Slow coarsening of B2-ordered domains at low temperatures: A kinetic Monte Carlo study

International Nuclear Information System (INIS)

Le Floc'h, D.; Bellon, P.; Athenes, M.

2000-01-01

The kinetics of the ordering and coarsening of B2-ordered domains is studied using atomistic kinetic Monte Carlo simulations. Special emphasis is put on the effect of annealing temperature, alloy composition, and atom dynamics on the coarsening behavior. When atomic diffusion proceeds by vacancy jumps to nearest-neighbor sites, a transient slow coarsening regime is observed at temperatures below half the order-disorder transition temperature T c . It results in apparent coarsening exponents that decrease with decreasing the annealing temperature. Values as low as 0.14 are measured at 0.25T c . Slow transients take place in both stoichiometric and nonstoichiometric alloys. These regimes are correlated with the transient creation of excess antisites during domain disappearance. Since antiphase boundary mobility decreases with increasing antisite concentration, this transient excess results in the slow coarsening observed in simulations. (c) 2000 The American Physical Society

Object kinetic Monte Carlo model for neutron and ion irradiation in tungsten: Impact of transmutation and carbon impurities

Science.gov (United States)

Castin, N.; Bonny, G.; Bakaev, A.; Ortiz, C. J.; Sand, A. E.; Terentyev, D.

2018-03-01

We upgrade our object kinetic Monte Carlo (OKMC) model, aimed at describing the microstructural evolution in tungsten (W) under neutron and ion irradiation. Two main improvements are proposed based on recently published atomistic data: (a) interstitial carbon impurities, and their interaction with radiation-induced defects (point defect clusters and loops), are more accurately parameterized thanks to ab initio findings; (b) W transmutation to rhenium (Re) upon neutron irradiation, impacting the diffusivity of radiation defects, is included, also relying on recent atomistic data. These essential amendments highly improve the portability of our OKMC model, providing a description for the formation of SIA-type loops under different irradiation conditions. The model is applied to simulate neutron and ion irradiation in pure W samples, in a wide range of fluxes and temperatures. We demonstrate that it performs a realistic prediction of the population of TEM-visible voids and loops, as compared to experimental evidence. The impact of the transmutation of W to Re, and of carbon trapping, is assessed.

Atomistic simulations of surfactant adsorption kinetics at interfaces

Science.gov (United States)

Iskrenova, Eugeniya; Patnaik, Soumya

2014-03-01

Heat transfer control and enhancement is an important and challenging problem in a variety of industrial and technological applications including aircraft thermal management. The role of additives in nucleate boiling and phase change in general has long been recognized and studied experimentally and modeled theoretically but in-depth description and atomistic understanding of the multiscale processes involved are still needed for better prediction and control of the heat transfer efficiency. Surfactant additives have been experimentally observed to either enhance or inhibit the boiling heat transfer depending on the surfactant concentration and chemistry and, on a molecular level, their addition leads to dynamic surface tension and changes in interfacial and transfer properties, thus contributing to the complexity of the problem. We present our atomistic modeling study of the interfacial adsorption kinetics of aqueous surfactant (sodium dodecyl sulfate) systems at a range of concentrations at room and boiling temperatures. Classical molecular dynamics and Umbrella Sampling simulations were used to study the surfactant transport properties and estimate the adsorption and desorption rates at liquid-vacuum and liquid-solid interfaces. The authors gratefully acknowledge funding from AFOSR Thermal Science Program and the Air Force Research Laboratory DoD Supercomputing Resource Center for computing time and resources.

A kinetic Monte Carlo method for the simulation of massive phase transformations

International Nuclear Information System (INIS)

Bos, C.; Sommer, F.; Mittemeijer, E.J.

2004-01-01

A multi-lattice kinetic Monte Carlo method has been developed for the atomistic simulation of massive phase transformations. Beside sites on the crystal lattices of the parent and product phase, randomly placed sites are incorporated as possible positions. These random sites allow the atoms to take favourable intermediate positions, essential for a realistic description of transformation interfaces. The transformation from fcc to bcc starting from a flat interface with the fcc(1 1 1)//bcc(1 1 0) and fcc[1 1 1-bar]//bcc[0 0 1-bar] orientation in a single component system has been simulated. Growth occurs in two different modes depending on the chosen values of the bond energies. For larger fcc-bcc energy differences, continuous growth is observed with a rough transformation front. For smaller energy differences, plane-by-plane growth is observed. In this growth mode two-dimensional nucleation is required in the next fcc plane after completion of the transformation of the previous fcc plane

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.

RNA folding kinetics using Monte Carlo and Gillespie algorithms.

Science.gov (United States)

Clote, Peter; Bayegan, Amir H

2018-04-01

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time for a K-step trajectory of the Monte Carlo algorithm is equal to [Formula: see text] times that of the Gillespie algorithm, where [Formula: see text] denotes the Boltzmann expected network degree. If the network is regular (i.e. every node has the same degree), then the mean first passage time (MFPT) computed by the Monte Carlo algorithm is equal to MFPT computed by the Gillespie algorithm multiplied by [Formula: see text]; however, this is not true for non-regular networks. In particular, RNA secondary structure folding kinetics, as computed by the Monte Carlo algorithm, is not equal to the folding kinetics, as computed by the Gillespie algorithm, although the mean first passage times are roughly correlated. Simulation software for RNA secondary structure folding according to the Monte Carlo and Gillespie algorithms is publicly available, as is our software to compute the expected degree of the network of secondary structures of a given RNA sequence-see http://bioinformatics.bc.edu/clote/RNAexpNumNbors .

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

Science.gov (United States)

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

2017-02-01

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

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.

Kinetic Monte Carlo simulation of phase-precipitation versus instability behavior in short period FeCr superlattices

Energy Technology Data Exchange (ETDEWEB)

Rodríguez-Martínez, F.J. [UCAM, Universidad Católica de Murcia, Campus de los Jerónimos, 30107 Guadalupe (Murcia) (Spain); Castejón-Mochón, J.F., E-mail: jfcastejon@ucam.edu [UCAM, Universidad Católica de Murcia, Campus de los Jerónimos, 30107 Guadalupe (Murcia) (Spain); Castrillo, P.; Berenguer-Vidal, R. [UCAM, Universidad Católica de Murcia, Campus de los Jerónimos, 30107 Guadalupe (Murcia) (Spain); Dopico, I.; Martin-Bragado, I. [IMDEA Materials Institute, Eric Kandel 2, 28906 Getafe (Madrid) (Spain)

2017-02-15

The structural evolution of FeCr superlattices has been studied using a quasi-atomistic Object Kinetic Monte Carlo model. Superlattices with different spatial periods have been simulated for anneal durations from few hours to several months at 500 °C. Relatively-long period superlattices stabilize into Fe-rich and Cr-rich layers with compositions close to those of bulk α and α′ phases. In contrast, superlattices with very short periods (4, 5, 6 nm) are observed to undergo instability and, for long annealing times, evolve into three-dimensionally decomposed regions, in qualitative agreement to recent experimental observations. The instability onset is delayed as the spatial period increases, and it occurs via interface roughness. This evolution can be explained as a minimization of the free-energy associated to the α/α′ interfaces. A comprehensive description of the evolution dynamics of FeCr-based structures is obtained with our model.

Modelling of radiation induced segregation in austenitic Fe alloys at the atomistic level

International Nuclear Information System (INIS)

Piochaud, Jean-Baptiste

2013-01-01

In pressurized water reactors, under irradiation internal structures are subject of irradiation assisted stress corrosion cracking which is influenced by radiation induced segregation (RIS). In this work RIS of 316 stainless steels is modelled considering a model ternary Fe-10Ni-20Cr alloy. For this purpose we have built an Fe-Ni-Cr pair interaction model to simulate RIS at the atomistic level using an atomistic kinetic Monte Carlo approach. The pair interactions have been deduced from density functional theory (DFT) data available in the pure fcc systems but also from DFT calculations we have performed in the Fe-10Ni-20Cr target alloy. Point defect formation energies were calculated and found to depend strongly on the local environment of the defect. As a consequence, a rather good estimation of these energies can be obtained from the knowledge of the number and respective positions of the Ni and Cr atoms in the vicinity of the defect. This work shows that a model based only on interaction parameters between elements positioned in perfect lattice sites (solute atoms and vacancy) cannot capture alone both the thermodynamic and the kinetic aspect of RIS. A more accurate of estimating the barriers encountered by the diffusing species is required than the one used in our model, which has to depend on the saddle point environment. This study therefore shows thus the need to estimate point defect migration energies using the DFT approach to calibrate a model that can be used in the framework of atomic kinetic Monte Carlo simulations. We also found that the reproduction by our pair interaction model of DFT data for the self-interstitial atoms was found to be incompatible with the modelling of RIS under electron irradiation. (author)

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

International Nuclear Information System (INIS)

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

2016-01-01

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. (paper)

SPQR: a Monte Carlo reactor kinetics code

International Nuclear Information System (INIS)

Cramer, S.N.; Dodds, H.L.

1980-02-01

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

Mechanism of Kinetically Controlled Capillary Condensation in Nanopores: A Combined Experimental and Monte Carlo Approach.

Science.gov (United States)

Hiratsuka, Tatsumasa; Tanaka, Hideki; Miyahara, Minoru T

2017-01-24

We find the rule of capillary condensation from the metastable state in nanoscale pores based on the transition state theory. The conventional thermodynamic theories cannot achieve it because the metastable capillary condensation inherently includes an activated process. We thus compute argon adsorption isotherms on cylindrical pore models and atomistic silica pore models mimicking the MCM-41 materials by the grand canonical Monte Carlo and the gauge cell Monte Carlo methods and evaluate the rate constant for the capillary condensation by the transition state theory. The results reveal that the rate drastically increases with a small increase in the chemical potential of the system, and the metastable capillary condensation occurs for any mesopores when the rate constant reaches a universal critical value. Furthermore, a careful comparison between experimental adsorption isotherms and the simulated ones on the atomistic silica pore models reveals that the rate constant of the real system also has a universal value. With this finding, we can successfully estimate the experimental capillary condensation pressure over a wide range of temperatures and pore sizes by simply applying the critical rate constant.

A kinetic Monte Carlo study on the role of defects and detachment in the formation and growth of In chains on Si(100)

International Nuclear Information System (INIS)

Albao, Marvin A; Chuang, F-C; Evans, J W

2009-01-01

Deposition on a Si(100) surface and subsequent self-assembly of In atoms into one-dimensional (1D) atomic chains at room temperature is investigated via kinetic Monte Carlo simulation of a suitable atomistic model. Model development is guided by recent experimental observations in which 1D In chains nucleate effectively exclusively at C-type defects, although In atoms can detach from chains. We find that a monotonically decreasing form of the scaled island size distribution (ISD) is consistent with a high defect density which facilitates persistent chain nucleation even at relatively high coverages. The predominance of heterogeneous nucleation may be attributed to several factors including low surface diffusion barriers, a high defect density, and relatively weak In-In binding.

Shaping the composition profiles in heteroepitaxial quantum dots: Interplay of thermodynamic and kinetic effects

Directory of Open Access Journals (Sweden)

C. Georgiou

2014-07-01

Full Text Available Atomistic Monte Carlo simulations, coupling thermodynamic and kinetic effects, resolve a longstanding controversy regarding the origin of composition profiles in heteroepitaxial SiGe quantum dots. It is shown that profiles with cores rich in the unstrained (Si component derive from near-equilibrium processes and intraisland diffusion. Profiles with cores rich in the strained (Ge component are of nonequilibrium nature, i.e., they are strain driven but kinetically limited. They are shaped by the distribution of kinetic barriers of atomic diffusion in the islands. The diffusion pathways are clearly revealed for the first time. Geometrical kinetics play a minor role.

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.

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

International Nuclear Information System (INIS)

Das, Biswajit; Gangopadhyay, Gautam

2012-01-01

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.

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

International Nuclear Information System (INIS)

Liedke, Bartosz

2011-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Liedke, Bartosz

2011-03-24

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

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.)

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.

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

KAUST Repository

Shao, Jing; Tang, Wei; Xia, Ru; Feng, Xiaoshuang; Chen, Peng; Qian, Jiasheng; Song, Changjiang

2015-01-01

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

Oxygen self-diffusion mechanisms in monoclinic Zr O2 revealed and quantified by density functional theory, random walk analysis, and kinetic Monte Carlo calculations

Science.gov (United States)

Yang, Jing; Youssef, Mostafa; Yildiz, Bilge

2018-01-01

In this work, we quantify oxygen self-diffusion in monoclinic-phase zirconium oxide as a function of temperature and oxygen partial pressure. A migration barrier of each type of oxygen defect was obtained by first-principles calculations. Random walk theory was used to quantify the diffusivities of oxygen interstitials by using the calculated migration barriers. Kinetic Monte Carlo simulations were used to calculate diffusivities of oxygen vacancies by distinguishing the threefold- and fourfold-coordinated lattice oxygen. By combining the equilibrium defect concentrations obtained in our previous work together with the herein calculated diffusivity of each defect species, we present the resulting oxygen self-diffusion coefficients and the corresponding atomistically resolved transport mechanisms. The predicted effective migration barriers and diffusion prefactors are in reasonable agreement with the experimentally reported values. This work provides insights into oxygen diffusion engineering in Zr O2 -related devices and parametrization for continuum transport modeling.

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

Science.gov (United States)

Serebrinsky, Santiago A

2011-03-01

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

Kinetic Monte Carlo model of defect transport and irradiation effects in La-doped CeO2

International Nuclear Information System (INIS)

Oaks, Aaron; Yun Di; Ye Bei; Chen Weiying; Stubbins, James F.

2011-01-01

A generalized Kinetic Monte Carlo code was developed to study oxygen mobility in UO 2 type nuclear fuels, using lanthanum doped CeO 2 as a surrogate material. Molecular Statics simulations were performed using interatomic potentials for CeO 2 developed by Gotte, Minervini, and Sayle to calculate local configuration-dependent oxygen vacancy migration energies. Kinetic Monte Carlo simulations of oxygen vacancy diffusion were performed at varying lanthanum dopant concentrations using the developed generalized Kinetic Monte Carlo code and the calculated configuration-dependent migration energies. All three interatomic potentials were found to confirm the lanthanum trapping effect. The results of these simulations were compared with experimental data and the Gotte potential was concluded to yield the most realistic diffusivity curve.

An atomistic analysis of the interface mobility in a massive transformation

International Nuclear Information System (INIS)

Bos, C.; Sommer, F.; Mittemeijer, E.J.

2005-01-01

A new multi-lattice kinetic Monte Carlo method has been used for an atomistic study on the interpretation of the interface mobility parameter for a massive face-centred cubic (fcc) to body-centred cubic (bcc) transformation in a single element system. For lateral growth of bcc in a system with an fcc(111)//bcc(110) and fcc[112-bar ]//bcc[001-bar ] interface orientation the overall activation energy for the interface mobility parameter is governed by energetically unfavourable atomic jumps. The atoms on the fcc lattice often cannot jump directly to bcc lattice sites because neighbouring atoms block the empty bcc sites. By single unfavourable jumps and by groups of unfavourable jumps a path from fcc to bcc is created. The necessity of these unfavourable jumps leads to an overall activation energy considerably larger than the activation energy barrier for a single atomic jump

Kinetic Monte Carlo simulation of intermixing during semiconductor heteroepitaxy

Science.gov (United States)

Rouhani, M. Djafari; Kassem, H.; Dalla Torre, J.; Landa, G.; Estève, D.

2002-03-01

We have used the kinetic Monte Carlo technique to investigate the intermixing mechanisms during the heteroepitaxial growth of semiconductors. We have shown that the temperature increases the intermixing between the substrate and deposited film, while an increasing growth rate inhibits this intermixing. We have also observed that intermixing is reduced when the energetics becomes unfavorable, i.e. with high lattice mismatches or hard-deposited materials.

Atomistic simulations in Si processing: Bridging the gap between atoms and experiments

International Nuclear Information System (INIS)

Marques, Luis A.; Pelaz, Lourdes; Lopez, Pedro; Aboy, Maria; Santos, Ivan; Barbolla, Juan

2005-01-01

With devices shrinking to nanometric scale, process simulation tools have to shift from continuum models to an atomistic description of the material. However, the limited sizes and time scales accessible for detailed atomistic techniques usually lead to the difficult task of relating the information obtained from simulations to experimental data. The solution consists of the use of a hierarchical simulation scheme: more fundamental techniques are employed to extract parameters and models that are then feed into less detailed simulators which allow direct comparison with experiments. This scheme will be illustrated with the modeling of the amorphization and recrystallization of Si, which has been defined as a key challenge in the last edition of the International Technology Roadmap for Semiconductors. The model is based on the bond defect or IV pair, which is used as the building block of the amorphous phase. The properties of this defect have been studied using ab initio methods and classical molecular dynamics techniques. It is shown that the recombination of this defect depends on the surrounding bond defects, which accounts for the cooperative nature of the amorphization and recrystallization processes. The implementation of this model in a kinetic Monte Carlo code allows extracting data directly comparable with experiments. This approach provides physical insight on the amorphization and recrystallization mechanisms and a tool for the optimization of solid-phase epitaxial-related processes

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

Science.gov (United States)

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

2017-01-01

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

How Monte Carlo heuristics aid to identify the physical processes of drug release kinetics.

Science.gov (United States)

Lecca, Paola

2018-01-01

We implement a Monte Carlo heuristic algorithm to model drug release from a solid dosage form. We show that with Monte Carlo simulations it is possible to identify and explain the causes of the unsatisfactory predictive power of current drug release models. It is well known that the power-law, the exponential models, as well as those derived from or inspired by them accurately reproduce only the first 60% of the release curve of a drug from a dosage form. In this study, by using Monte Carlo simulation approaches, we show that these models fit quite accurately almost the entire release profile when the release kinetics is not governed by the coexistence of different physico-chemical mechanisms. We show that the accuracy of the traditional models are comparable with those of Monte Carlo heuristics when these heuristics approximate and oversimply the phenomenology of drug release. This observation suggests to develop and use novel Monte Carlo simulation heuristics able to describe the complexity of the release kinetics, and consequently to generate data more similar to those observed in real experiments. Implementing Monte Carlo simulation heuristics of the drug release phenomenology may be much straightforward and efficient than hypothesizing and implementing from scratch complex mathematical models of the physical processes involved in drug release. Identifying and understanding through simulation heuristics what processes of this phenomenology reproduce the observed data and then formalize them in mathematics may allow avoiding time-consuming, trial-error based regression procedures. Three bullet points, highlighting the customization of the procedure. •An efficient heuristics based on Monte Carlo methods for simulating drug release from solid dosage form encodes is presented. It specifies the model of the physical process in a simple but accurate way in the formula of the Monte Carlo Micro Step (MCS) time interval.•Given the experimentally observed curve of

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.

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

International Nuclear Information System (INIS)

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.

2015-01-01

Implantation of 10 keV helium in 316L steel thin foils was performed in JANNuS-Orsay facility and modeled using a multiscale approach. Density Functional Theory (DFT) atomistic calculations [1] were used to obtain the properties of He and He-vacancy clusters, and the Binary Collision Approximation based code MARLOWE was applied to determine the damage and He-ion depth profiles as in [2,3]. The processes involved in the homogeneous He bubble nucleation and growth were defined and implemented in the Object Kinetic Monte Carlo code LAKIMOCA [4]. In particular as the He to dpa ratio was high, self-trapping of He clusters and the trap mutation of He-vacancy clusters had to be taken into account. With this multiscale approach, the formation of bubbles was modeled up to nanometer-scale size, where bubbles can be observed by Transmission Electron Microscopy. Their densities and sizes were studied as functions of fluence (up to 5 × 10 19 He/m 2 ) at two temperatures (473 and 723 K) and for different sample thicknesses (25–250 nm). It appears that the damage is not only due to the collision cascades but is also strongly controlled by the He accumulation in pressurized bubbles. Comparison with experimental data is discussed and sensible agreement is achieved

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...... to cross over from n = 1/4 at T approximately 0 to n = 1/2 with temperature for models with pinnings of types (a) and (b). For topological pinnings at T approximately 0, n is consistent with n = 1/8, a value conceivable for several levels of hierarchically interrelated domain-wall movement. When...

Kinetic Monte Carlo Study of Li Intercalation in LiFePO4.

Science.gov (United States)

Xiao, Penghao; Henkelman, Graeme

2018-01-23

Even as a commercial cathode material, LiFePO 4 remains of tremendous research interest for understanding Li intercalation dynamics. The partially lithiated material spontaneously separates into Li-poor and Li-rich phases at equilibrium. Phase segregation is a surprising property of LiFePO 4 given its high measured rate capability. Previous theoretical studies, aiming to describe Li intercalation in LiFePO 4 , include both atomic-scale density functional theory (DFT) calculations of static Li distributions and entire-particle-scale phase field models, based upon empirical parameters, studying the dynamics of the phase separation. Little effort has been made to bridge the gap between these two scales. In this work, DFT calculations are used to fit a cluster expansion for the basis of kinetic Monte Carlo calculations, which enables long time scale simulations with accurate atomic interactions. This atomistic model shows how the phases evolve in Li x FePO 4 without parameters from experiments. Our simulations reveal that an ordered Li 0.5 FePO4 phase with alternating Li-rich and Li-poor planes along the ac direction forms between the LiFePO 4 and FePO 4 phases, which is consistent with recent X-ray diffraction experiments showing peaks associated with an intermediate-Li phase. The calculations also help to explain a recent puzzling experiment showing that LiFePO 4 particles with high aspect ratios that are narrower along the [100] direction, perpendicular to the [010] Li diffusion channels, actually have better rate capabilities. Our calculations show that lateral surfaces parallel to the Li diffusion channels, as well as other preexisting sites that bind Li weakly, are important for phase nucleation and rapid cycling performance.

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

Energy Technology Data Exchange (ETDEWEB)

De Backer, A., E-mail: andree.debacker@ccfe.ac.uk [UMET, UMR 8207, Université Lille 1, Villeneuve d’Ascq (France); CCFE, Culham Centre for Fusion Energy, Abingdon, Oxon (United Kingdom); Adjanor, G.; Domain, C.; Lescoat, M.L. [EDF R& D, MMC Centre des Renardières, Moret-sur-Loing (France); Jublot-Leclerc, S.; Fortuna, F.; Gentils, A. [CSNSM, Univ Paris-Sud, CNRS/IN2P3, Orsay (France); Ortiz, C.J. [CIEMAT, Laboratorio Nacional de Fusión por Confinamiento Magnético, Madrid (Spain); Souidi, A. [Université Dr. Tahar Moulay de Saida, Saida (Algeria); Becquart, C.S. [UMET, UMR 8207, Université Lille 1, Villeneuve d’Ascq (France)

2015-06-01

Implantation of 10 keV helium in 316L steel thin foils was performed in JANNuS-Orsay facility and modeled using a multiscale approach. Density Functional Theory (DFT) atomistic calculations [1] were used to obtain the properties of He and He-vacancy clusters, and the Binary Collision Approximation based code MARLOWE was applied to determine the damage and He-ion depth profiles as in [2,3]. The processes involved in the homogeneous He bubble nucleation and growth were defined and implemented in the Object Kinetic Monte Carlo code LAKIMOCA [4]. In particular as the He to dpa ratio was high, self-trapping of He clusters and the trap mutation of He-vacancy clusters had to be taken into account. With this multiscale approach, the formation of bubbles was modeled up to nanometer-scale size, where bubbles can be observed by Transmission Electron Microscopy. Their densities and sizes were studied as functions of fluence (up to 5 × 10{sup 19} He/m{sup 2}) at two temperatures (473 and 723 K) and for different sample thicknesses (25–250 nm). It appears that the damage is not only due to the collision cascades but is also strongly controlled by the He accumulation in pressurized bubbles. Comparison with experimental data is discussed and sensible agreement is achieved.

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.

Estimation of Adjoint-Weighted Kinetics Parameters in Monte Carlo Wieland Calculations

International Nuclear Information System (INIS)

Choi, Sung Hoon; Shim, Hyung Jin

2013-01-01

The effective delayed neutron fraction, β eff , and the prompt neutron generation time, Λ, in the point kinetics equation are weighted by the adjoint flux to improve the accuracy of the reactivity estimate. Recently the Monte Carlo (MC) kinetics parameter estimation methods by using the self-consistent adjoint flux calculated in the MC forward simulations have been developed and successfully applied for the research reactor analyses. However these adjoint estimation methods based on the cycle-by-cycle genealogical table require a huge memory size to store the pedigree hierarchy. In this paper, we present a new adjoint estimation in which the pedigree of a single history is utilized by applying the MC Wielandt method. The effectiveness of the new method is demonstrated in the kinetics parameter estimations for infinite homogeneous two-group problems and the Godiva critical facility

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

International Nuclear Information System (INIS)

Cheng, Feng; He, Xiang; Chen, Zhao-Xu; Huang, Yu-Gai

2015-01-01

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

Kinetic Monte Carlo simulation of 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.

Kinetic Monte Carlo study of sensitiviy of OLED efficiency and lifetime to materials parameters

NARCIS (Netherlands)

Coehoorn, R.; Eersel, van H.; Bobbert, P.A.; Janssen, R.A.J.

2015-01-01

The performance of organic light-emitting diodes (OLEDs) is determined by a complex interplay of the optoelectronic processes in the active layer stack. In order to enable simulation-assisted layer stack development, a three-dimensional kinetic Monte Carlo OLED simulation method which includes the

Atomistic modelling of diffusional phase transformations with elastic strain

International Nuclear Information System (INIS)

Mason, D R; Rudd, R E; Sutton, A P

2004-01-01

Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Atomic interactions are modelled by Finnis-Sinclair potentials constructed for these simulations. Vacancy diffusion is modelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of k B T. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r 3 , it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice

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

International Nuclear Information System (INIS)

Al-Subeihi, Ala' A.A.; Alhusainy, Wasma; Kiwamoto, Reiko; Spenkelink, Bert; Bladeren, Peter J. van; Rietjens, Ivonne M.C.M.; Punt, Ans

2015-01-01

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

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

Passing waves from atomistic to continuum

Science.gov (United States)

Chen, Xiang; Diaz, Adrian; Xiong, Liming; McDowell, David L.; Chen, Youping

2018-02-01

Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

Dislocation climb models from atomistic scheme to dislocation dynamics

OpenAIRE

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

2016-01-01

We develop a mesoscopic dislocation dynamics model for vacancy-assisted dislocation climb by upscalings from a stochastic model on the atomistic scale. Our models incorporate microscopic mechanisms of (i) bulk diffusion of vacancies, (ii) vacancy exchange dynamics between bulk and dislocation core, (iii) vacancy pipe diffusion along the dislocation core, and (iv) vacancy attachment-detachment kinetics at jogs leading to the motion of jogs. Our mesoscopic model consists of the vacancy bulk dif...

