Granero Cabanero, D.

    2015-07-01

    The Monte Carlo method has become a fundamental tool for brachytherapy dosimetry mainly because no difficulties associated with experimental dosimetry. In brachytherapy the main handicap of experimental dosimetry is the high dose gradient near the present sources making small uncertainties in the positioning of the detectors lead to large uncertainties in the dose. This presentation will review mainly the procedure for calculating dose distributions around a fountain using the Monte Carlo method showing the difficulties inherent in these calculations. In addition we will briefly review other applications of the method of Monte Carlo in brachytherapy dosimetry, as its use in advanced calculation algorithms, calculating barriers or obtaining dose applicators around. (Author)

  19. On the use of stochastic approximation Monte Carlo for Monte Carlo integration

    KAUST Repository

    Liang, Faming

    2009-03-01

    The stochastic approximation Monte Carlo (SAMC) algorithm has recently been proposed as a dynamic optimization algorithm in the literature. In this paper, we show in theory that the samples generated by SAMC can be used for Monte Carlo integration via a dynamically weighted estimator by calling some results from the literature of nonhomogeneous Markov chains. Our numerical results indicate that SAMC can yield significant savings over conventional Monte Carlo algorithms, such as the Metropolis-Hastings algorithm, for the problems for which the energy landscape is rugged. © 2008 Elsevier B.V. All rights reserved.

  20. Decohesion Kinetics of PEDOT:PSS Conducting Polymer Films

    KAUST Repository

    Dupont, Stephanie R.

    2013-10-17

    The highly conductive polymer PEDOT:PSS is a widely used hole transport layer and transparent electrode in organic electronic devices. To date, the mechanical and fracture properties of this conductive polymer layer are not well understood. Notably, the decohesion rate of the PEDOT:PSS layer and its sensitivity to moist environments has not been reported, which is central in determining the lifetimes of organic electronic devices. Here, it is demonstrated that the decohesion rate is highly sensitive to the ambient moisture content, temperature, and mechanical stress. The kinetic mechanisms are elucidated using atomistic bond rupture models and the decohesion process is shown to be facilitated by a chemical reaction between water molecules from the environment and strained hydrogen bonds. Hydrogen bonds are the predominant bonding mechanism between individual PEDOT:PSS grains within the layer and cause a significant loss in cohesion when they are broken. Understanding the decohesion kinetics and mechanisms in these films is essential for the mechanical integrity of devices containing PEDOT:PSS layers and yields general guidelines for the design of more reliable organic electronic devices. Decohesion rate in PEDOT:PSS conducting films is studied under varied environmental conditions. The moisture content in the environment is the most important factor accelerating the decohesion in the PEDOT:PSS layer, which is detrimental for device reliability. The findings on the decohesion rate and mechanisms, elucidated by atomic kinetic models, are essential for the design of more reliable organic electronic devices containting PEDOT:PSS layers. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.