A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition

International Nuclear Information System (INIS)

Zheng Zheming; Stephens, Ryan M.; Braatz, Richard D.; Alkire, Richard C.; Petzold, Linda R.

2008-01-01

A hybrid multiscale kinetic Monte Carlo (HMKMC) method for speeding up the simulation of copper electrodeposition is presented. The fast diffusion events are simulated deterministically with a heterogeneous diffusion model which considers site-blocking effects of additives. Chemical reactions are simulated by an accelerated (tau-leaping) method for discrete stochastic simulation which adaptively selects exact discrete stochastic simulation for the appropriate reaction whenever that is necessary. The HMKMC method is seen to be accurate and highly efficient

Optimization of the Kinetic Activation-Relaxation Technique, an off-lattice and self-learning kinetic Monte-Carlo method

International Nuclear Information System (INIS)

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

2012-01-01

We present two major optimizations for the kinetic Activation-Relaxation Technique (k-ART), an off-lattice self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search THAT has been successfully applied to study a number of semiconducting and metallic systems. K-ART is parallelized in a non-trivial way: A master process uses several worker processes to perform independent event searches for possible events, while all bookkeeping and the actual simulation is performed by the master process. Depending on the complexity of the system studied, the parallelization scales well for tens to more than one hundred processes. For dealing with large systems, we present a near order 1 implementation. Techniques such as Verlet lists, cell decomposition and partial force calculations are implemented, and the CPU time per time step scales sublinearly with the number of particles, providing an efficient use of computational resources.

G4-STORK: A Geant4-based Monte Carlo reactor kinetics simulation code

International Nuclear Information System (INIS)

Russell, Liam; Buijs, Adriaan; Jonkmans, Guy

2014-01-01

Highlights: • G4-STORK is a new, time-dependent, Monte Carlo code for reactor physics applications. • G4-STORK was built by adapting and expanding on the Geant4 Monte Carlo toolkit. • G4-STORK was designed to simulate short-term fluctuations in reactor cores. • G4-STORK is well suited for simulating sub- and supercritical assemblies. • G4-STORK was verified through comparisons with DRAGON and MCNP. - Abstract: In this paper we introduce G4-STORK (Geant4 STOchastic Reactor Kinetics), a new, time-dependent, Monte Carlo particle tracking code for reactor physics applications. G4-STORK was built by adapting and expanding on the Geant4 Monte Carlo toolkit. The toolkit provides the fundamental physics models and particle tracking algorithms that track each particle in space and time. It is a framework for further development (e.g. for projects such as G4-STORK). G4-STORK derives reactor physics parameters (e.g. k eff ) from the continuous evolution of a population of neutrons in space and time in the given simulation geometry. In this paper we detail the major additions to the Geant4 toolkit that were necessary to create G4-STORK. These include a renormalization process that maintains a manageable number of neutrons in the simulation even in very sub- or supercritical systems, scoring processes (e.g. recording fission locations, total neutrons produced and lost, etc.) that allow G4-STORK to calculate the reactor physics parameters, and dynamic simulation geometries that can change over the course of simulation to illicit reactor kinetics responses (e.g. fuel temperature reactivity feedback). The additions are verified through simple simulations and code-to-code comparisons with established reactor physics codes such as DRAGON and MCNP. Additionally, G4-STORK was developed to run a single simulation in parallel over many processors using MPI (Message Passing Interface) pipes

Kinetics of niobium carbide precipitation in ferrite

International Nuclear Information System (INIS)

Gendt, D.

2001-01-01

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

Microcanonical Monte Carlo approach for computing melting curves by atomistic simulations

OpenAIRE

Davis, Sergio; Gutiérrez, Gonzalo

2017-01-01

We report microcanonical Monte Carlo simulations of melting and superheating of a generic, Lennard-Jones system starting from the crystalline phase. The isochoric curve, the melting temperature $T_m$ and the critical superheating temperature $T_{LS}$ obtained are in close agreement (well within the microcanonical temperature fluctuations) with standard molecular dynamics one-phase and two-phase methods. These results validate the use of microcanonical Monte Carlo to compute melting points, a ...

Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Arampatzis, Georgios; Katsoulakis, Markos A.

2014-01-01

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

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

Science.gov (United States)

Arampatzis, Georgios; Katsoulakis, Markos A

2014-03-28

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

Thin film growth behaviors on strained fcc(111) surface by kinetic Monte Carlo

International Nuclear Information System (INIS)

Doi, Y; Matsunaka, D; Shibutani, Y

2009-01-01

We study Ag islands grown on strained Ag(111) surfaces using kinetic Monte Carlo (KMC) simulations. We employed KMC parameters of activation energy and attempt frequency estimated by nudged elastic band (NEB) method and vibration analyses. We investigate influences of surface strain and substrate temperature on film growth. As the biaxial surface strain increases, the island density increases. As temperature increases, the shape of the island changes from dendric to hexagonal and the island density increases.

Conformational Diffusion and Helix Formation Kinetics

International Nuclear Information System (INIS)

Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

2000-01-01

The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

Conformational Diffusion and Helix Formation Kinetics

Energy Technology Data Exchange (ETDEWEB)

Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

2000-09-18

The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

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

Science.gov (United States)

Moradmand Jalali, Hamed; Bashiri, Hadis; Rasa, Hossein

2015-05-01

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. Copyright © 2015 Elsevier B.V. All rights reserved.

Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling

International Nuclear Information System (INIS)

Schaefer, C.; Jansen, A. P. J.

2013-01-01

We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.

Synchronous parallel kinetic Monte Carlo for continuum diffusion-reaction systems

International Nuclear Information System (INIS)

Martinez, E.; Marian, J.; Kalos, M.H.; Perlado, J.M.

2008-01-01

A novel parallel kinetic Monte Carlo (kMC) algorithm formulated on the basis of perfect time synchronicity is presented. The algorithm is intended as a generalization of the standard n-fold kMC method, and is trivially implemented in parallel architectures. In its present form, the algorithm is not rigorous in the sense that boundary conflicts are ignored. We demonstrate, however, that, in their absence, or if they were correctly accounted for, our algorithm solves the same master equation as the serial method. We test the validity and parallel performance of the method by solving several pure diffusion problems (i.e. with no particle interactions) with known analytical solution. We also study diffusion-reaction systems with known asymptotic behavior and find that, for large systems with interaction radii smaller than the typical diffusion length, boundary conflicts are negligible and do not affect the global kinetic evolution, which is seen to agree with the expected analytical behavior. Our method is a controlled approximation in the sense that the error incurred by ignoring boundary conflicts can be quantified intrinsically, during the course of a simulation, and decreased arbitrarily (controlled) by modifying a few problem-dependent simulation parameters

Kinetic Monte Carlo simulation of formation of microstructures in liquid droplets

International Nuclear Information System (INIS)

Block, M; Kunert, R; Schoell, E; Boeck, T; Teubner, Th

2004-01-01

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

Kinetic Monte Carlo modeling of the efficiency roll-off in a multilayer white organic light-emitting device

NARCIS (Netherlands)

Mesta, M.; van Eersel, H.; Coehoorn, R.; Bobbert, P.A.

2016-01-01

Triplet-triplet annihilation (TTA) and triplet-polaron quenching (TPQ) in organic light-emitting devices (OLEDs) lead to a roll-off of the internal quantum efficiency (IQE) with increasing current density J. We employ a kinetic Monte Carlo modeling study to analyze the measured IQE and color balance

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

International Nuclear Information System (INIS)

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/

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

Science.gov (United States)

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

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

International Nuclear Information System (INIS)

Montoya, M.; Rojas, J.; Saettone, E.

2007-01-01

The mass and kinetic energy distribution of nuclear fragments from the thermal neutron-induced fission of 235 U have been studied using a Monte Carlo simulation. Besides reproducing the pronounced broadening on the standard deviation of the final fragment kinetic energy distribution (σ 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 a 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. (Author)

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.

Effect of Polarization on the Mobility of C60: A Kinetic Monte Carlo Study.

Science.gov (United States)

Volpi, Riccardo; Kottravel, Sathish; Nørby, Morten Steen; Stafström, Sven; Linares, Mathieu

2016-02-09

We present a study of mobility field and temperature dependence for C60 with Kinetic Monte Carlo simulations. We propose a new scheme to take into account polarization effects in organic materials through atomic induced dipoles on nearby molecules. This leads to an energy correction for the single site energies and to an external reorganization happening after each hopping. The inclusion of polarization allows us to obtain a good agreement with experiments for both mobility field and temperature dependence.

Effects of substrate anisotropy and edge diffusion on submonolayer growth during molecular beam epitaxy: A Kinetic Monte Carlo study

International Nuclear Information System (INIS)

Devkota, J.; Shrestha, S.P.

2007-12-01

We have performed Kinetic Monte Carlo simulation work to study the effect of diffusion anisotropy, bonding anisotropy and edge diffusion on island formation at different temperatures during the sub-monolayer film growth in Molecular Beam Epitaxy. We use simple cubic solid on solid model and event based Bortz, Kalos and Labowitch (BKL) algorithm on the Kinetic Monte Carlo method to simulate the physical phenomena. We have found that the island morphology and growth exponent are found to be influenced by substrate anisotropy as well as edge diffusion, however they do not play a significant role in island elongation. The growth exponent and island size distribution are observed to be influenced by substrate anisotropy but are negligibly influenced by edge diffusion. We have found fractal islands when edge diffusion is excluded and compact islands when edge diffusion is included. (author)

Mobility field and mobility temperature dependence in PC61BM: A kinetic Monte-Carlo study

Science.gov (United States)

Sousa, Leonardo; Volpi, Riccardo; da Silva Filho, Demétrio Antônio; Linares, Mathieu

2017-12-01

A study of electron mobility in a PCBM system is performed by means of analytical considerations and Kinetic Monte Carlo simulations. Orbital energies are calculated at the ZINDO level of theory and successively corrected considering contributions from permanent charges and polarization interactions. The relative importance of these environmental effects is analyzed in details, furthermore the predicted mobilities are compared with experimental results and similar simulations performed in C60.

Kinetic Monte Carlo simulation of the efficiency roll-off, emission color, and degradation of organic light-emitting diodes

NARCIS (Netherlands)

Coehoorn, R.; van Eersel, H.; Bobbert, P.A.; Janssen, R.A.J.

2015-01-01

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

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

Science.gov (United States)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Crystal plasticity model for BCC iron atomistically informed by kinetics of correlated kinkpair nucleation on screw dislocation

Science.gov (United States)

Narayanan, Sankar; McDowell, David L.; Zhu, Ting

2014-04-01

The mobility of dislocation in body-centered cubic (BCC) metals is controlled by the thermally activated nucleation of kinks along the dislocation core. By employing a recent interatomic potential and the Nudged Elastic Band method, we predict the atomistic saddle-point state of 1/2 screw dislocation motion in BCC iron that involves the nucleation of correlated kinkpairs and the resulting double superkinks. This unique process leads to a single-humped minimum energy path that governs the one-step activation of a screw dislocation to move into the adjacent {110} Peierls valley, which contrasts with the double-humped energy path and the two-step transition predicted by other interatomic potentials. Based on transition state theory, we use the atomistically computed, stress-dependent kinkpair activation parameters to inform a coarse-grained crystal plasticity flow rule. Our atomistically-informed crystal plasticity model quantitatively predicts the orientation dependent stress-strain behavior of BCC iron single crystals in a manner that is consistent with experimental results. The predicted temperature and strain-rate dependencies of the yield stress agree with experimental results in the 200-350 K temperature regime, and are rationalized by the small activation volumes associated with the kinkpair-mediated motion of screw dislocations.

Monte Carlo simulation for fragment mass and kinetic energy distributions from the neutron-induced fission of {sup 235}U

Energy Technology Data Exchange (ETDEWEB)

Montoya, M.; Rojas, J. [Instituto Peruano de Energia Nuclear, Av. Canada 1470, Lima 41 (Peru); Saettone, E. [Facultad de Ciencias, Universidad Nacional de lngenieria, Av. Tupac Amaru 210, Apartado 31-139, Lima (Peru)

2007-07-01

The mass and kinetic energy distribution of nuclear fragments from the thermal neutron-induced fission of {sup 235}U 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}{sub 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 a 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. (Author)

Generative Models of Conformational Dynamics

OpenAIRE

Langmead, Christopher James

2014-01-01

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term ‘generative’ refers to a...

Kinetic Monte Carlo simulations of water ice porosity: extrapolations of deposition parameters from the laboratory to interstellar space

Science.gov (United States)

Clements, Aspen R.; Berk, Brandon; Cooke, Ilsa R.; Garrod, Robin T.

2018-02-01

Using an off-lattice kinetic Monte Carlo model we reproduce experimental laboratory trends in the density of amorphous solid water (ASW) for varied deposition angle, rate and surface temperature. Extrapolation of the model to conditions appropriate to protoplanetary disks and interstellar dark clouds indicate that these ices may be less porous than laboratory ices.

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)

Moradmand Jalali, Hamed; Bashiri, Hadis; Rasa, Hossein

2015-01-01

In the present study, the mechanism of free radical production by light-reflective agents in sunscreens (TiO 2 , ZnO and ZrO 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 2 (rutile and anatase), ZnO and ZrO 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

Atomistic approach to predict the glass-forming ability in Zr–Cu–Al ternary metallic glasses

Energy Technology Data Exchange (ETDEWEB)

Yu, C.Y. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, X.J. [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Zheng, G.P. [Department of Mechanical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong (China); Niu, X.R. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, C.T., E-mail: chainliu@cityu.edu.hk [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China)

2015-04-05

Highlights: • An atomistic approach has been developed to predict the glass forming ability (GFA) in Zr–Cu–Al ternary alloy system. • Both of the thermodynamic and structure-dependent kinetic effects to glass formation have been taken into account. • The first-principles calculation and molecular dynamics simulation have been performed. • The approach predicts the best glass former in the model Zr–Cu–Al alloy system. • The predicted GFA is consistent with various experimental results. - Abstract: Prediction of composition-dependent glass-forming ability (GFA) remains to be a key scientific challenge in the metallic-glass community, especially in multi-component alloy systems. In the present study, we apply an atomistic approach to predict the trend of GFA effectively in the Zr–Cu–Al ternary alloy system from alloy compositions alone. This approach is derived from the first-principles calculations based on the density-functional theory and molecular dynamic (MD) simulations. By considering of both the thermodynamic and atomic-structure induced kinetic effects, the predicted GFA trend from this approach shows an excellent agreement with experimental data available in this alloy system, manifesting its capability of seeking metallic glasses with superior GFA in ternary alloy systems.

Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Chatterjee, Abhijit; Vlachos, Dionisios G.

2006-01-01

The computational intensity of kinetic Monte Carlo (KMC) simulation is a major impediment in simulating large length and time scales. In recent work, an approximate method for KMC simulation of spatially uniform systems, termed the binomial τ-leap method, was introduced [A. Chatterjee, D.G. Vlachos, M.A. Katsoulakis, Binomial distribution based τ-leap accelerated stochastic simulation, J. Chem. Phys. 122 (2005) 024112], where molecular bundles instead of individual processes are executed over coarse-grained time increments. This temporal coarse-graining can lead to significant computational savings but its generalization to spatially lattice KMC simulation has not been realized yet. Here we extend the binomial τ-leap method to lattice KMC simulations by combining it with spatially adaptive coarse-graining. Absolute stability and computational speed-up analyses for spatial systems along with simulations provide insights into the conditions where accuracy and substantial acceleration of the new spatio-temporal coarse-graining method are ensured. Model systems demonstrate that the r-time increment criterion of Chatterjee et al. obeys the absolute stability limit for values of r up to near 1

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.

Extended pattern recognition scheme for self-learning kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Shah, Syed Islamuddin; Nandipati, Giridhar; Kara, Abdelkader; Rahman, Talat S

2012-01-01

We report the development of a pattern recognition scheme that takes into account both fcc and hcp adsorption sites in performing self-learning kinetic Monte Carlo (SLKMC-II) simulations on the fcc(111) surface. In this scheme, the local environment of every under-coordinated atom in an island is uniquely identified by grouping fcc sites, hcp sites and top-layer substrate atoms around it into hexagonal rings. As the simulation progresses, all possible processes, including those such as shearing, reptation and concerted gliding, which may involve fcc-fcc, hcp-hcp and fcc-hcp moves are automatically found, and their energetics calculated on the fly. In this article we present the results of applying this new pattern recognition scheme to the self-diffusion of 9-atom islands (M 9 ) on M(111), where M = Cu, Ag or Ni.

Kinetic Monte Carlo simulation of growth of Ge quantum dot multilayers with amorphous matrix

Energy Technology Data Exchange (ETDEWEB)

Endres, Jan, E-mail: endres.jan@gmail.com; Holý, Václav; Daniš, Stanislav [Charles University, Faculty of Mathematics and Physics (Czech Republic); Buljan, Maja [Ruđer Bošković Institute (Croatia)

2017-04-15

Kinetic Monte Carlo method is used to simulate the growth of germanium quantum dot multilayers with amorphous matrix. We modified a model for self-assembled growth of quantum dots in crystalline matrix for the case of the amorphous one. The surface morphology given as hills above the buried dots is the main driving force for the ordering of the quantum dots. In the simulations, we observed a short-range self-ordering in the lateral direction. The ordering in lateral and vertical direction depends strongly on the surface morphology, mostly on the strength how the deposited material replicates previous surfaces.

OBJECT KINETIC MONTE CARLO SIMULATIONS OF RADIATION DAMAGE IN TUNGSTEN SUBJECTED TO NEUTRON FLUX WITH PKA SPECTRUM CORRESPONDING TO THE HFIR

Energy Technology Data Exchange (ETDEWEB)

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

2015-12-31

The objective of this work is to study the damage accumulation in pure tungsten (W) subjected to neutron bombardment with a primary knock-on atom (PKA) spectrum corresponding to the High Flux Isotope Reactor (HFIR), using the object kinetic Monte Carlo (OKMC) method.

A kinetic theory for nonanalog Monte Carlo algorithms: Exponential transform with angular biasing

International Nuclear Information System (INIS)

Ueki, T.; Larsen, E.W.

1998-01-01

A new Boltzmann Monte Carlo (BMC) equation is proposed to describe the transport of Monte Carlo particles governed by a set of nonanalog rules for the transition of space, velocity, and weight. The BMC equation is a kinetic equation that includes weight as an extra independent variable. The solution of the BMC equation is the pointwise distribution of velocity and weight throughout the physical system. The BMC equation is derived for the simulation of a transmitted current, utilizing the exponential transform with angular biasing. The weight moments of the solution of the BMC equation are used to predict the score moments of the transmission current. (Also, it is shown that an adjoint BMC equation can be used for this purpose.) Integrating the solution of the forward BMC equation over space, velocity, and weight, the mean number of flights per history is obtained. This is used to determine theoretically the figure of merit for any choice of biasing parameters. Also, a maximum safe value of the exponential transform parameter is proposed, which ensure the finite variance of variance estimate (sample variance) for any penetration distance. Finally, numerical results that validate the new theory are provided

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.

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

International Nuclear Information System (INIS)

Gelß, Patrick; Matera, Sebastian; Schütte, Christof

2016-01-01

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

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.

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

Science.gov (United States)

Gelß, Patrick; Matera, Sebastian; Schütte, Christof

2016-06-01

In multiscale modeling of heterogeneous catalytic processes, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. Usually, this is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO2(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased stiffness.

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-06-01

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

Development of a Combined In Vitro Physiologically Based Kinetic (PBK) and Monte Carlo Modelling Approach to Predict Interindividual Human Variation in Phenol-Induced Developmental Toxicity.

Science.gov (United States)

Strikwold, Marije; Spenkelink, Bert; Woutersen, Ruud A; Rietjens, Ivonne M C M; Punt, Ans

2017-06-01

With our recently developed in vitro physiologically based kinetic (PBK) modelling approach, we could extrapolate in vitro toxicity data to human toxicity values applying PBK-based reverse dosimetry. Ideally information on kinetic differences among human individuals within a population should be considered. In the present study, we demonstrated a modelling approach that integrated in vitro toxicity data, PBK modelling and Monte Carlo simulations to obtain insight in interindividual human kinetic variation and derive chemical specific adjustment factors (CSAFs) for phenol-induced developmental toxicity. The present study revealed that UGT1A6 is the primary enzyme responsible for the glucuronidation of phenol in humans followed by UGT1A9. Monte Carlo simulations were performed taking into account interindividual variation in glucuronidation by these specific UGTs and in the oral absorption coefficient. Linking Monte Carlo simulations with PBK modelling, population variability in the maximum plasma concentration of phenol for the human population could be predicted. This approach provided a CSAF for interindividual variation of 2.0 which covers the 99th percentile of the population, which is lower than the default safety factor of 3.16 for interindividual human kinetic differences. Dividing the dose-response curve data obtained with in vitro PBK-based reverse dosimetry, with the CSAF provided a dose-response curve that reflects the consequences of the interindividual variability in phenol kinetics for the developmental toxicity of phenol. The strength of the presented approach is that it provides insight in the effect of interindividual variation in kinetics for phenol-induced developmental toxicity, based on only in vitro and in silico testing. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Structure of Cu64.5Zr35.5 metallic glass by reverse Monte Carlo simulations

International Nuclear Information System (INIS)

Fang, X. W.; Huang, Li; Wang, C. Z.; Ho, K. M.; Ding, Z. J.

2014-01-01

Reverse Monte Carlo simulations (RMC) have been widely used to generate three dimensional (3D) atomistic models for glass systems. To examine the reliability of the method for metallic glass, we use RMC to predict the atomic configurations of a “known” structure from molecular dynamics (MD) simulations, and then compare the structure obtained from the RMC with the target structure from MD. We show that when the structure factors and partial pair correlation functions from the MD simulations are used as inputs for RMC simulations, the 3D atomistic structure of the glass obtained from the RMC gives the short- and medium-range order in good agreement with those from the target structure by the MD simulation. These results suggest that 3D atomistic structure model of the metallic glass alloys can be reasonably well reproduced by RMC method with a proper choice of input constraints

Multi-scale modelling of ions in solution: from atomistic descriptions to chemical engineering

International Nuclear Information System (INIS)

Molina, J.J.

2011-01-01

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)

Kinetic Monte Carlo modeling of chemical reactions coupled with heat transfer.

Science.gov (United States)

Castonguay, Thomas C; Wang, Feng

2008-03-28

In this paper, we describe two types of effective events for describing heat transfer in a kinetic Monte Carlo (KMC) simulation that may involve stochastic chemical reactions. Simulations employing these events are referred to as KMC-TBT and KMC-PHE. In KMC-TBT, heat transfer is modeled as the stochastic transfer of "thermal bits" between adjacent grid points. In KMC-PHE, heat transfer is modeled by integrating the Poisson heat equation for a short time. Either approach is capable of capturing the time dependent system behavior exactly. Both KMC-PHE and KMC-TBT are validated by simulating pure heat transfer in a rod and a square and modeling a heated desorption problem where exact numerical results are available. KMC-PHE is much faster than KMC-TBT and is used to study the endothermic desorption of a lattice gas. Interesting findings from this study are reported.

Permutation invariant potential energy surfaces for polyatomic reactions using atomistic neural networks

International Nuclear Information System (INIS)

Kolb, Brian; Zhao, Bin; Guo, Hua; Li, Jun; Jiang, Bin

2016-01-01

The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H 2 → H 2 + H, H + H 2 O → H 2 + OH, and H + CH 4 → H 2 + CH 3 . A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggest this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved.

Off-lattice pattern recognition scheme for kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Nandipati, Giridhar; Kara, Abdelkader; Shah, Syed Islamuddin; Rahman, Talat S.

2012-01-01

We report the development of a pattern-recognition scheme for the off-lattice self-learning kinetic Monte Carlo (KMC) method, one that is simple and flexible enough that it can be applied to all types of surfaces. In this scheme, to uniquely identify the local environment and associated processes involving three-dimensional (3D) motion of an atom or atoms, space around a central atom is divided into 3D rectangular boxes. The dimensions and the number of 3D boxes are determined by the accuracy with which a process needs to be identified and a process is described as the central atom moving to a neighboring vacant box accompanied by the motion of any other atom or atoms in its surrounding boxes. As a test of this method to we apply it to examine the decay of 3D Cu islands on the Cu(100) and to the surface diffusion of a Cu monomer and a dimer on Cu(111) and compare the results and computational efficiency to those available in the literature.

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.

The Metropolis Monte Carlo method with CUDA enabled Graphic Processing Units

International Nuclear Information System (INIS)

Hall, Clifford; Ji, Weixiao; Blaisten-Barojas, Estela

2014-01-01

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.

Monte Carlo simulation of kinetic electron emission from metal due to impact of heavy ions

International Nuclear Information System (INIS)

Kawata, J.; Ohya, K.

1999-01-01

A Monte Carlo simulation is performed for study of the dependence of kinetic electron emission on nuclear charge of projectile Z 1 , using the nonlinear response theory with the density-functional (DF) formalism to calculate electron excitation cross section. The kinetic yield, energy distribution, excitation depth distribution and emission statistics of emitted electrons showed clear Z 1 oscillations, however, the Z 1 oscillations of them are different from that of the inelastic stopping power, in particular for high Z 1 , due to large elastic energy loss of the ions and secondary cascade process of primary excited electrons within the solid. For high Z 1 , the linear relationship does not exist between them and the inelastic stopping power, although they are closely related to it. The emission of high-energy primary electrons excited by the ion within shallow depth without experiencing the secondary cascade process, results in the Z 1 dependence in the energy distribution, excitation depth distribution and emission statistics of emitted electrons

A three-dimensional self-learning kinetic Monte Carlo model: application to Ag(111)

International Nuclear Information System (INIS)

Latz, Andreas; Brendel, Lothar; Wolf, Dietrich E

2012-01-01

The reliability of kinetic Monte Carlo (KMC) simulations depends on accurate transition rates. The self-learning KMC method (Trushin et al 2005 Phys. Rev. B 72 115401) combines the accuracy of rates calculated from a realistic potential with the efficiency of a rate catalog, using a pattern recognition scheme. This work expands the original two-dimensional method to three dimensions. The concomitant huge increase in the number of rate calculations on the fly needed can be avoided by setting up an initial database, containing exact activation energies calculated for processes gathered from a simpler KMC model. To provide two representative examples, the model is applied to the diffusion of Ag monolayer islands on Ag(111), and the homoepitaxial growth of Ag on Ag(111) at low temperatures.

Kinetic Monte Carlo simulations of three-dimensional self-assembled quantum dot islands

International Nuclear Information System (INIS)

Song Xin; Feng Hao; Liu Yu-Min; Yu Zhong-Yuan; Yin Hao-Zhi

2014-01-01

By three-dimensional kinetic Monte Carlo simulations, the effects of the temperature, the flux rate, the total coverage and the interruption time on the distribution and the number of self-assembled InAs/GaAs (001) quantum dot (QD) islands are studied, which shows that a higher temperature, a lower flux rate and a longer growth time correspond to a better island distribution. The relations between the number of islands and the temperature and the flux rate are also successfully simulated. It is observed that for the total coverage lower than 0.5 ML, the number of islands decreases with the temperature increasing and other growth parameters fixed and the number of islands increases with the flux rate increasing when the deposition is lower than 0.6 ML and the other parameters are fixed. (condensed matter: structural, mechanical, and thermal properties)

Atomistic-level non-equilibrium model for chemically reactive systems based on steepest-entropy-ascent quantum thermodynamics

International Nuclear Information System (INIS)

Li, Guanchen; Al-Abbasi, Omar; Von Spakovsky, Michael R

2014-01-01

This paper outlines an atomistic-level framework for modeling the non-equilibrium behavior of chemically reactive systems. The framework called steepest- entropy-ascent quantum thermodynamics (SEA-QT) is based on the paradigm of intrinsic quantum thermodynamic (IQT), which is a theory that unifies quantum mechanics and thermodynamics into a single discipline with wide applications to the study of non-equilibrium phenomena at the atomistic level. SEA-QT is a novel approach for describing the state of chemically reactive systems as well as the kinetic and dynamic features of the reaction process without any assumptions of near-equilibrium states or weak-interactions with a reservoir or bath. Entropy generation is the basis of the dissipation which takes place internal to the system and is, thus, the driving force of the chemical reaction(s). The SEA-QT non-equilibrium model is able to provide detailed information during the reaction process, providing a picture of the changes occurring in key thermodynamic properties (e.g., the instantaneous species concentrations, entropy and entropy generation, reaction coordinate, chemical affinities, reaction rate, etc). As an illustration, the SEA-QT framework is applied to an atomistic-level chemically reactive system governed by the reaction mechanism F + H 2 ↔ FH + H

Permutation invariant potential energy surfaces for polyatomic reactions using atomistic neural networks

Energy Technology Data Exchange (ETDEWEB)

Kolb, Brian [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Zhao, Bin; Guo, Hua, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Li, Jun [School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331 (China); Jiang, Bin [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

2016-06-14

The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H{sub 2} → H{sub 2} + H, H + H{sub 2}O → H{sub 2} + OH, and H + CH{sub 4} → H{sub 2} + CH{sub 3}. A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggest this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved.

The diffusion of a Ga atom on GaAs(001)β2(2 × 4): Local superbasin kinetic Monte Carlo

Science.gov (United States)

Lin, Yangzheng; Fichthorn, Kristen A.

2017-10-01

We use first-principles density-functional theory to characterize the binding sites and diffusion mechanisms for a Ga adatom on the GaAs(001)β 2(2 × 4) surface. Diffusion in this system is a complex process involving eleven unique binding sites and sixteen different hops between neighboring binding sites. Among the binding sites, we can identify four different superbasins such that the motion between binding sites within a superbasin is much faster than hops exiting the superbasin. To describe diffusion, we use a recently developed local superbasin kinetic Monte Carlo (LSKMC) method, which accelerates a conventional kinetic Monte Carlo (KMC) simulation by describing the superbasins as absorbing Markov chains. We find that LSKMC is up to 4300 times faster than KMC for the conditions probed in this study. We characterize the distribution of exit times from the superbasins and find that these are sometimes, but not always, exponential and we characterize the conditions under which the superbasin exit-time distribution should be exponential. We demonstrate that LSKMC simulations assuming an exponential superbasin exit-time distribution yield the same diffusion coefficients as conventional KMC.

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

International Nuclear Information System (INIS)

Neumann, Martin; Zoppi, Marco

2002-01-01

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

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.

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.

Kinetic energy classification and smoothing for compact B-spline basis sets in quantum Monte Carlo

Science.gov (United States)

Krogel, Jaron T.; Reboredo, Fernando A.

2018-01-01

Quantum Monte Carlo calculations of defect properties of transition metal oxides have become feasible in recent years due to increases in computing power. As the system size has grown, availability of on-node memory has become a limiting factor. Saving memory while minimizing computational cost is now a priority. The main growth in memory demand stems from the B-spline representation of the single particle orbitals, especially for heavier elements such as transition metals where semi-core states are present. Despite the associated memory costs, splines are computationally efficient. In this work, we explore alternatives to reduce the memory usage of splined orbitals without significantly affecting numerical fidelity or computational efficiency. We make use of the kinetic energy operator to both classify and smooth the occupied set of orbitals prior to splining. By using a partitioning scheme based on the per-orbital kinetic energy distributions, we show that memory savings of about 50% is possible for select transition metal oxide systems. For production supercells of practical interest, our scheme incurs a performance penalty of less than 5%.

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

Kinetic Monte-Carlo modeling of hydrogen retention and re-emission from Tore Supra deposits

International Nuclear Information System (INIS)

Rai, A.; Schneider, R.; Warrier, M.; Roubin, P.; Martin, C.; Richou, M.

2009-01-01

A multi-scale model has been developed to study the reactive-diffusive transport of hydrogen in porous graphite [A. Rai, R. Schneider, M. Warrier, J. Nucl. Mater. (submitted for publication). http://dx.doi.org/10.1016/j.jnucmat.2007.08.013.]. The deposits found on the leading edge of the neutralizer of Tore Supra are multi-scale in nature, consisting of micropores with typical size lower than 2 nm (∼11%), mesopores (∼5%) and macropores with a typical size more than 50 nm [C. Martin, M. Richou, W. Sakaily, B. Pegourie, C. Brosset, P. Roubin, J. Nucl. Mater. 363-365 (2007) 1251]. Kinetic Monte-Carlo (KMC) has been used to study the hydrogen transport at meso-scales. Recombination rate and the diffusion coefficient calculated at the meso-scale was used as an input to scale up and analyze the hydrogen transport at macro-scale. A combination of KMC and MCD (Monte-Carlo diffusion) method was used at macro-scales. Flux dependence of hydrogen recycling has been studied. The retention and re-emission analysis of the model has been extended to study the chemical erosion process based on the Kueppers-Hopf cycle [M. Wittmann, J. Kueppers, J. Nucl. Mater. 227 (1996) 186].

Kinetic Monte Carlo simulation of nanoparticle film formation via nanocolloid drying

Science.gov (United States)

Kameya, Yuki

2017-06-01

A kinetic Monte Carlo simulation of nanoparticle film formation via nanocolloid drying is presented. The proposed two-dimensional model addresses the dynamics of nanoparticles in the vertical plane of a drying nanocolloid film. The gas-liquid interface movement due to solvent evaporation was controlled by a time-dependent chemical potential, and the resultant particle dynamics including Brownian diffusion and aggregate growth were calculated. Simulations were performed at various Peclet numbers defined based on the rate ratio of solvent evaporation and nanoparticle diffusion. At high Peclet numbers, nanoparticles accumulated at the top layer of the liquid film and eventually formed a skin layer, causing the formation of a particulate film with a densely packed structure. At low Peclet numbers, enhanced particle diffusion led to significant particle aggregation in the bulk colloid, and the resulting film structure became highly porous. The simulated results showed some typical characteristics of a drying nanocolloid that had been reported experimentally. Finally, the potential of the model as well as the remaining challenges are discussed.

Origin of two time-scale regimes in potentiometric titration of metal oxides. A replica kinetic Monte Carlo study

International Nuclear Information System (INIS)

Zarzycki, Piotr P.; Rosso, Kevin M.

2009-01-01

Replica Kinetic Monte Carlo simulations were used to study the characteristic time scales of potentiometric titration of the metal oxides and (oxy)hydroxides. The effect of surface heterogeneity and surface transformation on the titration kinetics were also examined. Two characteristic relaxation times are often observed experimentally, with the trailing slower part attributed to surface non-uniformity, porosity, polymerization, amorphization, and other dynamic surface processes induced by unbalanced surface charge. However, our simulations show that these two characteristic relaxation times are intrinsic to the proton binding reaction for energetically homogeneous surfaces, and therefore surface heterogeneity or transformation do not necessarily need to be invoked. However, all such second-order surface processes are found to intensify the separation and distinction of the two kinetic regimes. The effect of surface energetic-topographic non-uniformity, as well dynamic surface transformation, interface roughening/smoothing were described in a statistical fashion. Furthermore, our simulations show that a shift in the point-of-zero charge is expected from increased titration speed and the pH-dependence of the titration measurement error is in excellent agreement with experimental studies.

Origin of two time-scale regimes in potentiometric titration of metal oxides. A replica kinetic Monte Carlo study.

Science.gov (United States)

Zarzycki, Piotr; Rosso, Kevin M

2009-06-16

Replica kinetic Monte Carlo simulations were used to study the characteristic time scales of potentiometric titration of the metal oxides and (oxy)hydroxides. The effect of surface heterogeneity and surface transformation on the titration kinetics were also examined. Two characteristic relaxation times are often observed experimentally, with the trailing slower part attributed to surface nonuniformity, porosity, polymerization, amorphization, and other dynamic surface processes induced by unbalanced surface charge. However, our simulations show that these two characteristic relaxation times are intrinsic to the proton-binding reaction for energetically homogeneous surfaces, and therefore surface heterogeneity or transformation does not necessarily need to be invoked. However, all such second-order surface processes are found to intensify the separation and distinction of the two kinetic regimes. The effect of surface energetic-topographic nonuniformity, as well dynamic surface transformation, interface roughening/smoothing were described in a statistical fashion. Furthermore, our simulations show that a shift in the point-of-zero charge is expected from increased titration speed, and the pH-dependence of the titration measurement error is in excellent agreement with experimental studies.

Kinetic energy of solid and liquid para-hydrogen: a path integral Monte Carlo simulation

International Nuclear Information System (INIS)

Zoppi, M.; Neumann, M.

1992-01-01

The translational (center of mass) kinetic energy of solid and liquid para-hydrogen have been recently measured by means of Deep Inelastic Neutron Scattering. We have evaluated the same quantity, in similar thermodynamic conditions, by means of Path Integral Monte Carlo computer simulation, modelling the system as composed of a set of spherical molecules interacting through a pairwise additive Lennard-Jones potential. In spite of the crude approximations on the interaction potential, the agreement is excellent. The pressure was also computed by means of the same simulations. This quantity, compared with the equation of state for solid para-hydrogen given by Driessen and Silvera, gives an agreement of a lesser quality and a negative value for the liquid state. We attribute this discrepancy to the limitations of the Lennard-Jones potential. (orig.)

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

Numerical modelling in material physics

International Nuclear Information System (INIS)

Proville, L.

2004-12-01

The author first briefly presents his past research activities: investigation of a dislocation sliding in solid solution by molecular dynamics, modelling of metal film growth by phase field and Monte Carlo kinetics, phase field model for surface self-organisation, phase field model for the Al 3 Zr alloy, calculation of anharmonic photons, mobility of bipolarons in superconductors. Then, he more precisely reports the mesoscopic modelling in phase field, and some atomistic modelling (dislocation sliding, Monte Carlo simulation of metal surface growth, anharmonic network optical spectrum modelling)

Levy-Lieb-Based Monte Carlo Study of the Dimensionality Behaviour of the Electronic Kinetic Functional

Directory of Open Access Journals (Sweden)

Seshaditya A.

2017-06-01

Full Text Available We consider a gas of interacting electrons in the limit of nearly uniform density and treat the one dimensional (1D, two dimensional (2D and three dimensional (3D cases. We focus on the determination of the correlation part of the kinetic functional by employing a Monte Carlo sampling technique of electrons in space based on an analytic derivation via the Levy-Lieb constrained search principle. Of particular interest is the question of the behaviour of the functional as one passes from 1D to 3D; according to the basic principles of Density Functional Theory (DFT the form of the universal functional should be independent of the dimensionality. However, in practice the straightforward use of current approximate functionals in different dimensions is problematic. Here, we show that going from the 3D to the 2D case the functional form is consistent (concave function but in 1D becomes convex; such a drastic difference is peculiar of 1D electron systems as it is for other quantities. Given the interesting behaviour of the functional, this study represents a basic first-principle approach to the problem and suggests further investigations using highly accurate (though expensive many-electron computational techniques, such as Quantum Monte Carlo.

Thermodynamics of grain boundary premelting in alloys. II. Atomistic simulation

International Nuclear Information System (INIS)

Williams, P.L.; Mishin, Y.

2009-01-01

We apply the semi-grand-canonical Monte Carlo method with an embedded-atom potential to study grain boundary (GB) premelting in Cu-rich Cu-Ag alloys. The Σ5 GB chosen for this study becomes increasingly disordered near the solidus line while its local chemical composition approaches the liquidus composition at the same temperature. This behavior indicates the formation of a thin layer of the liquid phase in the GB when the grain composition approaches the solidus. The thickness of the liquid layer remains finite and the GB can be overheated/oversaturated to metastable states slightly above the solidus. The premelting behavior found by the simulations is qualitatively consistent with the phase-field model of the same binary system presented in Part I of this work [Mishin Y, Boettinger WJ, Warren JA, McFadden GB. Acta Mater, in press]. Although this agreement is encouraging, we discuss several problems arising when atomistic simulations are compared with phase-field modeling.

Nano-scale study of phase separation in ferrite of long term thermally aged Mo-bearing duplex stainless steels - Atom probe tomography and Monte Carlo simulation

International Nuclear Information System (INIS)

Pareige, C.; Emo, J.; Pareige, P.; Saillet, S.; Domain, C.

2015-01-01

Duplex stainless steels (DSS), used in primary circuit of Pressurised Water Reactor (PWR), are prone to thermal ageing at service temperature, typically between 286 and 323 C. degrees. This ageing is due to the ferrite decomposition via two kinds of phase transformations: spinodal decomposition into Fe rich α zones and Cr rich α' zones and precipitation of G-phase enriched in Ni, Si, Mn and Mo. It has been shown by atom probe tomography (APT) that the G-phase particles form at the interface between α and α' regions thereby demonstrating that α-α' decomposition and G-phase precipitation are highly dependent. The synergy between the two decomposition processes should be related to both the thermodynamics of the system and the diffusion mechanisms active during ageing. This can be studied by atomistic kinetic Monte Carlo (AKMC) with a model that can reproduce the phase transformations which take place in ferrite of duplex stainless steels. This paper presents the first simulations of the kinetics of spinodal decomposition and G-phase precipitation occurring in ferrite of duplex stainless steels. The kinetics was simulated using a simple but effective atomic kinetic Monte Carlo model in a ternary alloy. The simulations reproduced the α/α' spinodal structure with precipitates at the α/α' interface. The comparison of simulated results with experiments shows that the simulations quantitatively reproduce the kinetics of phase transformation and the synergy observed experimentally between the spinodal decomposition and G-phase precipitation: the time evolution of the wavelength of the spinodal decomposition and the radius of G-phase precipitates were quantitatively reproduced. The simulations endorse the assumption that G-phase precipitation mainly results from the rejection of G-formers from α and α' domains. By following the vacancy pathway during simulation, we show that coarsening of the G-phase precipitates must proceed via

Monte Carlo kinetics simulations of ice-mantle formation on interstellar grains

Science.gov (United States)

Garrod, Robin

2015-08-01

The majority of interstellar dust-grain chemical kinetics models use rate equations, or alternative population-based simulation methods, to trace the time-dependent formation of grain-surface molecules and ice mantles. Such methods are efficient, but are incapable of considering explicitly the morphologies of the dust grains, the structure of the ices formed thereon, or the influence of local surface composition on the chemistry.A new Monte Carlo chemical kinetics model, MIMICK, is presented here, whose prototype results were published recently (Garrod 2013, ApJ, 778, 158). The model calculates the strengths and positions of the potential mimima on the surface, on the fly, according to the individual pair-wise (van der Waals) bonds between surface species, allowing the structure of the ice to build up naturally as surface diffusion and chemistry occur. The prototype model considered contributions to a surface particle's potential only from contiguous (or "bonded") neighbors; the full model considers contributions from surface constituents from short to long range. Simulations are conducted on a fully 3-D user-generated dust-grain with amorphous surface characteristics. The chemical network has also been extended from the simple water system previously published, and now includes 33 chemical species and 55 reactions. This allows the major interstellar ice components to be simulated, such as water, methane, ammonia and methanol, as well as a small selection of more complex molecules, including methyl formate (HCOOCH3).The new model results indicate that the porosity of interstellar ices are dependent on multiple variables, including gas density, the dust temperature, and the relative accretion rates of key gas-phase species. The results presented also have implications for the formation of complex organic molecules on dust-grain surfaces at very low temperatures.

Derivation of kinetic coefficients by atomistic methods for studying defect behavior in Mo

International Nuclear Information System (INIS)

Insepov, Z.; Rest, J.; Yacout, A.M.; Kuksin, A.Yu.; Norman, G.E.; Stegailov, V.V.; Starikov, S.V.; Yanilkin, A.V.

2012-01-01

Highlights: ► A multiscale concept couples molecular dynamics (MD) with ab initio and kinetic rate theory. ► Evolution of a system of self-interstitial atoms and vacancies in Mo is studied by MD. ► Formation of di-SIA clusters and SIA–vacancy recombination is analyzed. ► 1D diffusion of self-interstitials at various temperature and defect concentrations were studied. ► This paper provides a powerful predictive tool for simulating irradiation of nuclear materials. - Abstract: A multiscale concept for irradiated materials simulation is formulated based on coupling molecular dynamics simulations (MD) where the potential was obtained from ab initio data of energies of the basic defect structures, with kinetic mesoscale models. The evolution of a system containing self-interstitial atoms (SIAs) and vacancies in crystalline molybdenum is investigated by means of MD. The kinetics of formation of di-SIA clusters and SIA–vacancy recombination is analyzed via approaches used in the kinetic theory of radiation ageing. The effects of 1D diffusion of SIAs, temperature, and defect concentrations on the reaction rates are also studied. This approach can validate both the kinetic mechanisms and the appropriate kinetic coefficients, offering the potential to significantly reduce the uncertainty of the kinetic methodology and providing a powerful predictive tool for simulating irradiation behavior of nuclear materials.

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.

Steady state likelihood ratio sensitivity analysis for stiff kinetic Monte Carlo simulations.

Science.gov (United States)

Núñez, M; Vlachos, D G

2015-01-28

Kinetic Monte Carlo simulation is an integral tool in the study of complex physical phenomena present in applications ranging from heterogeneous catalysis to biological systems to crystal growth and atmospheric sciences. Sensitivity analysis is useful for identifying important parameters and rate-determining steps, but the finite-difference application of sensitivity analysis is computationally demanding. Techniques based on the likelihood ratio method reduce the computational cost of sensitivity analysis by obtaining all gradient information in a single run. However, we show that disparity in time scales of microscopic events, which is ubiquitous in real systems, introduces drastic statistical noise into derivative estimates for parameters affecting the fast events. In this work, the steady-state likelihood ratio sensitivity analysis is extended to singularly perturbed systems by invoking partial equilibration for fast reactions, that is, by working on the fast and slow manifolds of the chemistry. Derivatives on each time scale are computed independently and combined to the desired sensitivity coefficients to considerably reduce the noise in derivative estimates for stiff systems. The approach is demonstrated in an analytically solvable linear system.

Resistivity recovery simulations of electron-irradiated iron: Kinetic Monte Carlo versus cluster dynamics

International Nuclear Information System (INIS)

Dalla Torre, J.; Fu, C.-C.; Willaime, F.; Barbu, A.; Bocquet, J.-L.

2006-01-01

The isochronal resistivity recovery in high purity α-iron irradiated by electrons was successfully reproduced by a multiscale modelling approach. The stability and mobility of small self-defect clusters determined by ab initio methods were used as input data for an event based Kinetic Monte Carlo (KMC) model, used to explore the defect population evolution during the annealing and to extract the resistivity recovery peaks. In this paper, we investigate the possibility of using an efficient mesoscale model, the Cluster Dynamics (CD), instead of KMC in this approach. The comparison between the two methods for various CD initial conditions shows the importance of spatial correlations between defects, which are neglected in the CD model. However, using appropriate initial conditions, e.g. starting from the concentration of Frenkel pairs after the uncorrelated stage I E , the CD model captures the main characteristics of subsequent defect population evolution, and it can therefore be used for fast and semi-quantitative investigations

An efficient Monte Carlo algorithm for the fast equilibration and atomistic simulation of alkanethiol self-assembled monolayers on a Au(111) substrate.

Science.gov (United States)

Alexiadis, Orestis; Daoulas, Kostas Ch; Mavrantzas, Vlasis G

2008-01-31

A new Monte Carlo algorithm is presented for the simulation of atomistically detailed alkanethiol self-assembled monolayers (R-SH) on a Au(111) surface. Built on a set of simpler but also more complex (sometimes nonphysical) moves, the new algorithm is capable of efficiently driving all alkanethiol molecules to the Au(111) surface, thereby leading to full surface coverage, irrespective of the initial setup of the system. This circumvents a significant limitation of previous methods in which the simulations typically started from optimally packed structures on the substrate close to thermal equilibrium. Further, by considering an extended ensemble of configurations each one of which corresponds to a different value of the sulfur-sulfur repulsive core potential, sigmass, and by allowing for configurations to swap between systems characterized by different sigmass values, the new algorithm can adequately simulate model R-SH/Au(111) systems for values of sigmass ranging from 4.25 A corresponding to the Hautman-Klein molecular model (J. Chem. Phys. 1989, 91, 4994; 1990, 93, 7483) to 4.97 A corresponding to the Siepmann-McDonald model (Langmuir 1993, 9, 2351), and practically any chain length. Detailed results are presented quantifying the efficiency and robustness of the new method. Representative simulation data for the dependence of the structural and conformational properties of the formed monolayer on the details of the employed molecular model are reported and discussed; an investigation of the variation of molecular organization and ordering on the Au(111) substrate for three CH3-(CH2)n-SH/Au(111) systems with n=9, 15, and 21 is also included.

Atomistic modeling of ion beam induced amorphization in silicon

International Nuclear Information System (INIS)

Pelaz, Lourdes; Marques, Luis A.; Lopez, Pedro; Santos, Ivan; Aboy, Maria; Barbolla, Juan

2005-01-01

Ion beam induced amorphization in Si has attracted significant interest since the beginning of the use of ion implantation for the fabrication of Si devices. Nowadays, a renewed interest in the modeling of amorphization mechanisms at atomic level has arisen due to the use of preamorphizing implants and high dopant implantation doses for the fabrication of nanometric-scale Si devices. In this work, we briefly describe the existing phenomenological and defect-based amorphization models. We focus on the atomistic model we have developed to describe ion beam induced amorphization in Si. In our model, the building block for the amorphous phase is the bond defect or IV pair, whose stability increases with the number of surrounding IV pairs. This feature explains the regrowth behavior of different damage topologies and the kinetics of the crystalline to amorphous transition. The model provides excellent quantitative agreement with experimental results

Monte Carlo steps per spin vs. time in the master equation II: Glauber kinetics for the infinite-range ising model in a static magnetic field

Energy Technology Data Exchange (ETDEWEB)

Oh, Suhk Kun [Chungbuk National University, Chungbuk (Korea, Republic of)

2006-01-15

As an extension of our previous work on the relationship between time in Monte Carlo simulation and time in the continuous master equation in the infinit-range Glauber kinetic Ising model in the absence of any magnetic field, we explored the same model in the presence of a static magnetic field. Monte Carlo steps per spin as time in the MC simulations again turns out to be proportional to time in the master equation for the model in relatively larger static magnetic fields at any temperature. At and near the critical point in a relatively smaller magnetic field, the model exhibits a significant finite-size dependence, and the solution to the Suzuki-Kubo differential equation stemming from the master equation needs to be re-scaled to fit the Monte Carlo steps per spin for the system with different numbers of spins.

Kinetic Monte Carlo simulations of the effect of the exchange control layer thickness in CoPtCrB/CoPtCrSiO granular media

Science.gov (United States)

Almudallal, Ahmad M.; Mercer, J. I.; Whitehead, J. P.; Plumer, M. L.; van Ek, J.

2018-05-01

A hybrid Landau Lifshitz Gilbert/kinetic Monte Carlo algorithm is used to simulate experimental magnetic hysteresis loops for dual layer exchange coupled composite media. The calculation of the rate coefficients and difficulties arising from low energy barriers, a fundamental problem of the kinetic Monte Carlo method, are discussed and the methodology used to treat them in the present work is described. The results from simulations are compared with experimental vibrating sample magnetometer measurements on dual layer CoPtCrB/CoPtCrSiO media and a quantitative relationship between the thickness of the exchange control layer separating the layers and the effective exchange constant between the layers is obtained. Estimates of the energy barriers separating magnetically reversed states of the individual grains in zero applied field as well as the saturation field at sweep rates relevant to the bit write speeds in magnetic recording are also presented. The significance of this comparison between simulations and experiment and the estimates of the material parameters obtained from it are discussed in relation to optimizing the performance of magnetic storage media.

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

Science.gov (United States)

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

2016-12-01

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

Monte Carlo simulation of heavy ion induced kinetic electron emission from an Al surface

CERN Document Server

Ohya, K

2002-01-01

A Monte Carlo simulation is performed in order to study heavy ion induced kinetic electron emission from an Al surface. In the simulation, excitation of conduction band electrons by the projectile ion and recoiling target atoms is treated on the basis of the partial wave expansion method, and the cascade multiplication process of the excited electrons is simulated as well as collision cascade of the recoiling target atoms. Experimental electron yields near conventional threshold energies of heavy ions are simulated by an assumption of a lowering in the apparent surface barrier for the electrons. The present calculation derives components for electron excitations by the projectile ion, the recoiling target atoms and the electron cascades, from the calculated total electron yield. The component from the recoiling target atoms increases with increasing projectile mass, whereas the component from the electron cascade decreases. Although the components from the projectile ion and the electron cascade increase with...

Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations

Energy Technology Data Exchange (ETDEWEB)

Mermigkis, Panagiotis G.; Tsalikis, Dimitrios G. [Department of Chemical Engineering, University of Patras, GR 26500 Patras (Greece); Institute of Chemical Engineering and High Temperature Chemical Processes, GR 26500 Patras (Greece); Mavrantzas, Vlasis G., E-mail: vlasis@chemeng.upatras.gr [Department of Chemical Engineering, University of Patras, GR 26500 Patras (Greece); Institute of Chemical Engineering and High Temperature Chemical Processes, GR 26500 Patras (Greece); Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH-Z, CH-8092 Zurich (Switzerland)

2015-10-28

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, D{sub eff}, of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, D{sub eff} is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for D{sub eff} as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on D{sub eff} (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate

Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Mermigkis, Panagiotis G.; Tsalikis, Dimitrios G.; Mavrantzas, Vlasis G.

2015-01-01

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, D eff , of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, D eff is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for D eff as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on D eff (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated

Kinetic Monte Carlo simulations compared with continuum models and experimental properties of pattern formation during ion beam sputtering

International Nuclear Information System (INIS)

Chason, E; Chan, W L

2009-01-01

Kinetic Monte Carlo simulations model the evolution of surfaces during low energy ion bombardment using atomic level mechanisms of defect formation, recombination and surface diffusion. Because the individual kinetic processes are completely determined, the resulting morphological evolution can be directly compared with continuum models based on the same mechanisms. We present results of simulations based on a curvature-dependent sputtering mechanism and diffusion of mobile surface defects. The results are compared with a continuum linear instability model based on the same physical processes. The model predictions are found to be in good agreement with the simulations for predicting the early-stage morphological evolution and the dependence on processing parameters such as the flux and temperature. This confirms that the continuum model provides a reasonable approximation of the surface evolution from multiple interacting surface defects using this model of sputtering. However, comparison with experiments indicates that there are many features of the surface evolution that do not agree with the continuum model or simulations, suggesting that additional mechanisms are required to explain the observed behavior.

Atomistic and holistic understanding in physics

International Nuclear Information System (INIS)

Bohm, A.

1992-01-01

Understanding means always reduction to the simpler. In the atomistic understanding the reduction is to the simpler objects. One asks the question: what does it consist of? For instance, one asks: What does the molecule consist of? and the answer is: The molecule consists of electrons and nuclei. Or: what does the nucleus consist of? And the answer is: The nucleus consists of protons and neutrons. The parts in the atomistic understanding are the constituents. In the holistic understanding, the reduction is to the simpler functions, the simpler motions. One asks the question: What does it do? What does the molecule do? What does the nucleus do? And the answer is: The molecule rotates and oscillates. The nucleus rotates and oscillates

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

International Nuclear Information System (INIS)

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

2010-01-01

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

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.

Self-learning kinetic Monte Carlo simulations of self-diffusion of small Ag islands on the Ag(111) surface

International Nuclear Information System (INIS)

Shah, Syed Islamuddin; Nandipati, Giridhar; Rahman, Talat S; Karim, Altaf

2016-01-01

We studied self-diffusion of small two-dimensional Ag islands, containing up to ten atoms, on the Ag(111) surface using self-learning kinetic Monte Carlo (SLKMC) simulations. Activation barriers are calculated using the semi-empirical embedded atom method (EAM) potential. We find that two- to seven-atom islands primarily diffuse via concerted translation processes with small contributions from multi-atom and single-atom processes, while eight- to ten-atom islands diffuse via single-atom processes, especially edge diffusion, corner rounding and kink detachment, along with a minimal contribution from concerted processes. For each island size, we give a detailed description of the important processes, and their activation barriers, responsible for its diffusion. (paper)

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.

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

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

International Nuclear Information System (INIS)

Roentzsch, L.

2007-01-01

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

Automatic kinetic Monte-Carlo modeling for impurity atom diffusion in grain boundary structure of tungsten material

Directory of Open Access Journals (Sweden)

Atsushi M. Ito

2017-08-01

Full Text Available The diffusion process of hydrogen and helium in plasma-facing material depends on the grain boundary structures. Whether a grain boundary accelerates or limits the diffusion speed of these impurity atoms is not well understood. In the present work, we proposed the automatic modeling of a kinetic Monte-Carlo (KMC simulation to treat an asymmetric grain boundary structure that corresponds to target samples used in fusion material experiments for retention and permeation. In this method, local minimum energy sites and migration paths for impurity atoms in the grain boundary structure are automatically found using localized molecular dynamics. The grain boundary structure was generated with the Voronoi diagram. Consequently, we demonstrate that the KMC simulation for the diffusion process of impurity atoms in the generated grain boundary structure of tungsten material can be performed.

A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins

International Nuclear Information System (INIS)

Ceccarelli, Matteo; Ruggerone, Paolo; Vargiu, Attilio V

2012-01-01

Many relevant biological processes take place on time scales not reachable by standard all-atom computer simulations. The translocation of antibiotics through non-specific bacterial porins is an example. Microscopic effects compete to determine penetration routes and, consequently, free energy barriers to be overcome. Since bacteria can develop resistance to treatment also by reducing their antibiotic permeability, to understand the microscopic aspects of antibiotic translocation is an important step to rationalize drug design. Here, to investigate the translocation we propose a complete numerical model that combines the diffusion-controlled rate theory and a kinetic Monte Carlo scheme based on both experimental data and microscopically well-founded all-atom simulations. Within our model, an antibiotic translocating through an hour-glass-shaped channel can be described as a molecule moving on a potential of mean force featuring several affinity sites and a high central barrier. The implications of our results for the characterization of antibiotic translocation at in vivo concentrations are discussed. The presence of an affinity site close to the mouth of the channel seems to favor the translocation of antibiotics, the affinity site acting as a particle reservoir. Possible connections between results and the appearance of mutations in clinical strains are also outlined. (paper)

A new scaling approach for the mesoscale simulation of magnetic domain structures using Monte Carlo simulations

Energy Technology Data Exchange (ETDEWEB)

Radhakrishnan, B., E-mail: radhakrishnb@ornl.gov; Eisenbach, M.; Burress, T.A.

2017-06-15

Highlights: • Developed new scaling technique for dipole–dipole interaction energy. • Developed new scaling technique for exchange interaction energy. • Used scaling laws to extend atomistic simulations to micrometer length scale. • Demonstrated transition from mono-domain to vortex magnetic structure. • Simulated domain wall width and transition length scale agree with experiments. - Abstract: A new scaling approach has been proposed for the spin exchange and the dipole–dipole interaction energy as a function of the system size. The computed scaling laws are used in atomistic Monte Carlo simulations of magnetic moment evolution to predict the transition from single domain to a vortex structure as the system size increases. The width of a 180° – domain wall extracted from the simulated structures is in close agreement with experimentally values for an F–Si alloy. The transition size from a single domain to a vortex structure is also in close agreement with theoretically predicted and experimentally measured values for Fe.

Elastic dipoles of point defects from atomistic simulations

Science.gov (United States)

Varvenne, Céline; Clouet, Emmanuel

2017-12-01

The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

Kinetic Monte Carlo study on the evolution of silicon surface roughness under hydrogen thermal treatment

Energy Technology Data Exchange (ETDEWEB)

Wang, Gang; Wang, Yu; Wang, Junzhuan; Pan, Lijia; Yu, Linwei; Zheng, Youdou; Shi, Yi, E-mail: yshi@nju.edu.cn

2017-08-31

Highlights: • The KMC method is adopted to investigate the relationships between surface evolution and hydrogen thermal treatment conditions. • The reduction in surface roughness is divided into two stages at relatively low temperatures, both exhibiting exponential dependence on the time. • The optimized surface structure can be obtained by precisely adjusting thermal treatment temperatures and hydrogen pressures. - Abstract: The evolution of a two-dimensional silicon surface under hydrogen thermal treatment is studied by kinetic Monte Carlo simulations, focusing on the dependence of the migration behaviors of surface atoms on both the temperature and hydrogen pressure. We adopt different activation energies to analyze the influence of hydrogen pressure on the evolution of surface morphology at high temperatures. The reduction in surface roughness is divided into two stages, both exhibiting exponential dependence on the equilibrium time. Our results indicate that a high hydrogen pressure is conducive to obtaining optimized surfaces, as a strategy in the applications of three-dimensional devices.

Ab initio based kinetic Monte-Carlo simulations of phase transformations in FeCrAl

International Nuclear Information System (INIS)

Olsson, Paer

2015-01-01

Document available in abstract form only, full text follows: Corrosion and erosion in lead cooled reactors can be a serious issue due to the high operating temperature and the necessary flow rates. FeCrAl alloys are under consideration as cladding or as coating for stainless steel cladding tubes for lead cooled reactor concepts. The alumina scale that is formed, as Al segregates to the surface and Fe and Cr rich oxides break off, offers a highly protective layer against lead corrosion in a large range of temperatures. However, there are concerns about the phase stability of the alloy under irradiation conditions and of possible induced alpha-prime precipitation. Here a theoretical model of the ternary FeCrAl alloy is presented, based on density functional theory predictions and linked to a kinetic Monte-Carlo simulation framework. The effect of Al on the FeCr miscibility properties are discussed and the coupling of irradiation induced defects with the solutes are treated. Simulations of the micro-structure evolution are tentatively compared to available experiments. (authors)

First-principles kinetic Monte Carlo simulations of ammonia oxidation at RuO{sub 2}(110): Selectivity vs. semi-local DFT

Energy Technology Data Exchange (ETDEWEB)

Mangold, Claudia [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin (Germany); Reuter, Karsten [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin (Germany); Technische Universitaet, Muenchen (Germany)

2011-07-01

Reaching a detailed mechanistic understanding of high selectivity in surface catalytic processes is one of the central goals in present-day catalysis research. The Surface Science approach to this problem focuses on the investigation of well-defined model systems that reduce the complexity but still capture the relevant aspects. In this respect, the almost 100% selectivity reported in detailed experiments for the oxidation of NH{sub 3} to NO at RuO{sub 2}(110) presents an ideal benchmark for a quantitative theoretical analysis. To this end we perform detailed kinetic Monte Carlo simulations based on kinetic parameters derived from density-functional theory (DFT). The obtained turnover frequency for molecular nitrogen is in rather good agreement with the experimental data. However, even with an extended set of elementary processes we are not able to reproduce the experimental findings for the production of NO and therewith the selectivity. The central quantities that decisively determine the latter are the binding energy of NO and the N diffusion barrier. Suspecting the approximate energetics obtained with the employed semi-local DFT functional as reason for the discrepancy, we recalculate the kinetic parameters with different functionals and discuss the resulting effects in the kMC simulations.

Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

Directory of Open Access Journals (Sweden)

Christopher D. Taylor

2012-01-01

Full Text Available Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies of the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.

Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures

Science.gov (United States)

Yan, Xin; Gouissem, Afif; Guduru, Pradeep R.; Sharma, Pradeep

2017-10-01

Amorphous lithium-silicon (a-Li-Si), especially in nanostructure form, is an attractive high-capacity anode material for next-generation Li-ion batteries. During cycles of charging and discharging, a-Li-Si undergoes substantive inelastic deformation and exhibits microcracking. The mechanical response to repeated lithiation-delithiation eventually results in the loss of electrical contact and consequent decrease of capacity, thus underscoring the importance of studying the plasticity of a-Li-Si nanostructures. In recent years, a variety of phenomenological continuum theories have been introduced that purport to model plasticity and the electro-chemo-mechanical behavior of a-Li-Si. Unfortunately, the micromechanisms and atomistic considerations underlying plasticity in Li-Si material are not yet fully understood and this impedes the development of physics-based constitutive models. Conventional molecular dynamics, although extensively used to study this material, is grossly inadequate to resolve this matter. As is well known, conventional molecular dynamics simulations can only address phenomena with characteristic time scales of (at most) a microsecond. Accordingly, in such simulations, the mechanical behavior is deduced under conditions of very high strain rates (usually, 108s-1 or even higher). This limitation severely impacts a realistic assessment of rate-dependent effects. In this work, we attempt to circumvent the time-scale bottleneck of conventional molecular dynamics and provide novel insights into the mechanisms underpinning plastic deformation of Li-Si nanostructures. We utilize an approach that allows imposition of slow strain rates and involves the employment of a new and recently developed potential energy surface sampling method—the so-called autonomous basin climbing—to identify the local minima in the potential energy surface. Combined with other techniques, such as nudged elastic band, kinetic Monte Carlo and transition state theory, we assess

Atomistic modeling of L10 FePt: path to HAMR 5Tb/in2

Science.gov (United States)

Chen, Tianran; Benakli, Mourad; Rea, Chris

2015-03-01

Heat assisted magnetic recording (HAMR) is a promising approach for increasing the storage density of hard disk drives. To increase data density, information must be written in small grains, which requires materials with high anisotropy energy such as L10 FePt. On the other hand, high anisotropy implies high coercivity, making it difficult to write the data with existing recording heads. This issue can be overcome by the technique of HAMR, where a laser is used to heat the recording medium to reduce its coercivity while retaining good thermal stability at room temperature due to the large anisotropy energy. One of the keys to the success of HAMR is the precise control of writing process. In this talk, I will propose a Monte Carlo simulation, based on an atomistic model, that would allow us to study the magnetic properties of L10 FePt and dynamics of spin reversal for the writing process in HAMR.

Kinetic Monte Carlo Potts Model for Simulating a High Burnup Structure in UO2

International Nuclear Information System (INIS)

Oh, Jae-Yong; Koo, Yang-Hyun; Lee, Byung-Ho

2008-01-01

A Potts model, based on the kinetic Monte Carlo method, was originally developed for magnetic domain evolutions, but it was also proposed as a model for a grain growth in polycrystals due to similarities between Potts domain structures and grain structures. It has modeled various microstructural phenomena such as grain growths, a recrystallization, a sintering, and so on. A high burnup structure (HBS) is observed in the periphery of a high burnup UO 2 fuel. Although its formation mechanism is not clearly understood yet, its characteristics are well recognized: The HBS microstructure consists of very small grains and large bubbles instead of original as-sintered grains. A threshold burnup for the HBS is observed at a local burnup 60-80 Gwd/tM, and the threshold temperature is 1000-1200 .deg. C. Concerning a energy stability, the HBS can be created if the system energy of the HBS is lower than that of the original structure in an irradiated UO 2 . In this paper, a Potts model was implemented for simulating the HBS by calculating system energies, and the simulation results were compared with the HBS characteristics mentioned above

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.

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)

Zvejnieks, G.; Ibenskas, A.; Tornau, E.E.

2015-01-01

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

Mesoscopic kinetic Monte Carlo modeling of organic photovoltaic device characteristics

Science.gov (United States)

Kimber, Robin G. E.; Wright, Edward N.; O'Kane, Simon E. J.; Walker, Alison B.; Blakesley, James C.

2012-12-01

Measured mobility and current-voltage characteristics of single layer and photovoltaic (PV) devices composed of poly{9,9-dioctylfluorene-co-bis[N,N'-(4-butylphenyl)]bis(N,N'-phenyl-1,4-phenylene)diamine} (PFB) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) have been reproduced by a mesoscopic model employing the kinetic Monte Carlo (KMC) approach. Our aim is to show how to avoid the uncertainties common in electrical transport models arising from the need to fit a large number of parameters when little information is available, for example, a single current-voltage curve. Here, simulation parameters are derived from a series of measurements using a self-consistent “building-blocks” approach, starting from data on the simplest systems. We found that site energies show disorder and that correlations in the site energies and a distribution of deep traps must be included in order to reproduce measured charge mobility-field curves at low charge densities in bulk PFB and F8BT. The parameter set from the mobility-field curves reproduces the unipolar current in single layers of PFB and F8BT and allows us to deduce charge injection barriers. Finally, by combining these disorder descriptions and injection barriers with an optical model, the external quantum efficiency and current densities of blend and bilayer organic PV devices can be successfully reproduced across a voltage range encompassing reverse and forward bias, with the recombination rate the only parameter to be fitted, found to be 1×107 s-1. These findings demonstrate an approach that removes some of the arbitrariness present in transport models of organic devices, which validates the KMC as an accurate description of organic optoelectronic systems, and provides information on the microscopic origins of the device behavior.

Research on Monte Carlo improved quasi-static method for reactor space-time dynamics

International Nuclear Information System (INIS)

Xu Qi; Wang Kan; Li Shirui; Yu Ganglin

2013-01-01

With large time steps, improved quasi-static (IQS) method can improve the calculation speed for reactor dynamic simulations. The Monte Carlo IQS method was proposed in this paper, combining the advantages of both the IQS method and MC method. Thus, the Monte Carlo IQS method is beneficial for solving space-time dynamics problems of new concept reactors. Based on the theory of IQS, Monte Carlo algorithms for calculating adjoint neutron flux, reactor kinetic parameters and shape function were designed and realized. A simple Monte Carlo IQS code and a corresponding diffusion IQS code were developed, which were used for verification of the Monte Carlo IQS method. (authors)

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

International Nuclear Information System (INIS)

Nakashima, Kenichi; Stoller, Roger E; Xu, Haixuan

2015-01-01

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in irradiated materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1.0a 0 to 3.3a 0 have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomic level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a 0 by taking the average of the recombination distances from 80 simulation cases. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster. (paper)

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.

Atomistic studies of cation transport in tetragonal ZrO2 during zirconium corrosion

International Nuclear Information System (INIS)

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

2015-01-01

Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is a significant degradation mechanism of these alloys. During corrosion, the transport of oxidizing species in zirconium dioxide (ZrO 2 ) determines the corrosion kinetics. Previously, it has been argued that the outward diffusion of cations is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO 2 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 ZrO 2 . The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration of Zr interstitials at a grain boundary is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed. (authors)

AACSD: An atomistic analyzer for crystal structure and defects

Science.gov (United States)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Kinetic Monte Carlo simulations for transient thermal fields: Computational methodology and application to the submicrosecond laser processes in implanted silicon.

Science.gov (United States)

Fisicaro, G; Pelaz, L; Lopez, P; La Magna, A

2012-09-01

Pulsed laser irradiation of damaged solids promotes ultrafast nonequilibrium kinetics, on the submicrosecond scale, leading to microscopic modifications of the material state. Reliable theoretical predictions of this evolution can be achieved only by simulating particle interactions in the presence of large and transient gradients of the thermal field. We propose a kinetic Monte Carlo (KMC) method for the simulation of damaged systems in the extremely far-from-equilibrium conditions caused by the laser irradiation. The reference systems are nonideal crystals containing point defect excesses, an order of magnitude larger than the equilibrium density, due to a preirradiation ion implantation process. The thermal and, eventual, melting problem is solved within the phase-field methodology, and the numerical solutions for the space- and time-dependent thermal field were then dynamically coupled to the KMC code. The formalism, implementation, and related tests of our computational code are discussed in detail. As an application example we analyze the evolution of the defect system caused by P ion implantation in Si under nanosecond pulsed irradiation. The simulation results suggest a significant annihilation of the implantation damage which can be well controlled by the laser fluence.

Addressing uncertainty in atomistic machine learning

DEFF Research Database (Denmark)

Peterson, Andrew A.; Christensen, Rune; Khorshidi, Alireza

2017-01-01

Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predi......Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility...... of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We...... suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate...

Robust mode space approach for atomistic modeling of realistically large nanowire transistors

Science.gov (United States)

Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

2018-01-01

Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.

A kinetic Monte Carlo study of coarsening resistance of novel core/shell precipitates

International Nuclear Information System (INIS)

Zhang, Xuan; Gao, Wenpei; Bellon, Pascal; Averback, Robert S.; Zuo, Jian-Min

2014-01-01

A novel approach towards the design of coarsening-resistant nanoprecipitates in structural alloys was investigated by kinetic Monte Carlo (KMC) simulation. The approach is motivated by recent experimental results in Cu–Nb–W alloys showing that room temperature ion irradiation resulted in W nanoprecipitation, leading to exceptional stability of W-rich-core/Nb-rich-shell nanoprecipitates formed following thermal annealing (Zhang et al., 2013 [11]). Here, image simulations of atomically resolved scanning transmission electron microscopy are performed to establish that these W nanoprecipitates are highly ramified. Thermal precipitate coarsening in an A–B–C ternary alloy similar to Cu–Nb–W is then studied by KMC simulations, where the highly immiscible and refractory C solute atoms are initially distributed into fractal nanoprecipitates, or cores, which become coated by a shell of B atoms during elevated temperature annealing. Compared with nanoprecipitates generated by compact C cores, the ramified nanoprecipitates result in exceptionally high trapping efficiency of B solute atoms during thermal coarsening, and the efficiency increases with the cluster size. The KMC results are analyzed and rationalized by noting that, owing to the Gibbs–Thomson effect, when the curvatures of the shell of the precipitates are zero or negative, the microstructure is coarsening-resistant. Such morphology can be realized by facets, or by dynamic balance within positive, negative and zero curvatures

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.

Kinetic Monte Carlo Study of Ambipolar Lithium Ion and Electron-Polaron Diffusion into Nanostructured TiO2

International Nuclear Information System (INIS)

Yu, Jianguo; Sushko, Maria L.; Kerisit, Sebastien N.; Rosso, Kevin M.; Liu, Jun

2012-01-01

Nanostructured titania (TiO2) polymorphs have proved to be promising electrode materials for next generation lithium-ion batteries. However, there is still a lack of understanding of the fundamental microscopic processes that control charge transport in these materials. Here we present microscopic simulations of the collective dynamics of lithium-ion (Li+) and charge compensating electron polarons (e-) in rutile TiO2 nanoparticles in contact with idealized conductive matrix and electrolyte. Kinetic Monte Carlo simulations are used, parameterized by molecular dynamics-based predictions of activation energy barriers for Li+ and e- diffusion. Simulations reveal the central role of electrostatic coupling between Li+ and e- on their collective drift diffusion at the nanoscale. They also demonstrate that high contact area between conductive matrix and rutile nanoparticles leads to undesirable coupling-induced surface saturation effects during Li+ insertion, which limits the overall capacity and conductivity of the material. These results help provide guidelines for design of nanostructured electrode materials with improved electrochemical performance.

Kinetic Monte Carlo Modeling of Charge Carriers in Organic Electronic Devices: Suppression of the Self-Interaction Error

KAUST Repository

Li, Haoyuan

2017-05-18

Kinetic Monte Carlo (KMC) simulations have emerged as an important tool to help improve the efficiency of organic electronic devices by providing a better understanding of their device physics. In the KMC simulation of an organic device, the reliability of the results depends critically on the accuracy of the chosen charge-transfer rates, which are themselves strongly influenced by the site-energy differences. These site-energy differences include components coming from the electrostatic forces present in the system, which are often evaluated through electric potentials described by the Poisson equation. Here we show that the charge-carrier self-interaction errors that appear when evaluating the site-energy differences can lead to unreliable simulation results. To eliminate these errors, we propose two approaches that are also found to reduce the impact of finite-size effects. As a consequence, reliable results can be obtained at reduced computational costs. The proposed methodologies can be extended to other device simulation techniques as well.

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.

Monte Carlo studies of domain growth in two dimensions

International Nuclear Information System (INIS)

Yaldram, K.; Ahsan Khan, M.

1983-07-01

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)

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.

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

International Nuclear Information System (INIS)

Martin-Bragado, Ignacio

2013-01-01

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

Atomistically informed solute drag in Al–Mg

International Nuclear Information System (INIS)

Zhang, F; Curtin, W A

2008-01-01

Solute drag in solute-strengthened alloys, caused by diffusion of solute atoms around moving dislocations, controls the stress at deformation rates and temperatures useful for plastic forming processes. In the technologically important Al–Mg alloys, the solute drag stresses predicted by classical theories are much larger than experiments, which is resolved in general by eliminating the singularity of the dislocation core via Peierls–Nabarro-type models. Here, the drag stress versus dislocation velocity is computed numerically using a realistic dislocation core structure obtained from an atomistic model to investigate the role of the core and obtain quantitative stresses for comparison with experiment. The model solves a discrete diffusion equation in a reference frame moving with the dislocation, with input solute enthalpies and diffusion activation barriers in the core computed by or estimated from atomistic studies. At low dislocation velocities, the solute drag stress is controlled by bulk solute diffusion because the core diffusion occurs too quickly. In this regime, the drag stress can be obtained using a Peierls–Nabarro model with a core spreading parameter tuned to best match the atomistic models. At intermediate velocities, both bulk and core diffusion can contribute to the drag, leading to a complex stress–velocity relationship showing two peaks in stress. At high velocities, the drag stress is controlled solely by diffusion within and across the core. Like the continuum models, the drag stress is nearly linear in solute concentration. The Orowan relationship is used to connect dislocation velocity to deformation strain rate. Accounting for the dependence of mobile dislocation density on stress, the simulations are in good agreement with experiments on Al–Mg alloys over a range of concentrations and temperatures

Adhesive contact: from atomistic model to continuum model

International Nuclear Information System (INIS)

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 self-consistent 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. (atomic and molecular physics)

Computational modeling of the behavior of nuclear materials (2). Molecular simulations for nuclear materials. Current situation and future perspective

International Nuclear Information System (INIS)

Okita, Taira; Itakura, Mitsuhiro

2017-01-01

Molecular simulations for nuclear materials aim to reproduce atomistic-scale phenomena induced by irradiation and infer the change in material properties. In the present work, recent progress in this field is presented. In particular, the following three topics are explained: (1) Quantification of lattice defects formation process induced by fast neutron collision. (2) Identification of dislocation-channeling mechanism induced by interactions between defect clusters and dislocations. (3) Modeling of the three dimensional movement of defect clusters using molecular dynamics and kinetic Monte Carlo simulations. (author)

A 3D kinetic Monte Carlo simulation study of resistive switching processes in Ni/HfO2/Si-n+-based RRAMs

International Nuclear Information System (INIS)

Aldana, S; García-Fernández, P; Jiménez-Molinos, F; Gómez-Campos, F; Roldán, J B; Rodríguez-Fernández, Alberto; Romero-Zaliz, R; González, M B; Campabadal, F

2017-01-01

A new RRAM simulation tool based on a 3D kinetic Monte Carlo algorithm has been implemented. The redox reactions and migration of cations are developed taking into consideration the temperature and electric potential 3D distributions within the device dielectric at each simulation time step. The filamentary conduction has been described by obtaining the percolation paths formed by metallic atoms. Ni/HfO 2 /Si-n + unipolar devices have been fabricated and measured. The different experimental characteristics of the devices under study have been reproduced with accuracy by means of simulations. The main physical variables can be extracted at any simulation time to clarify the physics behind resistive switching; in particular, the final conductive filament shape can be studied in detail. (paper)

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; Virginia Polytechnic Institute and State University; Savara, Aditya

2017-01-01

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of “KMC stiffness” (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps / cpu-time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order to achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events -- allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm designed for use in achieving and simulating steady-state conditions in KMC simulations. Lastly, as shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.

Diffusion of small Cu islands on the Ni(111) surface: A self-learning kinetic Monte Carlo study

Science.gov (United States)

Acharya, Shree Ram; Shah, Syed Islamuddin; Rahman, Talat S.

2017-08-01

We elucidate the diffusion kinetics of a heteroepitaxial system consisting of two-dimensional small (1-8 atoms) Cu islands on the Ni(111) surface at (100-600) K using the Self-Learning Kinetic Monte Carlo (SLKMC-II) method. Study of the statics of the system shows that compact CuN (3≤N≤8) clusters made up of triangular units on fcc occupancy sites are the energetically most stable structures of those clusters. Interestingly, we find a correlation between the height of the activation energy barrier (Ea) and the location of the transition state (TS). The Ea of processes for Cu islands on the Ni(111) surface are in general smaller than those of their counterpart Ni islands on the same surface. We find this difference to correlate with the relative strength of the lateral interaction of the island atoms in the two systems. While our database consists of hundreds of possible processes, we identify and discuss the energetics of those that are the most dominant, or are rate-limiting, or most contributory to the diffusion of the islands. Since the Ea of single- and multi-atom processes that convert compact island shapes into non-compact ones are larger (with a significantly smaller Ea for their reverse processes) than that for the collective (concerted) motion of the island, the later dominate in the system kinetics - except for the cases of the dimer, pentamer and octamer. Short-jump involving one atom, long jump dimer-shearing, and long-jump corner shearing (via a single-atom) are, respectively, the dominating processes in the diffusion of the dimer, pentamer and octamer. Furthermore single-atom corner-rounding are the rate-limiting processes for the pentamer and octamer islands. Comparison of the energetics of selected processes and lateral interactions obtained from semi-empirical interatomic potentials with those from density functional theory show minor quantitative differences and overall qualitative agreement.

Grown-in beryllium diffusion in indium gallium arsenide: An ab initio, continuum theory and kinetic Monte Carlo study

International Nuclear Information System (INIS)

Liu, Wenyuan; Sk, Mahasin Alam; Manzhos, Sergei; Martin-Bragado, Ignacio; Benistant, Francis; Cheong, Siew Ann

2017-01-01

A roadblock in utilizing InGaAs for scaled-down electronic devices is its anomalous dopant diffusion behavior; specifically, existing models are not able to explain available experimental data on beryllium diffusion consistently. In this paper, we propose a more comprehensive model, taking self-interstitial migration and Be interaction with Ga and In into account. Density functional theory (DFT) calculations are first used to calculate the energy parameters and charge states of possible diffusion mechanisms. Based on the DFT results, continuum modeling and kinetic Monte Carlo simulations are then performed. The model is able to reproduce experimental Be concentration profiles. Our results suggest that the Frank-Turnbull mechanism is not likely, instead, kick-out reactions are the dominant mechanism. Due to a large reaction energy difference, the Ga interstitial and the In interstitial play different roles in the kick-out reactions, contrary to what is usually assumed. The DFT calculations also suggest that the influence of As on Be diffusion may not be negligible.

Monte Carlo - Advances and Challenges

International Nuclear Information System (INIS)

Brown, Forrest B.; Mosteller, Russell D.; Martin, William R.

2008-01-01

Abstract only, full text follows: With ever-faster computers and mature Monte Carlo production codes, there has been tremendous growth in the application of Monte Carlo methods to the analysis of reactor physics and reactor systems. In the past, Monte Carlo methods were used primarily for calculating k eff of a critical system. More recently, Monte Carlo methods have been increasingly used for determining reactor power distributions and many design parameters, such as β eff , l eff , τ, reactivity coefficients, Doppler defect, dominance ratio, etc. These advanced applications of Monte Carlo methods are now becoming common, not just feasible, but bring new challenges to both developers and users: Convergence of 3D power distributions must be assured; confidence interval bias must be eliminated; iterated fission probabilities are required, rather than single-generation probabilities; temperature effects including Doppler and feedback must be represented; isotopic depletion and fission product buildup must be modeled. This workshop focuses on recent advances in Monte Carlo methods and their application to reactor physics problems, and on the resulting challenges faced by code developers and users. The workshop is partly tutorial, partly a review of the current state-of-the-art, and partly a discussion of future work that is needed. It should benefit both novice and expert Monte Carlo developers and users. In each of the topic areas, we provide an overview of needs, perspective on past and current methods, a review of recent work, and discussion of further research and capabilities that are required. Electronic copies of all workshop presentations and material will be available. The workshop is structured as 2 morning and 2 afternoon segments: - Criticality Calculations I - convergence diagnostics, acceleration methods, confidence intervals, and the iterated fission probability, - Criticality Calculations II - reactor kinetics parameters, dominance ratio, temperature

Atomistically-informed dislocation dynamics in FCC crystals

International Nuclear Information System (INIS)

Martinez, E.; Marian, J.; Arsenlis, A.; Victoria, M.; Martinez, E.; Victoria, M.; Perlado, J.M.

2008-01-01

Full text of publication follows. We will present 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 fundings to the plastic behaviour of' monocrystalline fcc metals. (authors)

Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling.

Science.gov (United States)

Núñez, M; Robie, T; Vlachos, D G

2017-10-28

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

Ab initio and Atomic kinetic Monte Carlo modelling of segregation in concentrated FeCrNi alloys

Science.gov (United States)

Piochaud, J. B.; Becquart, C. S.; Domain, C.

2014-06-01

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 multiscale 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 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 and radiation induce segregation will be presented. The effect of Si on the segregation will also be discussed.

Tripoli-4, a three-dimensional poly-kinetic particle transport Monte-Carlo code

International Nuclear Information System (INIS)

Both, J.P.; Lee, Y.K.; Mazzolo, A.; Peneliau, Y.; Petit, O.; Roesslinger, B.; Soldevila, M.

2003-01-01

In this updated of the Monte-Carlo transport code Tripoli-4, we list and describe its current main features. The code computes coupled neutron-photon propagation as well as the electron-photon cascade shower. While providing the user with common biasing techniques, it also implements an automatic weighting scheme. Tripoli-4 enables the user to compute the following physical quantities: a flux, a multiplication factor, a current, a reaction rate, a dose equivalent rate as well as deposit of energy and recoil energies. For each interesting physical quantity, a Monte-Carlo simulation offers different types of estimators. Tripoli-4 has support for execution in parallel mode. Special features and applications are also presented

Tripoli-4, a three-dimensional poly-kinetic particle transport Monte-Carlo code

Energy Technology Data Exchange (ETDEWEB)

Both, J P; Lee, Y K; Mazzolo, A; Peneliau, Y; Petit, O; Roesslinger, B; Soldevila, M [CEA Saclay, Dir. de l' Energie Nucleaire (DEN/DM2S/SERMA/LEPP), 91 - Gif sur Yvette (France)

2003-07-01

In this updated of the Monte-Carlo transport code Tripoli-4, we list and describe its current main features. The code computes coupled neutron-photon propagation as well as the electron-photon cascade shower. While providing the user with common biasing techniques, it also implements an automatic weighting scheme. Tripoli-4 enables the user to compute the following physical quantities: a flux, a multiplication factor, a current, a reaction rate, a dose equivalent rate as well as deposit of energy and recoil energies. For each interesting physical quantity, a Monte-Carlo simulation offers different types of estimators. Tripoli-4 has support for execution in parallel mode. Special features and applications are also presented.

Monte Carlo simulation of fission yields, kinetic energy, fission neutron spectrum and decay γ-ray spectrum for 232Th(n,f) reaction induced by 3H(d,n) 4He neutron source

International Nuclear Information System (INIS)

Zheng Wei; Zeen Yao; Changlin Lan; Yan Yan; Yunjian Shi; Siqi Yan; Jie Wang; Junrun Wang; Jingen Chen; Chinese Academy of Sciences, Shanghai

2015-01-01

Monte Carlo transport code Geant4 has been successfully utilised to study of neutron-induced fission reaction for 232 Th in the transport neutrons generated from 3 H(d,n) 4 He neutron source. The purpose of this work is to examine the applicability of Monte Carlo simulations for the computation of fission reaction process. For this, Monte Carlo simulates and calculates the characteristics of fission reaction process of 232 Th(n,f), such as the fission yields distribution, kinetic energy distribution, fission neutron spectrum and decay γ-ray spectrum. This is the first time to simulate the process of neutron-induced fission reaction using Geant4 code. Typical computational results of neutron-induced fission reaction of 232 Th(n,f) reaction are presented. The computational results are compared with the previous experimental data and evaluated nuclear data to confirm the certain physical process model in Geant4 of scientific rationality. (author)

Long time scale simulation of a grain boundary in copper

DEFF Research Database (Denmark)

Pedersen, A.; Henkelman, G.; Schiøtz, Jakob

2009-01-01

A general, twisted and tilted, grain boundary in copper has been simulated using the adaptive kinetic Monte Carlo method to study the atomistic structure of the non-crystalline region and the mechanism of annealing events that occur at low temperature. The simulated time interval spanned 67 mu s...... was also observed. In the final low-energy configurations, the thickness of the region separating the crystalline grains corresponds to just one atomic layer, in good agreement with reported experimental observations. The simulated system consists of 1307 atoms and atomic interactions were described using...

Analysis of polytype stability in PVT grown silicon carbide single crystal using competitive lattice model Monte Carlo simulations

Directory of Open Access Journals (Sweden)

Hui-Jun Guo

2014-09-01

Full Text Available Polytype stability is very important for high quality SiC single crystal growth. However, the growth conditions for the 4H, 6H and 15R polytypes are similar, and the mechanism of polytype stability is not clear. The kinetics aspects, such as surface-step nucleation, are important. The kinetic Monte Carlo method is a common tool to study surface kinetics in crystal growth. However, the present lattice models for kinetic Monte Carlo simulations cannot solve the problem of the competitive growth of two or more lattice structures. In this study, a competitive lattice model was developed for kinetic Monte Carlo simulation of the competition growth of the 4H and 6H polytypes of SiC. The site positions are fixed at the perfect crystal lattice positions without any adjustment of the site positions. Surface steps on seeds and large ratios of diffusion/deposition have positive effects on the 4H polytype stability. The 3D polytype distribution in a physical vapor transport method grown SiC ingot showed that the facet preserved the 4H polytype even if the 6H polytype dominated the growth surface. The theoretical and experimental results of polytype growth in SiC suggest that retaining the step growth mode is an important factor to maintain a stable single 4H polytype during SiC growth.

Kinetics of electron-positron pair plasmas using an adaptive Monte Carlo method

International Nuclear Information System (INIS)

Pilla, R.P.; Shaham, J.

1997-01-01

A new algorithm for implementing the adaptive Monte Carlo method is given. It is used to solve the Boltzmann equations that describe the time evolution of a nonequilibrium electron-positron pair plasma containing high-energy photons. These are coupled nonlinear integro-differential equations. The collision kernels for the photons as well as pairs are evaluated for Compton scattering, pair annihilation and creation, bremsstrahlung, and Coulomb collisions. They are given as multidimensional integrals which are valid for all energies. For an homogeneous and isotropic plasma with no particle escape, the equilibrium solution is expressed analytically in terms of the initial conditions. For two specific cases, for which the photon and the pair spectra are initially constant or have a power-law distribution within the given limits, the time evolution of the plasma is analyzed using the new method. The final spectra are found to be in a good agreement with the analytical solutions. The new algorithm is faster than the Monte Carlo scheme based on uniform sampling and more flexible than the numerical methods used in the past, which do not involve Monte Carlo sampling. It is also found to be very stable. Some astrophysical applications of this technique are discussed. copyright 1997 The American Astronomical Society

Definition and detection of contact in atomistic simulations

NARCIS (Netherlands)

Solhjoo, Soheil; Vakis, Antonis I.

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,

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,

Radiative Transfer Reconsidered as a Quantum Kinetic Theory

Indian Academy of Sciences (India)

Radiative transfer—quantum kinetic theory—anomalous dispersion. 1. ... able for the elaboration of transport codes (e.g. based on the Monte-Carlo technique ... this function is not a true probability density function but rather a quasiprobability.

Multiresolution Modeling of Semidilute Polymer Solutions: Coarse-Graining Using Wavelet-Accelerated Monte Carlo

Directory of Open Access Journals (Sweden)

Animesh Agarwal

2017-09-01

Full Text Available We present a hierarchical coarse-graining framework for modeling semidilute polymer solutions, based on the wavelet-accelerated Monte Carlo (WAMC method. This framework forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even standard coarse-grained simulations. Previously, it was applied to simulations examining the structure of individual polymer chains in solution using up to four levels of coarse-graining (Ismail et al., J. Chem. Phys., 2005, 122, 234901 and Ismail et al., J. Chem. Phys., 2005, 122, 234902, recovering the correct scaling behavior in the coarse-grained representation. In the present work, we extend this method to the study of polymer solutions, deriving the bonded and non-bonded potentials between coarse-grained superatoms from the single chain statistics. A universal scaling function is obtained, which does not require recalculation of the potentials as the scale of the system is changed. To model semi-dilute polymer solutions, we assume the intermolecular potential between the coarse-grained beads to be equal to the non-bonded potential, which is a reasonable approximation in the case of semidilute systems. Thus, a minimal input of microscopic data is required for simulating the systems at the mesoscopic scale. We show that coarse-grained polymer solutions can reproduce results obtained from the more detailed atomistic system without a significant loss of accuracy.

Ionic diffusion in quartz studied by transport measurements, SIMS and atomistic simulations

International Nuclear Information System (INIS)

Sartbaeva, Asel; Wells, Stephen A; Redfern, Simon A T; Hinton, Richard W; Reed, Stephen J B

2005-01-01

Ionic diffusion in the quartz-β-eucryptite system is studied by DC transport measurements, SIMS and atomistic simulations. Transport data show a large transient increase in ionic current at the α-β phase transition of quartz (the Hedvall effect). The SIMS data indicate two diffusion processes, one involving rapid Li + motion and the other involving penetration of Al and Li atoms into quartz at the phase transition. Atomistic simulations explain why the fine microstructure of twin domain walls in quartz near the transition does not hinder Li + diffusion

Structural and functional analysis of glycoprotein butyrylcholinesterase using atomistic molecular dynamics

Science.gov (United States)

Bernardi, Austen; Faller, Roland

Atomistic molecular dynamics (MD) has proven to be a powerful tool for studying the structure and dynamics of biological systems on nanosecond to microsecond time scales and nanometer length scales. In this work we study the effects of modifying the glycan distribution on the structure and function of full length monomeric butyrylcholinesterase (BChE). BChE exists as a monomer, dimer, or tetramer, and is a therapeutic glycoprotein with nine asparagine glycosylation sites per monomer. Each monomer acts as a stoichiometric scavenger for organophosphorus (OP) nerve agents (e.g. sarin, soman). Glycan distributions are highly heterogeneous and have been shown experimentally to affect certain glycoproteins' stability and reactivity. We performed structural analysis of various biologically relevant glycoforms of BChE using classical atomistic MD. Functional analysis was performed through binding energy simulations using umbrella sampling with BChE and OP cofactors. Additionally, we assess the quality of the glycans' conformational sampling. We found that the glycan distribution has a significant effect on the structure and function of BChE on timescales available to atomistic MD. This project is funded by the DTRA Grant HDTRA1-15-1-0054.

Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

International Nuclear Information System (INIS)

Ogawa, Hiroshi

2015-01-01

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

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

Science.gov (United States)

Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

2017-08-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

Atomistic models of Cu diffusion in CuInSe2 under variations in composition

Science.gov (United States)

Sommer, David E.; Dunham, Scott T.

2018-03-01

We construct an analytic model for the composition dependence of the vacancy-mediated Cu diffusion coefficient in undoped CuInSe2 using parameters from density functional theory. The applicability of this model is supported numerically with kinetic lattice Monte Carlo and Onsager transport tensors. We discuss how this model relates to experimental measurements of Cu diffusion, arguing that our results can account for significant contributions to the bulk diffusion of Cu tracers in non-stoichiometric CuInSe2.

A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics

Science.gov (United States)

Byun, Hye Suk; El-Naggar, Mohamed Y.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2017-10-01

Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.

Atomistic mechanisms of ReRAM cell operation and reliability

Science.gov (United States)

Pandey, Sumeet C.

2018-01-01

We present results from first-principles-based modeling that captures functionally important physical phenomena critical to cell materials selection, operation, and reliability for resistance-switching memory technologies. An atomic-scale description of retention, the low- and high-resistance states (RS), and the sources of intrinsic cell-level variability in ReRAM is discussed. Through the results obtained from density functional theory, non-equilibrium Green’s function, molecular dynamics, and kinetic Monte Carlo simulations; the role of variable-charge vacancy defects and metal impurities in determining the RS, the LRS-stability, and electron-conduction in such RS is reported. Although, the statistical electrical characteristics of the oxygen-vacancy (Ox-ReRAM) and conductive-bridging RAM (M-ReRAM) are notably different, the underlying similar electrochemical phenomena describing retention and formation/dissolution of RS are being discussed.

An Ab Initio and Kinetic Monte Carlo Simulation Study of Lithium Ion Diffusion on Graphene

Directory of Open Access Journals (Sweden)

Kehua Zhong

2017-07-01

Full Text Available The Li+ diffusion coefficients in Li+-adsorbed graphene systems were determined by combining first-principle calculations based on density functional theory with Kinetic Monte Carlo simulations. The calculated results indicate that the interactions between Li ions have a very important influence on lithium diffusion. Based on energy barriers directly obtained from first-principle calculations for single-Li+ and two-Li+ adsorbed systems, a new equation predicting energy barriers with more than two Li ions was deduced. Furthermore, it is found that the temperature dependence of Li+ diffusion coefficients fits well to the Arrhenius equation, rather than meeting the equation from electrochemical impedance spectroscopy applied to estimate experimental diffusion coefficients. Moreover, the calculated results also reveal that Li+ concentration dependence of diffusion coefficients roughly fits to the equation from electrochemical impedance spectroscopy in a low concentration region; however, it seriously deviates from the equation in a high concentration region. So, the equation from electrochemical impedance spectroscopy technique could not be simply used to estimate the Li+ diffusion coefficient for all Li+-adsorbed graphene systems with various Li+ concentrations. Our work suggests that interactions between Li ions, and among Li ion and host atoms will influence the Li+ diffusion, which determines that the Li+ intercalation dependence of Li+ diffusion coefficient should be changed and complex.

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

Science.gov (United States)

Kumar, Rajesh; Parashar, Avinash

2016-01-07

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.

Kinetic Monte Carlo modeling of the efficiency roll-off in a multilayer white organic light-emitting device

Energy Technology Data Exchange (ETDEWEB)

Mesta, M.; Coehoorn, R.; Bobbert, P. A. [Department of Applied Physics, Technische Universiteit Eindhoven, P.O. Box 513, NL-5600 MB Eindhoven (Netherlands); Eersel, H. van [Simbeyond B.V., P.O. Box 513, NL-5600 MB Eindhoven (Netherlands)

2016-03-28

Triplet-triplet annihilation (TTA) and triplet-polaron quenching (TPQ) in organic light-emitting devices (OLEDs) lead to a roll-off of the internal quantum efficiency (IQE) with increasing current density J. We employ a kinetic Monte Carlo modeling study to analyze the measured IQE and color balance as a function of J in a multilayer hybrid white OLED that combines fluorescent blue with phosphorescent green and red emission. We investigate two models for TTA and TPQ involving the phosphorescent green and red emitters: short-range nearest-neighbor quenching and long-range Förster-type quenching. Short-range quenching predicts roll-off to occur at much higher J than measured. Taking long-range quenching with Förster radii for TTA and TPQ equal to twice the Förster radii for exciton transfer leads to a fair description of the measured IQE-J curve, with the major contribution to the roll-off coming from TPQ. The measured decrease of the ratio of phosphorescent to fluorescent component of the emitted light with increasing J is correctly predicted. A proper description of the J-dependence of the ratio of red and green phosphorescent emission needs further model refinements.

Kinetic Monte Carlo modeling of the efficiency roll-off in a multilayer white organic light-emitting device

Science.gov (United States)

Mesta, M.; van Eersel, H.; Coehoorn, R.; Bobbert, P. A.

2016-03-01

Triplet-triplet annihilation (TTA) and triplet-polaron quenching (TPQ) in organic light-emitting devices (OLEDs) lead to a roll-off of the internal quantum efficiency (IQE) with increasing current density J. We employ a kinetic Monte Carlo modeling study to analyze the measured IQE and color balance as a function of J in a multilayer hybrid white OLED that combines fluorescent blue with phosphorescent green and red emission. We investigate two models for TTA and TPQ involving the phosphorescent green and red emitters: short-range nearest-neighbor quenching and long-range Förster-type quenching. Short-range quenching predicts roll-off to occur at much higher J than measured. Taking long-range quenching with Förster radii for TTA and TPQ equal to twice the Förster radii for exciton transfer leads to a fair description of the measured IQE-J curve, with the major contribution to the roll-off coming from TPQ. The measured decrease of the ratio of phosphorescent to fluorescent component of the emitted light with increasing J is correctly predicted. A proper description of the J-dependence of the ratio of red and green phosphorescent emission needs further model refinements.

Kinetic Monte Carlo modeling of the efficiency roll-off in a multilayer white organic light-emitting device

International Nuclear Information System (INIS)

Mesta, M.; Coehoorn, R.; Bobbert, P. A.; Eersel, H. van

2016-01-01

Triplet-triplet annihilation (TTA) and triplet-polaron quenching (TPQ) in organic light-emitting devices (OLEDs) lead to a roll-off of the internal quantum efficiency (IQE) with increasing current density J. We employ a kinetic Monte Carlo modeling study to analyze the measured IQE and color balance as a function of J in a multilayer hybrid white OLED that combines fluorescent blue with phosphorescent green and red emission. We investigate two models for TTA and TPQ involving the phosphorescent green and red emitters: short-range nearest-neighbor quenching and long-range Förster-type quenching. Short-range quenching predicts roll-off to occur at much higher J than measured. Taking long-range quenching with Förster radii for TTA and TPQ equal to twice the Förster radii for exciton transfer leads to a fair description of the measured IQE-J curve, with the major contribution to the roll-off coming from TPQ. The measured decrease of the ratio of phosphorescent to fluorescent component of the emitted light with increasing J is correctly predicted. A proper description of the J-dependence of the ratio of red and green phosphorescent emission needs further model refinements.

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.)

Ab initio and atomic kinetic Monte Carlo modelling of segregation in concentrated FeCrNi alloys

International Nuclear Information System (INIS)

Piochaud, J.B.; Becquart, C.S.; Domain, C.

2013-01-01

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-Fe 70 Cr 20 Ni 10 ). 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 Fe 70 Cr 20 Ni 10 , 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

Plasma kinetic effects on atomistic mix in one dimension and at structured interfaces (II)

Science.gov (United States)

Albright, Brian; Yin, Lin; Cooley, James; Haack, Jeffrey; Douglas, Melissa

2017-10-01

The Marble campaign seeks to develop a platform for studying mix evolution in turbulent, inhomogeneous, high-energy-density plasmas at the NIF. Marble capsules contain engineered CD foams, the pores of which are filled with hydrogen and tritium. During implosion, hydrodynamic stirring and plasma diffusivity mix tritium fuel into the surrounding CD plasma, leading to both DD and DT fusion neutron production. In this presentation, building upon prior work, kinetic particle-in-cell simulations using the VPIC code are used to examine kinetic effects on thermonuclear burn in Marble-like settings. Departures from Maxwellian distributions are observed near the interface and TN burn rates and inferred temperatures from synthetic neutron time of flight diagnostics are compared with those from treating the background species as Maxwellian. Work performed under the auspices of the U.S. DOE by the Los Alamos National Security, LLC Los Alamos National Laboratory and supported by the ASC and Science programs.

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...

A coupled atomistics and discrete dislocation plasticity simulation of nanoindentation into single crystal thin films

International Nuclear Information System (INIS)

Miller, Ronald E.; Shilkrot, L.E.; Curtin, William A.

2004-01-01

The phenomenon of 2D nanoindentation of circular 'Brinell' indenter into a single crystal metal thin film bonded to a rigid substrate is investigated. The simulation method is the coupled atomistics and discrete dislocation (CADD) model recently developed by the authors. The CADD model couples a continuum region containing any number of discrete dislocations to an atomistic region, and permits accurate, automatic detection and passing of dislocations between the atomistic and continuum regions. The CADD model allows for a detailed study of nanoindentation to large penetration depths (up to 60 A here) using only a small region of atoms just underneath the indenter where dislocation nucleation, cross-slip, and annihilation occur. Indentation of a model hexagonal aluminum crystal shows: (i) the onset of homogeneous dislocation nucleation at points away from the points of maximum resolved shear stress; (ii) size-dependence of the material hardness, (iii) the role of dislocation dissociation on deformation; (iv) reverse plasticity, including nucleation of dislocations on unloading and annihilation; (v) permanent deformation, including surface uplift, after full unloading; (vi) the effects of film thickness on the load-displacement response; and (vii) the differences between displacement and force controlled loading. This application demonstrates the power of the CADD method in capturing both long-range dislocation plasticity and short-range atomistic phenomena. The use of CADD permits for a clear study of the physical and mechanical influence of both complex plastic flow and non-continuum atomistic-level processes on the macroscopic response of material under indentation loading

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...

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.

Comparison of continuum and atomistic methods for the analysis of InAs/GaAs quantum dots

DEFF Research Database (Denmark)

Barettin, D.; Pecchia, A.; Penazzi, G.

2011-01-01

We present a comparison of continuum k · p and atomistic empirical Tight Binding methods for the analysis of the optoelectronic properties of InAs/GaAs quantum dots.......We present a comparison of continuum k · p and atomistic empirical Tight Binding methods for the analysis of the optoelectronic properties of InAs/GaAs quantum dots....

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.

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

Science.gov (United States)

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Atomistic simulations of bulk, surface and interfacial polymer properties

Science.gov (United States)

Natarajan, Upendra

In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin

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

KAUST Repository

Li, Haoyuan; Li, Yuan; Li, Hong; Bredas, Jean-Luc

2017-01-01

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

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

KAUST Repository

Li, Haoyuan

2017-01-16

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

Crystal growth kinetics in undercooled melts of pure Ge, Si and Ge-Si alloys

Science.gov (United States)

Herlach, Dieter M.; Simons, Daniel; Pichon, Pierre-Yves

2018-01-01

We report on measurements of crystal growth dynamics in semiconducting pure Ge and pure Si melts and in Ge100-xSix (x = 25, 50, 75) alloy melts as a function of undercooling. Electromagnetic levitation techniques are applied to undercool the samples in a containerless way. The growth velocity is measured by the utilization of a high-speed camera technique over an extended range of undercooling. Solidified samples are examined with respect to their microstructure by scanning electron microscopic investigations. We analyse the experimental results of crystal growth kinetics as a function of undercooling within the sharp interface theory developed by Peter Galenko. Transitions of the atomic attachment kinetics are found at large undercoolings, from faceted growth to dendrite growth. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

Nanostructure evolution of neutron-irradiated reactor pressure vessel steels: Revised 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); Messina, L. [DEN-Service de Recherches de Métallurgie Physique, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette (France); KTH Royal Institute of Technology, Roslagstullsbacken 21, SE-114 21 Stockholm (Sweden); Becquart, C.S. [Unité Matériaux Et Transformations (UMET), UMR 8207, Université de Lille 1, ENSCL, F-59600 Villeneuve d’Ascq Cedex (France); Olsson, P. [KTH Royal Institute of Technology, Roslagstullsbacken 21, SE-114 21 Stockholm (Sweden); Malerba, L. [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, B-2400 Mol (Belgium)

2017-02-15

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

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.

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

International Nuclear Information System (INIS)

Schebarchov, D.; Schulze, T. P.; Hendy, S. C.

2014-01-01

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

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

KAUST Repository

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2013-01-01

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

On-the-Fly Kinetic Monte Carlo Simulation of Aqueous Phase Advanced Oxidation Processes.

Science.gov (United States)

Guo, Xin; Minakata, Daisuke; Crittenden, John

2015-08-04

We have developed an on-the-fly kinetic Monte Carlo (KMC) model to predict the degradation mechanisms and fates of intermediates and byproducts that are produced during aqueous-phase advanced oxidation processes (AOPs). The on-the-fly KMC model is composed of a reaction pathway generator, a reaction rate constant estimator, a mechanistic reduction module, and a KMC solver. The novelty of this work is that we develop the pathway as we march forward in time rather than developing the pathway before we use the KMC method to solve the equations. As a result, we have fewer reactions to consider, and we have greater computational efficiency. We have verified this on-the-fly KMC model for the degradation of polyacrylamide (PAM) using UV light and titanium dioxide (i.e., UV/TiO2). Using the on-the-fly KMC model, we were able to predict the time-dependent profiles of the average molecular weight for PAM. The model provided detailed and quantitative insights into the time evolution of the molecular weight distribution and reaction mechanism. We also verified our on-the-fly KMC model for the destruction of (1) acetone, (2) trichloroethylene (TCE), and (3) polyethylene glycol (PEG) for the ultraviolet light and hydrogen peroxide AOP. We demonstrated that the on-the-fly KMC model can achieve the same accuracy as the computer-based first-principles KMC (CF-KMC) model, which has already been validated in our earlier work. The on-the-fly KMC is particularly suitable for molecules with large molecular weights (e.g., polymers) because the degradation mechanisms for large molecules can result in hundreds of thousands to even millions of reactions. The ordinary differential equations (ODEs) that describe the degradation pathways cannot be solved using traditional numerical methods, but the KMC can solve these equations.

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)

Adaptive spacetime method using Riemann jump conditions for coupled atomistic-continuum dynamics

International Nuclear Information System (INIS)

Kraczek, B.; Miller, S.T.; Haber, R.B.; Johnson, D.D.

2010-01-01

We combine the Spacetime Discontinuous Galerkin (SDG) method for elastodynamics with the mathematically consistent Atomistic Discontinuous Galerkin (ADG) method in a new scheme that concurrently couples continuum and atomistic models of dynamic response in solids. The formulation couples non-overlapping continuum and atomistic models across sharp interfaces by weakly enforcing jump conditions, for both momentum balance and kinematic compatibility, using Riemann values to preserve the characteristic structure of the underlying hyperbolic system. Momentum balances to within machine-precision accuracy over every element, on each atom, and over the coupled system, with small, controllable energy dissipation in the continuum region that ensures numerical stability. When implemented on suitable unstructured spacetime grids, the continuum SDG model offers linear computational complexity in the number of elements and powerful adaptive analysis capabilities that readily bridge between atomic and continuum scales in both space and time. A special trace operator for the atomic velocities and an associated atomistic traction field enter the jump conditions at the coupling interface. The trace operator depends on parameters that specify, at the scale of the atomic spacing, the position of the coupling interface relative to the atoms. In a key finding, we demonstrate that optimizing these parameters suppresses spurious reflections at the coupling interface without the use of non-physical damping or special boundary conditions. We formulate the implicit SDG-ADG coupling scheme in up to three spatial dimensions, and describe an efficient iterative solution scheme that outperforms common explicit schemes, such as the Velocity Verlet integrator. Numerical examples, in 1dxtime and employing both linear and nonlinear potentials, demonstrate the performance of the SDG-ADG method and show how adaptive spacetime meshing reconciles disparate time steps and resolves atomic-scale signals in

A kinetic Monte Carlo model with improved charge injection model for the photocurrent characteristics of organic solar cells

Science.gov (United States)

Kipp, Dylan; Ganesan, Venkat

2013-06-01

We develop a kinetic Monte Carlo model for photocurrent generation in organic solar cells that demonstrates improved agreement with experimental illuminated and dark current-voltage curves. In our model, we introduce a charge injection rate prefactor to correct for the electrode grid-size and electrode charge density biases apparent in the coarse-grained approximation of the electrode as a grid of single occupancy, charge-injecting reservoirs. We use the charge injection rate prefactor to control the portion of dark current attributed to each of four kinds of charge injection. By shifting the dark current between electrode-polymer pairs, we align the injection timescales and expand the applicability of the method to accommodate ohmic energy barriers. We consider the device characteristics of the ITO/PEDOT/PSS:PPDI:PBTT:Al system and demonstrate the manner in which our model captures the device charge densities unique to systems with small injection energy barriers. To elucidate the defining characteristics of our model, we first demonstrate the manner in which charge accumulation and band bending affect the shape and placement of the various current-voltage regimes. We then discuss the influence of various model parameters upon the current-voltage characteristics.

Generative Models of Conformational Dynamics

Science.gov (United States)

Langmead, Christopher James

2014-01-01

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term ‘generative’ refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GrAphical Models of Energy LANdscapes), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc) from long timescale simulation data. PMID:24446358

Monte Carlo codes and Monte Carlo simulator program

International Nuclear Information System (INIS)

Higuchi, Kenji; Asai, Kiyoshi; Suganuma, Masayuki.

1990-03-01

Four typical Monte Carlo codes KENO-IV, MORSE, MCNP and VIM have been vectorized on VP-100 at Computing Center, JAERI. The problems in vector processing of Monte Carlo codes on vector processors have become clear through the work. As the result, it is recognized that these are difficulties to obtain good performance in vector processing of Monte Carlo codes. A Monte Carlo computing machine, which processes the Monte Carlo codes with high performances is being developed at our Computing Center since 1987. The concept of Monte Carlo computing machine and its performance have been investigated and estimated by using a software simulator. In this report the problems in vectorization of Monte Carlo codes, Monte Carlo pipelines proposed to mitigate these difficulties and the results of the performance estimation of the Monte Carlo computing machine by the simulator are described. (author)

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.

Atomistic modeling of zirconium hydride precipitation: methodology for deriving a tight-binding potential

International Nuclear Information System (INIS)

Dufresne, Alice

2014-01-01

The zirconium-hydrogen system is of nuclear safety interest, as the hydride precipitation leads to the cladding embrittlement, which is made of zirconium-based alloys. The cladding is the first safety barrier confining the radioactive products: its integrity shall be kept during the entire fuel-assemblies life, in reactor, including accidental situation, and post-operation (transport and storage). Many uncertainties remain regarding the hydrides precipitation kinetics and the local stress impact on their precipitation. The atomic scale modeling of this system would bring clarifications on the relevant mechanisms. The usual atomistic modeling methods are based on thermo-statistic approaches, whose precision and reliability depend on the interatomic potential used. However, there was no potential allowing a rigorous study of the Zr-H system. The present work has indeed addressed this issue: a new tight-binding potential for zirconium hydrides modeling is now available. Moreover, this thesis provides a detailed manual for deriving such potentials accounting for spd hybridization, and fitted here on DFT results. This guidebook has be written in light of modeling a pure transition metal followed by a metal-covalent coupling (metallic carbides, nitrides and silicides). (author)

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...

The Ehrlich–Schwoebel barrier on an oxide surface: a combined Monte-Carlo and in situ scanning tunneling microscopy approach

International Nuclear Information System (INIS)

Gianfrancesco, Anthony G; Tselev, Alexander; Baddorf, Arthur P; Kalinin, Sergei V; Vasudevan, Rama K

2015-01-01

The controlled growth of epitaxial films of complex oxides requires an atomistic understanding of key parameters determining final film morphology, such as termination dependence on adatom diffusion, and height of the Ehrlich–Schwoebel (ES) barrier. Here, through an in situ scanning tunneling microscopy study of mixed-terminated La_5_/_8Ca_3_/_8MnO_3 (LCMO) films, we image adatoms and observe pile-up at island edges. Image analysis allows determination of the population of adatoms at the edge of islands and fractions on A-site and B-site terminations. A simple Monte-Carlo model, simulating the random walk of adatoms on a sinusoidal potential landscape using Boltzmann statistics is used to reproduce the experimental data, and provides an estimate of the ES barrier as ∼0.18 ± 0.04 eV at T = 1023 K, similar to those of metal adatoms on metallic surfaces. These studies highlight the utility of in situ imaging, in combination with basic Monte-Carlo methods, in elucidating the factors which control the final film growth in complex oxides. (paper)

The Ehrlich-Schwoebel barrier on an oxide surface: a combined Monte-Carlo and in situ scanning tunneling microscopy approach.

Science.gov (United States)

Gianfrancesco, Anthony G; Tselev, Alexander; Baddorf, Arthur P; Kalinin, Sergei V; Vasudevan, Rama K

2015-11-13

The controlled growth of epitaxial films of complex oxides requires an atomistic understanding of key parameters determining final film morphology, such as termination dependence on adatom diffusion, and height of the Ehrlich-Schwoebel (ES) barrier. Here, through an in situ scanning tunneling microscopy study of mixed-terminated La5/8Ca3/8MnO3 (LCMO) films, we image adatoms and observe pile-up at island edges. Image analysis allows determination of the population of adatoms at the edge of islands and fractions on A-site and B-site terminations. A simple Monte-Carlo model, simulating the random walk of adatoms on a sinusoidal potential landscape using Boltzmann statistics is used to reproduce the experimental data, and provides an estimate of the ES barrier as ∼0.18 ± 0.04 eV at T = 1023 K, similar to those of metal adatoms on metallic surfaces. These studies highlight the utility of in situ imaging, in combination with basic Monte-Carlo methods, in elucidating the factors which control the final film growth in complex oxides.

The Ehrlich-Schwoebel barrier on an oxide surface: a combined Monte-Carlo and in situ scanning tunneling microscopy approach

Science.gov (United States)

Gianfrancesco, Anthony G.; Tselev, Alexander; Baddorf, Arthur P.; Kalinin, Sergei V.; Vasudevan, Rama K.

2015-11-01

The controlled growth of epitaxial films of complex oxides requires an atomistic understanding of key parameters determining final film morphology, such as termination dependence on adatom diffusion, and height of the Ehrlich-Schwoebel (ES) barrier. Here, through an in situ scanning tunneling microscopy study of mixed-terminated La5/8Ca3/8MnO3 (LCMO) films, we image adatoms and observe pile-up at island edges. Image analysis allows determination of the population of adatoms at the edge of islands and fractions on A-site and B-site terminations. A simple Monte-Carlo model, simulating the random walk of adatoms on a sinusoidal potential landscape using Boltzmann statistics is used to reproduce the experimental data, and provides an estimate of the ES barrier as ˜0.18 ± 0.04 eV at T = 1023 K, similar to those of metal adatoms on metallic surfaces. These studies highlight the utility of in situ imaging, in combination with basic Monte-Carlo methods, in elucidating the factors which control the final film growth in complex oxides.

New Hybrid Monte Carlo methods for efficient sampling. From physics to biology and statistics

International Nuclear Information System (INIS)

Akhmatskaya, Elena; Reich, Sebastian

2011-01-01

We introduce a class of novel hybrid methods for detailed simulations of large complex systems in physics, biology, materials science and statistics. These generalized shadow Hybrid Monte Carlo (GSHMC) methods combine the advantages of stochastic and deterministic simulation techniques. They utilize a partial momentum update to retain some of the dynamical information, employ modified Hamiltonians to overcome exponential performance degradation with the system’s size and make use of multi-scale nature of complex systems. Variants of GSHMCs were developed for atomistic simulation, particle simulation and statistics: GSHMC (thermodynamically consistent implementation of constant-temperature molecular dynamics), MTS-GSHMC (multiple-time-stepping GSHMC), meso-GSHMC (Metropolis corrected dissipative particle dynamics (DPD) method), and a generalized shadow Hamiltonian Monte Carlo, GSHmMC (a GSHMC for statistical simulations). All of these are compatible with other enhanced sampling techniques and suitable for massively parallel computing allowing for a range of multi-level parallel strategies. A brief description of the GSHMC approach, examples of its application on high performance computers and comparison with other existing techniques are given. Our approach is shown to resolve such problems as resonance instabilities of the MTS methods and non-preservation of thermodynamic equilibrium properties in DPD, and to outperform known methods in sampling efficiency by an order of magnitude. (author)

MCSAD: Improved algorithm for Monte Carlo Simulation of Atom Displacements in solid materials

International Nuclear Information System (INIS)

Correa-Alfonso, C. M.; Pinnera, I.; Cruz, C. M.; Abreu, Y.; Leyva, A.

2011-01-01

In order to directly simulate the stochastic occurrence of atom displacements (AD) formation processes during gamma and electron irradiation, an improved Monte Carlo calculation code is presented. In MCSAD, AD processes were considered only on the basis of single elastic scattering interactions among fast primary and/or secondary electrons with matrix atoms. The AD distribution was statistically sampled and simulated in the framework of the Monte Carlo Method to perform discrete single electron scattering processes (ES), particularly those leading to AD events. As study case, the high critical temperature superconducting material YBa 2 Cu 3 O 7-x (YBCO) is presented. The AD in-depth distributions at different incident photons kinetic energies were obtained. Furthermore, the AD contribution from each atomic species to total AD distribution was achieved. In addition the AD energy profiles with the scattered electron kinetic energies were carried out. A comparison with the theoretical expressions proposed by Oen-Holmes-Cahn [1,2] is presented and discussed. (Author)

The Paradox of Migration and the Interests of the Atomistic Nation ...

African Journals Online (AJOL)

The Paradox of Migration and the Interests of the Atomistic Nation- States: The Southern ... Internationally as well as regionally, States are concerned with issues of ... within the nationstates in general, and in their labour markets in particular.

Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

Science.gov (United States)

Paul, Fabian; Noé, Frank; Weikl, Thomas R

2018-03-27

Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109 Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.

Atomic kinetic Monte Carlo model based on ab initio data: Simulation of microstructural evolution under irradiation of dilute Fe-CuNiMnSi alloys

International Nuclear Information System (INIS)

Vincent, E.; Becquart, C.S.; Domain, C.

2007-01-01

The embrittlement of pressure vessel steels under radiation has been long ago correlated with the presence of Cu solutes. Other solutes such as Ni, Mn and Si are now suspected to contribute also to the embrittlement. The interactions of these solutes with radiation induced point defects thus need to be characterized properly in order to understand the elementary mechanisms behind the formation of the clusters formed upon radiation. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si) in order to build a database used to parameterise an atomic kinetic Monte Carlo model. Some results of irradiation damage in dilute Fe-CuNiMnSi alloys obtained with this model are presented

Atomic kinetic Monte Carlo model based on ab initio data: Simulation of microstructural evolution under irradiation of dilute Fe CuNiMnSi alloys

Science.gov (United States)

Vincent, E.; Becquart, C. S.; Domain, C.

2007-02-01

The embrittlement of pressure vessel steels under radiation has been long ago correlated with the presence of Cu solutes. Other solutes such as Ni, Mn and Si are now suspected to contribute also to the embrittlement. The interactions of these solutes with radiation induced point defects thus need to be characterized properly in order to understand the elementary mechanisms behind the formation of the clusters formed upon radiation. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si) in order to build a database used to parameterise an atomic kinetic Monte Carlo model. Some results of irradiation damage in dilute Fe-CuNiMnSi alloys obtained with this model are presented.

Construction of a kinetics model for liquid-solid transitions built from atomistic simulations

Science.gov (United States)

Benedict, Lorin; Zepeda-Ruiz, Luis; Haxhimali, Tomorr; Hamel, Sebastien; Sadigh, Babak; Chernov, Alexander; Belof, Jonathan

We discuss work in progress towards a kinetics model for dynamically-driven liquid-solid transitions built from MD simulations. The growth of solid particles within a liquid is studied for a range of conditions, and careful attention is paid to the construction of an accurate multi-phase (equilibrium) equation of state for the system under consideration, in order to provide a framework upon which the non-equilibrium physics is based. His work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Lawrence Livermore National Security, LLC.

Microscopic Rate Constants of Crystal Growth from Molecular Dynamic Simulations Combined with Metadynamics

Directory of Open Access Journals (Sweden)

Dániel Kozma

2012-01-01

Full Text Available Atomistic simulation of crystal growth can be decomposed into two steps: the determination of the microscopic rate constants and a mesoscopic kinetic Monte Carlo simulation. We proposed a method to determine kinetic rate constants of crystal growth. We performed classical molecular dynamics on the equilibrium liquid/crystal interface of argon. Metadynamics was used to explore the free energy surface of crystal growth. A crystalline atom was selected at the interface, and it was displaced to the liquid phase by adding repulsive Gaussian potentials. The activation free energy of this process was calculated as the maximal potential energy density of the Gaussian potentials. We calculated the rate constants at different interfacial structures using the transition state theory. In order to mimic real crystallization, we applied a temperature difference in the calculations of the two opposite rate constants, and they were applied in kinetic Monte Carlo simulation. The novelty of our technique is that it can be used for slow crystallization processes, while the simple following of trajectories can be applied only for fast reactions. Our method is a possibility for determination of elementary rate constants of crystal growth that seems to be necessary for the long-time goal of computer-aided crystal design.

Atomistic nucleation sites of Pt nanoparticles on N-doped carbon nanotubes.

Science.gov (United States)

Sun, Chia-Liang; Pao, Chih-Wen; Tsai, Huang-Ming; Chiou, Jau-Wern; Ray, Sekhar C; Wang, Houng-Wei; Hayashi, Michitoshi; Chen, Li-Chyong; Lin, Hong-Ji; Lee, Jyh-Fu; Chang, Li; Tsai, Min-Hsiung; Chen, Kuei-Hsien; Pong, Way-Faung

2013-08-07

The atomistic nucleation sites of Pt nanoparticles (Pt NPs) on N-doped carbon nanotubes (N-CNTs) were investigated using C and N K-edge and Pt L3-edge X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure (EXAFS) spectroscopy. Transmission electron microscopy and XANES/EXAFS results revealed that the self-organized Pt NPs on N-CNTs are uniformly distributed because of the relatively high binding energies of the adsorbed Pt atoms at the imperfect sites. During the atomistic nucleation process of Pt NPs on N-CNTs, stable Pt-C and Pt-N bonds are presumably formed, and charge transfer occurs at the surface/interface of the N-CNTs. The findings in this study were consistent with density functional theory calculations performed using cluster models for the undoped, substitutional-N-doped and pyridine-like-N-doped CNTs.

The specific bias in dynamic Monte Carlo simulations of nuclear reactors

International Nuclear Information System (INIS)

Yamamoto, T.; Endo, H.; Ishizu, T.; Tatewaki, I.

2013-01-01

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 critical. 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 an over-estimation of the final power level. It should be noted that the bias will not be eliminated by refining the 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. (authors)

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

Atomistic simulations of dislocation processes in copper

DEFF Research Database (Denmark)

Vegge, T.; Jacobsen, K.W.

2002-01-01

We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example......, the stability of screw dislocation dipoles is discussed. We show that the presence of jogs will strongly influence cross slip barriers and dipole stability. We furthermore present some new results on jogged edge dislocations and edge dislocation dipoles. The jogs are found to be extended, and simulations...

Atomistic simulation studies of iron sulphide, platinum antimonide and platinum arsenide

CSIR Research Space (South Africa)

Ngoepe, PE

2005-09-01

Full Text Available The authors present the results of atomistic simulations using derived interatomic potentials for the pyrite-structured metal chalcogenides FeS2, PtSb2 and PtAs2. Structural and elastic constants were calculated and compared with experimental...

Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal

International Nuclear Information System (INIS)

Huang, Liangliang; Gubbins, Keith E.; Seredych, Mykola; Bandosz, Teresa J.; Duin, Adri C. T. van; Lu, Xiaohua

2013-01-01

The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H 2 S and H 2 O/H 2 S mixtures on GO materials and compare the results with experiment. We find that H 2 S molecules dissociate on the carbonyl functional groups, and H 2 O, CO 2 , and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H 2 O/H 2 S mixtures, H 2 O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H 2 S 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

Monte Carlo and Quasi-Monte Carlo Sampling

CERN Document Server

Lemieux, Christiane

2009-01-01

Presents essential tools for using quasi-Monte Carlo sampling in practice. This book focuses on issues related to Monte Carlo methods - uniform and non-uniform random number generation, variance reduction techniques. It covers several aspects of quasi-Monte Carlo methods.

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.

Coupling Strategies Investigation of Hybrid Atomistic-Continuum Method Based on State Variable Coupling

Directory of Open Access Journals (Sweden)

Qian Wang

2017-01-01

Full Text Available Different configurations of coupling strategies influence greatly the accuracy and convergence of the simulation results in the hybrid atomistic-continuum method. This study aims to quantitatively investigate this effect and offer the guidance on how to choose the proper configuration of coupling strategies in the hybrid atomistic-continuum method. We first propose a hybrid molecular dynamics- (MD- continuum solver in LAMMPS and OpenFOAM that exchanges state variables between the atomistic region and the continuum region and evaluate different configurations of coupling strategies using the sudden start Couette flow, aiming to find the preferable configuration that delivers better accuracy and efficiency. The major findings are as follows: (1 the C→A region plays the most important role in the overlap region and the “4-layer-1” combination achieves the best precision with a fixed width of the overlap region; (2 the data exchanging operation only needs a few sampling points closer to the occasions of interactions and decreasing the coupling exchange operations can reduce the computational load with acceptable errors; (3 the nonperiodic boundary force model with a smoothing parameter of 0.1 and a finer parameter of 20 can not only achieve the minimum disturbance near the MD-continuum interface but also keep the simulation precision.

An in-depth description of bipolar resistive switching in Cu/HfOx/Pt devices, a 3D kinetic Monte Carlo simulation approach

Science.gov (United States)

Aldana, S.; Roldán, J. B.; García-Fernández, P.; Suñe, J.; Romero-Zaliz, R.; Jiménez-Molinos, F.; Long, S.; Gómez-Campos, F.; Liu, M.

2018-04-01

A simulation tool based on a 3D kinetic Monte Carlo algorithm has been employed to analyse bipolar conductive bridge RAMs fabricated with Cu/HfOx/Pt stacks. Resistive switching mechanisms are described accounting for the electric field and temperature distributions within the dielectric. The formation and destruction of conductive filaments (CFs) are analysed taking into consideration redox reactions and the joint action of metal ion thermal diffusion and electric field induced drift. Filamentary conduction is considered when different percolation paths are formed in addition to other conventional transport mechanisms in dielectrics. The simulator was tuned by using the experimental data for Cu/HfOx/Pt bipolar devices that were fabricated. Our simulation tool allows for the study of different experimental results, in particular, the current variations due to the electric field changes between the filament tip and the electrode in the High Resistance State. In addition, the density of metallic atoms within the CF can also be characterized along with the corresponding CF resistance description.

A continuum-atomistic simulation of heat transfer in micro- and nano-flows

International Nuclear Information System (INIS)

Liu Jin; Chen Shiyi; Nie Xiaobo; Robbins, Mark O.

2007-01-01

We develop a hybrid atomistic-continuum scheme for simulating micro- and nano-flows with heat transfer. The approach is based on spatial 'domain decomposition' in which molecular dynamics (MD) is used in regions where atomistic details are important, while classical continuum fluid dynamics is used in the remaining regions. The two descriptions are matched in a coupling region where we ensure continuity of mass, momentum, energy and their fluxes. The scheme for including the energy equation is implemented in 1-D and 2-D, and used to study steady and unsteady heat transfer in channel flows with and without nano roughness. Good agreement between hybrid results and analytical or pure MD results is found, demonstrating the accuracy of this multiscale method and its potential applications in thermal engineering

Atomistic approach for modeling metal-semiconductor interfaces

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via the I–V curve. In particular, it will be demonstrated how doping — and bias — modifies the Schottky barrier, and how finite size models (the slab approach) are unable to describe these interfaces......We present a general framework for simulating interfaces using an atomistic approach based on density functional theory and non-equilibrium Green's functions. The method includes all the relevant ingredients, such as doping and an accurate value of the semiconductor band gap, required to model...

Atomistic Galois insertions for flow sensitive integrity

DEFF Research Database (Denmark)

Nielson, Flemming; Nielson, Hanne Riis

2017-01-01

Several program verification techniques assist in showing that software adheres to the required security policies. Such policies may be sensitive to the flow of execution and the verification may be supported by combinations of type systems and Hoare logics. However, this requires user assistance...... and to obtain full automation we shall explore the over-approximating nature of static analysis. We demonstrate that the use of atomistic Galois insertions constitutes a stable framework in which to obtain sound and fully automatic enforcement of flow sensitive integrity. The framework is illustrated...

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

Directory of Open Access Journals (Sweden)

M. Chiapetto

2016-12-01

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

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

Science.gov (United States)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

In-silico analysis on biofabricating vascular networks using kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Sun, Yi; Yang, Xiaofeng; Wang, Qi

2014-01-01

We present a computational modeling approach to study the fusion of multicellular aggregate systems in a novel scaffold-less biofabrication process, known as ‘bioprinting’. In this novel technology, live multicellular aggregates are used as fundamental building blocks to make tissues or organs (collectively known as the bio-constructs,) via the layer-by-layer deposition technique or other methods; the printed bio-constructs embedded in maturogens, consisting of nutrient-rich bio-compatible hydrogels, are then placed in bioreactors to undergo the cellular aggregate fusion process to form the desired functional bio-structures. Our approach reported here is an agent-based modeling method, which uses the kinetic Monte Carlo (KMC) algorithm to evolve the cellular system on a lattice. In this method, the cells and the hydrogel media, in which cells are embedded, are coarse-grained to material’s points on a three-dimensional (3D) lattice, where the cell–cell and cell–medium interactions are quantified by adhesion and cohesion energies. In a multicellular aggregate system with a fixed number of cells and fixed amount of hydrogel media, where the effect of cell differentiation, proliferation and death are tactically neglected, the interaction energy is primarily dictated by the interfacial energy between cell and cell as well as between cell and medium particles on the lattice, respectively, based on the differential adhesion hypothesis. By using the transition state theory to track the time evolution of the multicellular system while minimizing the interfacial energy, KMC is shown to be an efficient time-dependent simulation tool to study the evolution of the multicellular aggregate system. In this study, numerical experiments are presented to simulate fusion and cell sorting during the biofabrication process of vascular networks, in which the bio-constructs are fabricated via engineering designs. The results predict the feasibility of fabricating the vascular

In-silico analysis on biofabricating vascular networks using kinetic Monte Carlo simulations.

Science.gov (United States)

Sun, Yi; Yang, Xiaofeng; Wang, Qi

2014-03-01

We present a computational modeling approach to study the fusion of multicellular aggregate systems in a novel scaffold-less biofabrication process, known as 'bioprinting'. In this novel technology, live multicellular aggregates are used as fundamental building blocks to make tissues or organs (collectively known as the bio-constructs,) via the layer-by-layer deposition technique or other methods; the printed bio-constructs embedded in maturogens, consisting of nutrient-rich bio-compatible hydrogels, are then placed in bioreactors to undergo the cellular aggregate fusion process to form the desired functional bio-structures. Our approach reported here is an agent-based modeling method, which uses the kinetic Monte Carlo (KMC) algorithm to evolve the cellular system on a lattice. In this method, the cells and the hydrogel media, in which cells are embedded, are coarse-grained to material's points on a three-dimensional (3D) lattice, where the cell-cell and cell-medium interactions are quantified by adhesion and cohesion energies. In a multicellular aggregate system with a fixed number of cells and fixed amount of hydrogel media, where the effect of cell differentiation, proliferation and death are tactically neglected, the interaction energy is primarily dictated by the interfacial energy between cell and cell as well as between cell and medium particles on the lattice, respectively, based on the differential adhesion hypothesis. By using the transition state theory to track the time evolution of the multicellular system while minimizing the interfacial energy, KMC is shown to be an efficient time-dependent simulation tool to study the evolution of the multicellular aggregate system. In this study, numerical experiments are presented to simulate fusion and cell sorting during the biofabrication process of vascular networks, in which the bio-constructs are fabricated via engineering designs. The results predict the feasibility of fabricating the vascular structures

Meaningful timescales from Monte Carlo simulations of particle systems with hard-core interactions

Energy Technology Data Exchange (ETDEWEB)

Costa, Liborio I., E-mail: liborio78@gmail.com

2016-12-01

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

Electrochemical deposition on surface nanometric defects: Thermodynamics and grand canonical Monte Carlo simulations

International Nuclear Information System (INIS)

Luque, Noelia B.; Reinaudi, Luis; Serra, Pablo; Leiva, Ezequiel P.M.

2009-01-01

A thermodynamic analysis is performed on electrochemical metal deposition in the cavity of a foreign substrate. In particular, the deposition of Cu and Ag in nanometer-sized holes on Au(1 1 1) is studied by means of off-lattice atomistic Grand Canonical Monte Carlo simulations, using embedded atom method potentials. The present simulation conditions emulate experiments of electrochemical metal deposition in nanocavities, as performed in the literature. Depending on the system, remarkable differences are found in the way in which the defects are decorated, as well as in their energetics. When the interaction of the adsorbate atoms with the substrate is less favorable than the bulk interaction of the adsorbate, clusters are found that grow stepwise over the level of the surface. In the opposite case, the filling of the cavity occurs stepwise, without the occurrence of cluster growth above the surface level. The results of the simulations present a good qualitative agreement with experimental results from the literature

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...

Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

Science.gov (United States)

Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

1999-01-01

We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. 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 developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

Atomistic characterization of pseudoelasticity and shape memory in NiTi nanopillars

International Nuclear Information System (INIS)

Zhong Yuan; Gall, Ken; Zhu Ting

2012-01-01

Molecular dynamics simulations are performed to study the atomistic mechanisms governing the pseudoelasticity and shape memory in nickel–titanium (NiTi) nanostructures. For a 〈1 1 0〉 – oriented nanopillar subjected to compressive loading–unloading, we observe either a pseudoelastic or shape memory response, depending on the applied strain and temperature that control the reversibility of phase transformation and deformation twinning. We show that irreversible twinning arises owing to the dislocation pinning of twin boundaries, while hierarchically twinned microstructures facilitate the reversible twinning. The nanoscale size effects are manifested as the load serration, stress plateau and large hysteresis loop in stress–strain curves that result from the high stresses required to drive the nucleation-controlled phase transformation and deformation twinning in nanosized volumes. Our results underscore the importance of atomistically resolved modeling for understanding the phase and deformation reversibilities that dictate the pseudoelasticity and shape memory behavior in nanostructured shape memory alloys.

Beyond the Cahn-Hilliard equation: a vacancy-based kinetic theory

International Nuclear Information System (INIS)

Nastar, M.

2011-01-01

A Self-Consistent Mean Field (SCMF) kinetic theory including an explicit description of the vacancy diffusion mechanism is developed. The present theory goes beyond the usual local equilibrium hypothesis. It is applied to the study of the early time spinodal decomposition in alloys. The resulting analytical expression of the structure function highlights the contribution of the vacancy diffusion mechanism. Instead of the single amplification rate of the Cahn-Hillard linear theory, the linearized SCMF kinetic equations involve three constant rates, first one describing the vacancy relaxation kinetics, second one related to the kinetic coupling between local concentrations and pair correlations and the third one representing the spinodal amplification rate. Starting from the same vacancy diffusion model, we perform kinetic Monte Carlo simulations of a Body Centered Cubic (BCC) demixting alloy. The resulting spherically averaged structure function is compared to the SCMF predictions. Both qualitative and quantitative agreements are satisfying. (authors)

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

Monte Carlo simulation of asymmetrical growth of cube-shaped nanoparticles

International Nuclear Information System (INIS)

Wang Yuanyuan; Xie Huaqing; Wu Zihua; Xing Jiaojiao

2016-01-01

We simulated the asymmetrical growth of cube-shaped nanoparticles by applying the Monte Carlo method. The influence of the specific mechanisms on the crystal growth of nanoparticles has been phenomenologically described by efficient growth possibilities along different directions (or crystal faces). The roles of the thermodynamic and kinetic factors have been evaluated in three phenomenological models. The simulation results would benefit the understanding about the cause and manner of the asymmetrical growth of nanoparticles. (paper)

Monte Carlo technique for very large ising models

Science.gov (United States)

Kalle, C.; Winkelmann, V.

1982-08-01

Rebbi's multispin coding technique is improved and applied to the kinetic Ising model with size 600*600*600. We give the central part of our computer program (for a CDC Cyber 76), which will be helpful also in a simulation of smaller systems, and describe the other tricks necessary to go to large lattices. The magnetization M at T=1.4* T c is found to decay asymptotically as exp(-t/2.90) if t is measured in Monte Carlo steps per spin, and M( t = 0) = 1 initially.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

Science.gov (United States)

Yang, Shengfeng; Chen, Youping

2015-03-08

In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

Atomistic simulations of graphite etching at realistic time scales.

Science.gov (United States)

Aussems, D U B; Bal, K M; Morgan, T W; van de Sanden, M C M; Neyts, E C

2017-10-01

Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 20 m -2 s -1 . The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.

Off-lattice self-learning kinetic Monte Carlo: application to 2D cluster diffusion on the fcc(111) surface

International Nuclear Information System (INIS)

Kara, Abdelkader; Yildirim, Handan; Rahman, Talat S; Trushin, Oleg

2009-01-01

We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed self-learning KMC (SLKMC) (Trushin et al 2005 Phys. Rev. B 72 115401) is released, leaving atoms free to occupy 'off-lattice' positions to accommodate several processes responsible for small-cluster diffusion, periphery atom motion and heteroepitaxial growth. This technique combines the ideas embedded in the SLKMC method with a new pattern-recognition scheme fitted to an off-lattice model in which relative atomic positions are used to characterize and store configurations. Application of a combination of the 'drag' and the repulsive bias potential (RBP) methods for saddle point searches allows the treatment of concerted cluster, and multiple- and single-atom, motions on an equal footing. This tandem approach has helped reveal several new atomic mechanisms which contribute to cluster migration. We present applications of this off-lattice SLKMC to the diffusion of 2D islands of Cu (containing 2-30 atoms) on Cu and Ag(111), using the interatomic potential from the embedded-atom method. For the hetero-system Cu/Ag(111), this technique has uncovered mechanisms involving concerted motions such as shear, breathing and commensurate-incommensurate occupancies. Although the technique introduces complexities in storage and retrieval, it does not introduce noticeable extra computational cost.

Simulating Surface-Enhanced Hyper-Raman Scattering Using Atomistic Electrodynamics-Quantum Mechanical Models.

Science.gov (United States)

Hu, Zhongwei; Chulhai, Dhabih V; Jensen, Lasse

2016-12-13

Surface-enhanced hyper-Raman scattering (SEHRS) is the two-photon analogue of surface-enhanced Raman scattering (SERS), which has proven to be a powerful tool to study molecular structures and surface enhancements. However, few theoretical approaches to SEHRS exist and most neglect the atomistic descriptions of the metal surface and molecular resonance effects. In this work, we present two atomistic electrodynamics-quantum mechanical models to simulate SEHRS. The first is the discrete interaction model/quantum mechanical (DIM/QM) model, which combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule. The second model is a dressed-tensors method that describes the molecule as a point-dipole and point-quadrupole object interacting with the enhanced local field and field-gradients (FG) from the nanoparticle. In both of these models, the resonance effects are treated efficiently by means of damped quadratic response theory. Using these methods, we simulate SEHRS spectra for benzene and pyridine. Our results show that the FG effects in SEHRS play an important role in determining both the surface selection rules and the enhancements. We find that FG effects are more important in SEHRS than in SERS. We also show that the spectral features of small molecules can be accurately described by accounting for the interactions between the molecule and the local field and FG of the nanoparticle. However, at short distances between the metal and molecule, we find significant differences in the SEHRS enhancements predicted using the DIM/QM and the dressed-tensors methods.

Subdiffusion kinetics of nanoprecipitate growth and destruction in solid solutions

Science.gov (United States)

Sibatov, R. T.; Svetukhin, V. V.

2015-06-01

Based on fractional differential generalizations of the Ham and Aaron-Kotler precipitation models, we study the kinetics of subdiffusion-limited growth and dissolution of new-phase precipitates. We obtain the time dependence of the number of impurities and dimensions of new-phase precipitates. The solutions agree with the Monte Carlo simulation results.

Adaptive resolution simulation of an atomistic protein in MARTINI water

International Nuclear Information System (INIS)

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

Multiscale modeling of polyisoprene on graphite

International Nuclear Information System (INIS)

Pandey, Yogendra Narayan; Brayton, Alexander; Doxastakis, Manolis; Burkhart, Craig; Papakonstantopoulos, George J.

2014-01-01

The local dynamics and the conformational properties of polyisoprene next to a smooth graphite surface constructed by graphene layers are studied by a multiscale methodology. First, fully atomistic molecular dynamics simulations of oligomers next to the surface are performed. Subsequently, Monte Carlo simulations of a systematically derived coarse-grained model generate numerous uncorrelated structures for polymer systems. A new reverse backmapping strategy is presented that reintroduces atomistic detail. Finally, multiple extensive fully atomistic simulations with large systems of long macromolecules are employed to examine local dynamics in proximity to graphite. Polyisoprene repeat units arrange close to a parallel configuration with chains exhibiting a distribution of contact lengths. Efficient Monte Carlo algorithms with the coarse-grain model are capable of sampling these distributions for any molecular weight in quantitative agreement with predictions from atomistic models. Furthermore, molecular dynamics simulations with well-equilibrated systems at all length-scales support an increased dynamic heterogeneity that is emerging from both intermolecular interactions with the flat surface and intramolecular cooperativity. This study provides a detailed comprehensive picture of polyisoprene on a flat surface and consists of an effort to characterize such systems in atomistic detail

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.

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.

An atomistic model for cross-linked HNBR elastomers used in seals

Science.gov (United States)

Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

2015-03-01

Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

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.

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

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 ...

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

NARCIS (Netherlands)

Kooi, BJ

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

Continuum modeling of post-implantation damage and the effective plus factor in crystalline silicon at room temperature

International Nuclear Information System (INIS)

Chan, H.Y.; Srinivasan, M.P.; Benistant, F.; Mok, K.R.; Chan, Lap; Jin, H.M.

2006-01-01

The role of computer simulation in predicting intrinsic diffusion effects is amplified with the shrinkage of MOS devices. In this work, post-implant damage distributions are obtained from atomistic Monte Carlo (MC) simulations. Based on diffusion-limiting kinetics, the evolution of the damage at room temperature with time is studied. It is shown that evolution of the point defects follow the Ostwald ripening process, where larger defect clusters grow at the expense of smaller ones. A qualitative study of the effective plus factor is also conducted, taking into account various clustering and recombination processes. Clustering is found to significantly affect the remaining amount of damage, which in turn affects subsequent diffusion processes

Kinetic-energy distribution for symmetric fission of 236U

International Nuclear Information System (INIS)

Brissot, R.; Bocquet, J.P.; Ristori, C.; Crancon, J.; Guet, C.R.; Nifenecker, H.A.; Montoya, M.

1980-01-01

Fission fragment kinetic-energy distributions have been measured at the Grenoble high-flux reactor with the Lohengrin facility. Spurious events were eliminated in the symmetric region by a coherence test based on a time-of-flight measurement of fragment velocities. A Monte-Carlo calculation is then performed to correct the experimental data for neutron evaporation. The difference between the most probable kinetic energy in symmetric fission and the fission in which the heavy fragment is 'magic' (Zsub(H)=50) is found to be approximately =30 MeV. The results suggest that for the symmetric case the total excitation energy available at scission is shared equally among the fragments. (author)

Adaptive jump barrier height in Monte Carlo configuration kinetics.

Energy Technology Data Exchange (ETDEWEB)

Leitner, Martin; Pfeiler, Wolfgang; Pueschl, Wolfgang [Dynamics of Condensed Systems, Faculty of Physics, University of Vienna, Strudlhofgasse 4, A-1090 Wien (Austria); Vogtenhuber, Doris [Computational Materials Science, Faculty of Physics, University of Vienna, Sensengasse 8, A-1090 Wien (Austria)

2008-07-01

In usual MC simulations of configuration kinetics atom jump probabilities are calculated from energies of the initial and/or final bound states of the moving atom, leaving aside the exact energy of the intermediate saddle point state. This energy may however be critically influenced by the local atomic environment. We propose a strategy to explicitly take account of this influence. The basis is ab initio calculation of representative jump paths in the framework of the nudged elastic band method. From these results, an influence function is derived which modifies the energy of the saddle point and therefore the effective jump barrier height as calculated from the initial and final states according to a cluster expansion scheme. The overall effect is demonstrated on the NiAl system.

Decohesion Kinetics of PEDOT:PSS Conducting Polymer Films

KAUST Repository

Dupont, Stephanie R.; Novoa, Fernando; Voroshazi, Eszter; Dauskardt, Reinhold H.

2013-01-01

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.

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.

Monte Carlo simulation of tomography techniques using the platform Gate

International Nuclear Information System (INIS)

Barbouchi, Asma

2007-01-01

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

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

NARCIS (Netherlands)

Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.

2016-01-01

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell

Uncertainty quantification for hyperbolic and kinetic equations

CERN Document Server

Pareschi, Lorenzo

2017-01-01

This book explores recent advances in uncertainty quantification for hyperbolic, kinetic, and related problems. The contributions address a range of different aspects, including: polynomial chaos expansions, perturbation methods, multi-level Monte Carlo methods, importance sampling, and moment methods. The interest in these topics is rapidly growing, as their applications have now expanded to many areas in engineering, physics, biology and the social sciences. Accordingly, the book provides the scientific community with a topical overview of the latest research efforts.

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.

The effects of one-dimensional glide on the reaction kinetics of interstitial clusters

DEFF Research Database (Denmark)

Heinisch, H.L.; Singh, B.N.; Golubov, S.I.

2000-01-01

is therefore 'mixed 1D/3D migration' along a 3D path consisting of 1D segments, The defect reaction kinetics under mixed 1D/3D diffusion are different from pure 1D diffusion and pure 3D diffusion, both of which can be formulated within analytical rate theory models of microstructure evolution under irradiation....... Atomic-scale kinetic Monte Carlo (kMC) defect migration simulations are used to investigate the effects of mixed 1D/3D migration on defect reaction kinetics as a guide for implementing mixed 1D/3D migration into the analytical rate theory. The functional dependence of the sink strength on the size...

Kinetic Monte Carlo simulation of three-dimensional shape evolution with void formation using Solid-by-Solid model: Application to via and trench filling

International Nuclear Information System (INIS)

Kaneko, Yutaka; Hiwatari, Yasuaki; Ohara, Katsuhiko; Asa, Fujio

2013-01-01

In this paper we present the Kinetic Monte Carlo simulation system for the simulation of three-dimensional shape evolution with void formation as a model for electrodeposition. The basic system is the Solid-by-Solid model which is an extension of the conventional Solid-on-Solid model for crystal growth to include void formation. The advantage of the Solid-by-Solid model is that complex three-dimensional shape evolution accompanying void formation (from point defects to macro voids) can be simulated without the difficulty of treating moving boundaries. This model has been extended to include the solution part in which the migration of ions is simulated by the coarse-grained random walk. A multi-scale method is employed to generate the concentration gradient in the diffusion layer. The extended model is applied to the simulation of via and trench fillings by copper electrodeposition. Three kinds of additives are included: suppressors, accelerators and chloride ions. The mechanism of void formation, effects of additives and their influence on the bottom-up filling are discussed within the framework of this model

Atomistic simulation of graphene-based polymer nanocomposites

International Nuclear Information System (INIS)

Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

2016-01-01

Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

Dynamic aspects of dislocation motion: atomistic simulations

International Nuclear Information System (INIS)

Bitzek, Erik; Gumbsch, Peter

2005-01-01

Atomistic simulations of accelerating edge and screw dislocations were carried out to study the dynamics of dislocations in a face centered cubic metal. Using two different embedded atom potentials for nickel and a simple slab geometry, the Peierls stress, the effective mass, the line tension and the drag coefficient were determined. A dislocation intersecting an array of voids is used to study dynamic effects in dislocation-obstacle interactions. A pronounced effect caused by inertial overshooting is found. A dynamic line tension model is developed which reproduces the simulation results. The model can be used to easily estimate the magnitude of inertial effects in the interaction of dislocations with localized obstacles for different obstacle strengths, -spacings and temperatures

Quantum Corrections to the 'Atomistic' MOSFET Simulations

Science.gov (United States)

Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

2000-01-01

We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

Growth kinetics of metastable (331) nanofacet on Au and Pt(110) surfaces

International Nuclear Information System (INIS)

Ndongmouo, U.T.; Houngninou, E.; Hontinfinde, F.

2006-12-01

A theoretical epitaxial growth model with realistic barriers for surface diffusion is investigated by means of kinetic Monte Carlo simulations to study the growth modes of metastable (331) nanofacets on Au and Pt(110) surfaces. The results show that under experimental atomic fluxes, the (331) nanofacets grow by 2D nucleation at low temperature in the submonolayer regime. A metastable growth phase diagram that can be useful to experimentalists is presented and looks similar to the one found for the stationary growth of the bcc(001) surface in the kinetic 6-vertex model. (author)

Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

Science.gov (United States)

Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

2000-01-01

We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

DoGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

DEFF Research Database (Denmark)

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector

2017-01-01

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would...... be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools...

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)

Patinet, S.

2009-12-01

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)

An atomistic interpretation of Planck's 1900 derivation of his radiation law

International Nuclear Information System (INIS)

Irons, F.E.

2000-01-01

In deriving his radiation law in 1900, Max Planck employed a simple harmonic oscillator to model the exchange of energy between radiation and matter. Traditionally the harmonic oscillator has been viewed as modelling an entity which is itself oscillating, although a suitable oscillating entity has not been forthcoming. (Opinion is divided between a material oscillator, an imaginary oscillator and a need to revise Planck's derivation to apply to cavity modes of oscillation). We offer a novel, atomistic interpretation of Planck's derivation wherein the harmonic oscillator models a transition between the internal quantum states of an atom|not a normal electronic atom characterised by possible energies 0 and hν, but an atom populated by subatomic bosons (such as pions) and characterised by multiple occupancy of quantum states and possible energies nhν (n = 0;1;2; ...). We show how Planck's derivation can be varied to accommodate electronic atoms. A corollary to the atomistic interpretation is that Planck's derivation can no longer be construed as support for the postulate that material oscillating entities can have only those energies that are multiples of hν. Copyright (2000) CSIRO Australia

Optimal kernel shape and bandwidth for atomistic support of continuum stress

International Nuclear Information System (INIS)

Ulz, Manfred H; Moran, Sean J

2013-01-01

The treatment of atomistic scale interactions via molecular dynamics simulations has recently found favour for multiscale modelling within engineering. The estimation of stress at a continuum point on the atomistic scale requires a pre-defined kernel function. This kernel function derives the stress at a continuum point by averaging the contribution from atoms within a region surrounding the continuum point. This averaging volume, and therefore the associated stress at a continuum point, is highly dependent on the bandwidth and shape of the kernel. In this paper we propose an effective and entirely data-driven strategy for simultaneously computing the optimal shape and bandwidth for the kernel. We thoroughly evaluate our proposed approach on copper using three classical elasticity problems. Our evaluation yields three key findings: firstly, our technique can provide a physically meaningful estimation of kernel bandwidth; secondly, we show that a uniform kernel is preferred, thereby justifying the default selection of this kernel shape in future work; and thirdly, we can reliably estimate both of these attributes in a data-driven manner, obtaining values that lead to an accurate estimation of the stress at a continuum point. (paper)

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.

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...

3d visualization of atomistic simulations on every desktop

Science.gov (United States)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-08-01

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

3d visualization of atomistic simulations on every desktop

International Nuclear Information System (INIS)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-01-01

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

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

Kinetic modeling of the photocatalytic degradation of clofibric acid in a slurry reactor.

Science.gov (United States)

Manassero, Agustina; Satuf, María Lucila; Alfano, Orlando Mario

2015-01-01

A kinetic study of the photocatalytic degradation of the pharmaceutical clofibric acid is presented. Experiments were carried out under UV radiation employing titanium dioxide in water suspension. The main reaction intermediates were identified and quantified. Intrinsic expressions to represent the kinetics of clofibric acid and the main intermediates were derived. The modeling of the radiation field in the reactor was carried out by Monte Carlo simulation. Experimental runs were performed by varying the catalyst concentration and the incident radiation. Kinetic parameters were estimated from the experiments by applying a non-linear regression procedure. Good agreement was obtained between model predictions and experimental data, with an error of 5.9 % in the estimations of the primary pollutant concentration.

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

Science.gov (United States)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

Recent developments of JAEA's Monte Carlo Code MVP for reactor physics applications

International Nuclear Information System (INIS)

Nagaya, Y.; Okumura, K.; Mori, T.

2013-01-01

MVP is a general-purpose continuous-energy Monte Carlo code for neutron and photon transport calculations that has been developed since the late 1980's at Japan Atomic Energy Agency (JAEA, formerly JAERI). The MVP code is designed for nuclear reactor applications such as reactor core design/analysis, criticality safety and reactor shielding. This paper describes the MVP code and present its latest developments. Among the new capabilities of MVP we find: -) the perturbation method has been implemented for the change in k(eff); -) the eigenvalue calculations can be performed with an explicit treatment of delayed neutrons in which their fission spectra are taken into account; -) the capability of tallying the scattering matrix (group-to-group scattering cross sections); -) the implementation of an exact model for resonance elastic scattering; and -) a Monte Carlo perturbation technique is used to calculate reactor kinetics parameters

Monte Carlo simulations of lattice models for single polymer systems

Science.gov (United States)

Hsu, Hsiao-Ping

2014-10-01

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length N ˜ O(10^4). Based on the standard simple cubic lattice model (SCLM) with fixed bond length and the bond fluctuation model (BFM) with bond lengths in a range between 2 and sqrt{10}, we investigate the conformations of polymer chains described by self-avoiding walks on the simple cubic lattice, and by random walks and non-reversible random walks in the absence of excluded volume interactions. In addition to flexible chains, we also extend our study to semiflexible chains for different stiffness controlled by a bending potential. The persistence lengths of chains extracted from the orientational correlations are estimated for all cases. We show that chains based on the BFM are more flexible than those based on the SCLM for a fixed bending energy. The microscopic differences between these two lattice models are discussed and the theoretical predictions of scaling laws given in the literature are checked and verified. Our simulations clarify that a different mapping ratio between the coarse-grained models and the atomistically realistic description of polymers is required in a coarse-graining approach due to the different crossovers to the asymptotic behavior.

Monte Carlo simulations of lattice models for single polymer systems

International Nuclear Information System (INIS)

Hsu, Hsiao-Ping

2014-01-01

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length N∼O(10 4 ). Based on the standard simple cubic lattice model (SCLM) with fixed bond length and the bond fluctuation model (BFM) with bond lengths in a range between 2 and √(10), we investigate the conformations of polymer chains described by self-avoiding walks on the simple cubic lattice, and by random walks and non-reversible random walks in the absence of excluded volume interactions. In addition to flexible chains, we also extend our study to semiflexible chains for different stiffness controlled by a bending potential. The persistence lengths of chains extracted from the orientational correlations are estimated for all cases. We show that chains based on the BFM are more flexible than those based on the SCLM for a fixed bending energy. The microscopic differences between these two lattice models are discussed and the theoretical predictions of scaling laws given in the literature are checked and verified. Our simulations clarify that a different mapping ratio between the coarse-grained models and the atomistically realistic description of polymers is required in a coarse-graining approach due to the different crossovers to the asymptotic behavior

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

DEFF Research Database (Denmark)

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

2011-01-01

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

Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification

Science.gov (United States)

Swinburne, Thomas D.; Perez, Danny

2018-05-01

A massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.

A first principles kinetic Monte Carlo investigation of the adsorption and mobility of gadolinium on the (100) surface of tungsten

International Nuclear Information System (INIS)

Samin, Adib J.; Zhang, Jinsuo

2017-01-01

An accurate characterization of lanthanide adsorption and mobility on tungsten surfaces is important for pyroprocessing. In the present study, the adsorption and diffusion of gadolinium on the (100) surface of tungsten was investigated. It was found that the hollow sites were the most energetically favorable for the adsorption. It was further observed that a magnetic moment was induced following the adsorption of gadolinium on the tungsten surface and that the system with adsorbed hollow sites had the largest magnetization. A pathway for the surface diffusion of gadolinium was determined to occur by hopping between the nearest neighbor hollow sites via the bridge site and the activation energy for the hop was calculated to be 0.75 eV. The surface diffusion process was further assessed using two distinct kinetic Monte Carlo models; one that accounted for lateral adsorbate interactions up to the second nearest neighbor and one that did not account for such interatomic interactions in the adlayer. When the lateral interactions were included in the simulations, the diffusivity was observed to have a strong dependence on coverage (for the coverage values being studied). The effects of lateral interactions were further observed in a one-dimensional simulation of the diffusion equation where the asymmetry in the surface coverage profile upon its approach to a steady state distribution was clear in comparison with the simulations which did not account for those interactions.

Investigation of resistance switching in SiO x RRAM cells using a 3D multi-scale kinetic Monte Carlo simulator

Science.gov (United States)

Sadi, Toufik; Mehonic, Adnan; Montesi, Luca; Buckwell, Mark; Kenyon, Anthony; Asenov, Asen

2018-02-01

We employ an advanced three-dimensional (3D) electro-thermal simulator to explore the physics and potential of oxide-based resistive random-access memory (RRAM) cells. The physical simulation model has been developed recently, and couples a kinetic Monte Carlo study of electron and ionic transport to the self-heating phenomenon while accounting carefully for the physics of vacancy generation and recombination, and trapping mechanisms. The simulation framework successfully captures resistance switching, including the electroforming, set and reset processes, by modeling the dynamics of conductive filaments in the 3D space. This work focuses on the promising yet less studied RRAM structures based on silicon-rich silica (SiO x ) RRAMs. We explain the intrinsic nature of resistance switching of the SiO x layer, analyze the effect of self-heating on device performance, highlight the role of the initial vacancy distributions acting as precursors for switching, and also stress the importance of using 3D physics-based models to capture accurately the switching processes. The simulation work is backed by experimental studies. The simulator is useful for improving our understanding of the little-known physics of SiO x resistive memory devices, as well as other oxide-based RRAM systems (e.g. transition metal oxide RRAMs), offering design and optimization capabilities with regard to the reliability and variability of memory cells.

A first principles kinetic Monte Carlo investigation of the adsorption and mobility of gadolinium on the (100) surface of tungsten

Energy Technology Data Exchange (ETDEWEB)

Samin, Adib J., E-mail: samin.2@osu.edu; Zhang, Jinsuo

2017-05-15

An accurate characterization of lanthanide adsorption and mobility on tungsten surfaces is important for pyroprocessing. In the present study, the adsorption and diffusion of gadolinium on the (100) surface of tungsten was investigated. It was found that the hollow sites were the most energetically favorable for the adsorption. It was further observed that a magnetic moment was induced following the adsorption of gadolinium on the tungsten surface and that the system with adsorbed hollow sites had the largest magnetization. A pathway for the surface diffusion of gadolinium was determined to occur by hopping between the nearest neighbor hollow sites via the bridge site and the activation energy for the hop was calculated to be 0.75 eV. The surface diffusion process was further assessed using two distinct kinetic Monte Carlo models; one that accounted for lateral adsorbate interactions up to the second nearest neighbor and one that did not account for such interatomic interactions in the adlayer. When the lateral interactions were included in the simulations, the diffusivity was observed to have a strong dependence on coverage (for the coverage values being studied). The effects of lateral interactions were further observed in a one-dimensional simulation of the diffusion equation where the asymmetry in the surface coverage profile upon its approach to a steady state distribution was clear in comparison with the simulations which did not account for those interactions.

Investigation of resistance switching in SiO x RRAM cells using a 3D multi-scale kinetic Monte Carlo simulator.

Science.gov (United States)

Sadi, Toufik; Mehonic, Adnan; Montesi, Luca; Buckwell, Mark; Kenyon, Anthony; Asenov, Asen

2018-02-28

We employ an advanced three-dimensional (3D) electro-thermal simulator to explore the physics and potential of oxide-based resistive random-access memory (RRAM) cells. The physical simulation model has been developed recently, and couples a kinetic Monte Carlo study of electron and ionic transport to the self-heating phenomenon while accounting carefully for the physics of vacancy generation and recombination, and trapping mechanisms. The simulation framework successfully captures resistance switching, including the electroforming, set and reset processes, by modeling the dynamics of conductive filaments in the 3D space. This work focuses on the promising yet less studied RRAM structures based on silicon-rich silica (SiO x ) RRAMs. We explain the intrinsic nature of resistance switching of the SiO x layer, analyze the effect of self-heating on device performance, highlight the role of the initial vacancy distributions acting as precursors for switching, and also stress the importance of using 3D physics-based models to capture accurately the switching processes. The simulation work is backed by experimental studies. The simulator is useful for improving our understanding of the little-known physics of SiO x resistive memory devices, as well as other oxide-based RRAM systems (e.g. transition metal oxide RRAMs), offering design and optimization capabilities with regard to the reliability and variability of memory cells.

Direct simulation Monte Carlo method for the Uehling-Uhlenbeck-Boltzmann equation.

Science.gov (United States)

Garcia, Alejandro L; Wagner, Wolfgang

2003-11-01

In this paper we describe a direct simulation Monte Carlo algorithm for the Uehling-Uhlenbeck-Boltzmann equation in terms of Markov processes. This provides a unifying framework for both the classical Boltzmann case as well as the Fermi-Dirac and Bose-Einstein cases. We establish the foundation of the algorithm by demonstrating its link to the kinetic equation. By numerical experiments we study its sensitivity to the number of simulation particles and to the discretization of the velocity space, when approximating the steady-state distribution.

SCT: a suite of programs for comparing atomistic models with small-angle scattering data.

Science.gov (United States)

Wright, David W; Perkins, Stephen J

2015-06-01

Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.

General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium Green's function

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce...... an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-Vbias curve simulations. We apply...... interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid...

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

International Nuclear Information System (INIS)

Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

2014-01-01

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

Simulation of the microstructural evolution under irradiation of dilute Fe-CuNiMnSi alloys by atomic kinetic monte Carlo model based on ab initio data

International Nuclear Information System (INIS)

Vincent, E.; Domain, C.; Vincent, E.; Becquart, C.S.

2008-01-01

Full text of publication follows. The embrittlement and the hardening of pressure vessel steels under radiation has been correlated with the presence solutes such as Cu, Ni, Mn and Si. Indeed it has been observed that under irradiation, these solutes tend to gather to form more or less dilute clusters. The interactions of these solutes with radiation induced point defects thus need to be characterised properly in order to understand the elementary mechanisms behind the formation of these clusters. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects (vacancies as well as interstitials) with solute atoms in dilute FeX alloys (X Cu, Mn, Ni or Si) in order to build a database used to parameterize an atomic kinetic Monte Carlo model. The model has been applied to simulate thermal ageing as well as irradiation conditions in dilute Fe-CuNiMnSi alloys. Results obtained with this model will be presented. (authors)

PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

Directory of Open Access Journals (Sweden)

Radhakrishna Bettadapura

2015-10-01

Full Text Available There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data, and 3D reconstructed cryo-electron microscopy (3D EM maps (albeit at coarser resolution of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2 fit (Polar Fast Fourier Fitting for the best possible structural alignment of atomistic structures with 3D EM. While PF(2 fit enables only a rigid, six dimensional (6D alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

Atomistic simulation and continuum modeling of graphene nanoribbons under uniaxial tension

International Nuclear Information System (INIS)

Lu, Qiang; Gao, Wei; Huang, Rui

2011-01-01

Atomistic simulations are performed to study the nonlinear mechanical behavior of graphene nanoribbons under quasistatic uniaxial tension, emphasizing the effects of edge structures (armchair and zigzag, without and with hydrogen passivation) on elastic modulus and fracture strength. The numerical results are analyzed within a theoretical model of thermodynamics, which enables determination of the bulk strain energy density, the edge energy density and the hydrogen adsorption energy density as nonlinear functions of the applied strain based on static molecular mechanics simulations. These functions can be used to describe mechanical behavior of graphene nanoribbons from the initial linear elasticity to fracture. It is found that the initial Young's modulus of a graphene nanoribbon depends on the ribbon width and the edge chirality. Furthermore, it is found that the nominal strain to fracture is considerably lower for graphene nanoribbons with armchair edges than for ribbons with zigzag edges. Molecular dynamics simulations reveal two distinct fracture nucleation mechanisms: homogeneous nucleation for the zigzag-edged graphene nanoribbons and edge-controlled heterogeneous nucleation for the armchair-edged ribbons. The modeling and simulations in this study highlight the atomistic mechanisms for the nonlinear mechanical behavior of graphene nanoribbons with the edge effects, which is potentially important for developing integrated graphene-based devices

An atomistic fingerprint algorithm for learning ab initio molecular force fields

Science.gov (United States)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Multiscale modelling of nanostructures

International Nuclear Information System (INIS)

Vvedensky, Dimitri D

2004-01-01

Most materials phenomena are manifestations of processes that are operative over a vast range of length and time scales. A complete understanding of the behaviour of materials thereby requires theoretical and computational tools that span the atomic-scale detail of first-principles methods and the more coarse-grained description provided by continuum equations. Recent efforts have focused on combining traditional methodologies-density functional theory, molecular dynamics, Monte Carlo methods and continuum descriptions-within a unified multiscale framework. This review covers the techniques that have been developed to model various aspects of materials behaviour with the ultimate aim of systematically coupling the atomistic to the continuum descriptions. The approaches described typically have been motivated by particular applications but can often be applied in wider contexts. The self-assembly of quantum dot ensembles will be used as a case study for the issues that arise and the methods used for all nanostructures. Although quantum dots can be obtained with all the standard growth methods and for a variety of material systems, their appearance is a quite selective process, involving the competition between equilibrium and kinetic effects, and the interplay between atomistic and long-range interactions. Most theoretical models have addressed particular aspects of the ordering kinetics of quantum dot ensembles, with far fewer attempts at a comprehensive synthesis of this inherently multiscale phenomenon. We conclude with an assessment of the current status of multiscale modelling strategies and highlight the main outstanding issues. (topical review)

Point Genetics: A New Concept to Assess Neutron Kinetics

International Nuclear Information System (INIS)

Klein Meulekamp, R.; Kuijper, J.C.; Schikorr, M.

2005-01-01

Point genetic equations are introduced. These equations are similar to the well-known point kinetic equations but characterize and couple individual fission generations in subcritical systems. Point genetic equations are able to describe dynamic behavior of source-driven subcritical systems on shorter timescales than is possible with point kinetic equations. Point genetic parameters can be used as a first-order characterization of the system and can be calculated using standard Monte Carlo techniques; the implementation in other calculational schemes seems straightforward. A Godiva sphere is considered to show the applicability of the point genetic equations in describing a detector response on short timescales. For this system the point genetic parameters are calculated and compared with reference calculations. Typical dynamic source behavior is considered by studying a transient in which the neutron source energy decreases from 20 to 1 MeV. For all cases studied, the point genetic equations are compared to full space-time kinetic solutions, and it is shown that point genetics performs well

Inter-ribbon tunneling in graphene: An atomistic Bardeen approach

Energy Technology Data Exchange (ETDEWEB)

Van de Put, Maarten L., E-mail: maarten.vandeput@uantwerpen.be; Magnus, Wim [Department of Physics, Universiteit Antwerpen, B-2020 Antwerpen (Belgium); imec, B-3001 Heverlee (Belgium); Vandenberghe, William G.; Fischetti, Massimo V. [Department of Material Science, University of Texas at Dallas, Texas 75080 (United States); Sorée, Bart [Department of Physics, Universiteit Antwerpen, B-2020 Antwerpen (Belgium); imec, B-3001 Heverlee (Belgium); Department of Electrical Engineering, KU Leuven, B-3001 Leuven (Belgium)

2016-06-07

A weakly coupled system of two crossed graphene nanoribbons exhibits direct tunneling due to the overlap of the wavefunctions of both ribbons. We apply the Bardeen transfer Hamiltonian formalism, using atomistic band structure calculations to account for the effect of the atomic structure on the tunneling process. The strong quantum-size confinement of the nanoribbons is mirrored by the one-dimensional character of the electronic structure, resulting in properties that differ significantly from the case of inter-layer tunneling, where tunneling occurs between bulk two-dimensional graphene sheets. The current-voltage characteristics of the inter-ribbon tunneling structures exhibit resonance, as well as stepwise increases in current. Both features are caused by the energetic alignment of one-dimensional peaks in the density-of-states of the ribbons. Resonant tunneling occurs if the sign of the curvature of the coupled energy bands is equal, whereas a step-like increase in the current occurs if the signs are opposite. Changing the doping modulates the onset-voltage of the effects as well as their magnitude. Doping through electrostatic gating makes these structures promising for application towards steep slope switching devices. Using the atomistic empirical pseudopotentials based Bardeen transfer Hamiltonian method, inter-ribbon tunneling can be studied for the whole range of two-dimensional materials, such as transition metal dichalcogenides. The effects of resonance and of step-like increases in the current we observe in graphene ribbons are also expected in ribbons made from these alternative two-dimensional materials, because these effects are manifestations of the one-dimensional character of the density-of-states.

Experimentally driven atomistic model of 1,2 polybutadiene

Energy Technology Data Exchange (ETDEWEB)

Gkourmpis, Thomas, E-mail: thomas.gkourmpis@borealisgroup.com [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Mitchell, Geoffrey R. [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Centre for Rapid and Sustainable Product Development, Institute Polytechnic Leiria, Marinha Grande (Portugal)

2014-02-07

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

Ab-initio and atomistic study of the ferroelectric properties of Cu doped potassium niobate

Energy Technology Data Exchange (ETDEWEB)

Koerbel, Sabine; Elsaesser, Christian [Fraunhofer-Institut fuer Werkstoffmechanik IWM, Woehlerstrasse 11, 79108 Freiburg (Germany)

2011-07-01

KNbO{sub 3} is one end member of the solid solution (K,Na)NbO{sub 3} (KNN), which has promising ferroelectric properties to become a future lead-free substitute for lead zirconate titanate Pb(Zr,Ti)O{sub 3} (PZT) in piezoelectric actors and sensors. Both KNN and PZT exhibit a phase transition with composition and a morphotropic phase boundary, at which enhanced piezoelectric coefficients are obtained. The material properties of PZT and KNN are commonly optimized by doping. E.g., CuO can be added when fabricating KNN as a sintering aid. Ab initio density functional theory and atomistic simulation using a classical shell model potential have been combined to investigate low Cu concentrations in the KNbO{sub 3}-CuNbO{sub 3} system. The atomistic model predicts a morphotropic phase boundary at a few percent Cu, analogous to the one found in the LiNbO{sub 3}-KNbO{sub 3} system.

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

International Nuclear Information System (INIS)

Tabe, Michiharu; Tan, Hoang Nhat; Mizuno, Takeshi; Muruganathan, Manoharan; Anh, Le The; Mizuta, Hiroshi; Nuryadi, Ratno; Moraru, Daniel

2016-01-01

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.

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.

Characterizing Quality Factor of Niobium Resonators Using a Markov Chain Monte Carlo Approach

Energy Technology Data Exchange (ETDEWEB)

Basu Thakur, Ritoban; Tang, Qing Yang; McGeehan, Ryan; Carter, Faustin; Shirokoff, Erik

2017-06-01

The next generation of radiation detectors in high precision Cosmology, Astronomy, and particle-astrophysics experiments will rely heavily on superconducting microwave resonators and kinetic inductance devices. Understanding the physics of energy loss in these devices, in particular at low temperatures and powers, is vital. We present a comprehensive analysis framework, using Markov Chain Monte Carlo methods, to characterize loss due to two-level system in concert with quasi-particle dynamics in thin-film Nb resonators in the GHz range.

Heterogeneous precipitation of niobium carbide in the ferrite by Monte Carlo simulations

International Nuclear Information System (INIS)

Hin, C.

2005-12-01

The precipitation of niobium carbides in industrial steels is commonly used to control the recrystallization process or the amount of interstitial atoms in solid solution. It is then important to understand the precipitation kinetics and especially the competition between homogeneous and heterogeneous precipitation, since both of them have been observed experimentally, depending on they alloy composition, microstructure and thermal treatments. We propose Monte Carlo simulations of NbC precipitation in □-iron, based on a simple atomic description of the main parameters which control the kinetic pathway: - Realistic diffusion properties, with a rapid diffusion of C atoms by interstitial jumps and a slower diffusion of Fe and Nb atoms by vacancy jumps; - A model of grain boundaries which reproduces the segregation properties of Nb and C; - A model of dislocation which interacts with solute atoms through local segregation energies and long range elastic field; - A point defect source which drives the vacancy concentration towards its equilibrium value. Depending on the precipitation conditions, Monte Carlo simulations predict different kinetic behaviors, including a transient precipitation of metastable carbides, an early segregation stage of C, wetting phenomena at grain boundaries and on dislocations and a competition between homogeneous and heterogeneous NbC precipitation. Concerning the last point, we highlight that long range elastic field due to dislocation favors clearly the heterogeneous precipitation on dislocations. To understand this effect, we have developed a heterogeneous nucleation model including the calculation of the local concentration of solute atoms around the dislocation, the change of the solubility limit relative to the solubility limit in bulk and the energy of precipitates in an elastic field. We have concluded that elastic field favors the heterogeneous precipitation through the fall in nucleation barrier. (author)

An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

Energy Technology Data Exchange (ETDEWEB)

Wang, Zhi [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Jiang, Xiang-Wei; Li, Shu-Shen [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Wang, Lin-Wang, E-mail: lwwang@lbl.gov [Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2014-03-24

We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10{sup 5} atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose.

An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

International Nuclear Information System (INIS)

Wang, Zhi; Jiang, Xiang-Wei; Li, Shu-Shen; Wang, Lin-Wang

2014-01-01

We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10 5 atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose

Crystalline cellulose elastic modulus predicted by atomistic models of uniform deformation and nanoscale indentation

Science.gov (United States)

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

The elastic modulus of cellulose Iß in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive...

Finite element analysis of an atomistically derived cohesive model for brittle fracture

International Nuclear Information System (INIS)

Lloyd, J T; McDowell, D L; Zimmerman, J A; Jones, R E; Zhou, X W

2011-01-01

In order to apply information from molecular dynamics (MD) simulations in problems governed by engineering length and time scales, a coarse graining methodology must be used. In previous work by Zhou et al (2009 Acta Mater. 57 4671–86), a traction-separation cohesive model was developed using results from MD simulations with atomistic-to-continuum measures of stress and displacement. Here, we implement this cohesive model within a combined finite element/cohesive surface element framework (referred to as a finite element approach or FEA), and examine the ability for the atomistically informed FEA to directly reproduce results from MD. We find that FEA shows close agreement of both stress and crack opening displacement profiles at the cohesive interface, although some differences do exist that can be attributed to the stochastic nature of finite temperature MD. The FEA methodology is then used to study slower loading rates that are computationally expensive for MD. We find that the crack growth process initially exhibits a rate-independent relationship between crack length and boundary displacement, followed by a rate-dependent regime where, at a given amount of boundary displacement, a lower applied strain rate produces a longer crack length. Our method is also extended to larger length scales by simulating a compact tension fracture-mechanics specimen with sub-micrometer dimensions. Such a simulation shows a computational speedup of approximately four orders of magnitude over conventional atomistic simulation, while exhibiting the expected fracture-mechanics response. Finally, differences between FEA and MD are explored with respect to ensemble and temperature effects in MD, and their impact on the cohesive model and crack growth behavior. These results enable us to make several recommendations to improve the methodology used to derive cohesive laws from MD simulations. In light of this work, which has critical implications for efforts to derive continuum laws

Monte Carlo methods

Directory of Open Access Journals (Sweden)

Bardenet Rémi

2013-07-01

Full Text Available Bayesian inference often requires integrating some function with respect to a posterior distribution. Monte Carlo methods are sampling algorithms that allow to compute these integrals numerically when they are not analytically tractable. We review here the basic principles and the most common Monte Carlo algorithms, among which rejection sampling, importance sampling and Monte Carlo Markov chain (MCMC methods. We give intuition on the theoretical justification of the algorithms as well as practical advice, trying to relate both. We discuss the application of Monte Carlo in experimental physics, and point to landmarks in the literature for the curious reader.

Enhanced Generic Phase-field Model of Irradiation Materials: Fission Gas Bubble Growth Kinetics in Polycrystalline UO2

Energy Technology Data Exchange (ETDEWEB)

Li, Yulan; Hu, Shenyang Y.; Montgomery, Robert O.; Gao, Fei; Sun, Xin

2012-05-30

Experiments show that inter-granular and intra-granular gas bubbles have different growth kinetics which results in heterogeneous gas bubble microstructures in irradiated nuclear fuels. A science-based model predicting the heterogeneous microstructure evolution kinetics is desired, which enables one to study the effect of thermodynamic and kinetic properties of the system on gas bubble microstructure evolution kinetics and morphology, improve the understanding of the formation mechanisms of heterogeneous gas bubble microstructure, and provide the microstructure to macroscale approaches to study their impact on thermo-mechanical properties such as thermo-conductivity, gas release, volume swelling, and cracking. In our previous report 'Mesoscale Benchmark Demonstration, Problem 1: Mesoscale Simulations of Intra-granular Fission Gas Bubbles in UO2 under Post-irradiation Thermal Annealing', we developed a phase-field model to simulate the intra-granular gas bubble evolution in a single crystal during post-irradiation thermal annealing. In this work, we enhanced the model by incorporating thermodynamic and kinetic properties at grain boundaries, which can be obtained from atomistic simulations, to simulate fission gas bubble growth kinetics in polycrystalline UO2 fuels. The model takes into account of gas atom and vacancy diffusion, vacancy trapping and emission at defects, gas atom absorption and resolution at gas bubbles, internal pressure in gas bubbles, elastic interaction between defects and gas bubbles, and the difference of thermodynamic and kinetic properties in matrix and grain boundaries. We applied the model to simulate gas atom segregation at grain boundaries and the effect of interfacial energy and gas mobility on gas bubble morphology and growth kinetics in a bi-crystal UO2 during post-irradiation thermal annealing. The preliminary results demonstrate that the model can produce the equilibrium thermodynamic properties and the morphology of gas

The spatial kinetic analysis of accelerator-driven subcritical reactor

International Nuclear Information System (INIS)

Takahashi, H.; An, Y.; Chen, X.

1998-02-01

The operation of the accelerator driven reactor with subcritical condition provides a more flexible choice of the reactor materials and of design parameters. A deep subcriticality is chosen sometime from the analysis of point kinetics. When a large reactor is operated in deep subcritical condition by using a localized spallation source, the power distribution has strong spatial dependence, and point kinetics does not provide proper analysis for reactor safety. In order to analyze the spatial and energy dependent kinetic behavior in the subcritical reactor, the authors developed a computation code which is composed of two parts, the first one is for creating the group cross section and the second part solves the multi-group kinetic diffusion equations. The reactor parameters such as the cross section of fission, scattering, and energy transfer among the several energy groups and regions are calculated by using a code modified from the Monte Carlo codes MCNPA and LAHET instead of the usual analytical method of ANISN, TWOTRAN codes. Thus the complicated geometry of the accelerator driven reactor core can be precisely taken into account. The authors analyzed the subcritical minor actinide transmutor studied by Japan Atomic Energy Research Institute (JAERI) using the code

Nanoclusters in bcc-Fe containing vacancies, copper and nickel: Structure and energetics

International Nuclear Information System (INIS)

Al-Motasem, A.T.; Posselt, M.; Bergner, F.

2011-01-01

Highlights: → Fe-Cu-Ni model alloys for RPV steels. → Atomistic simulation, mainly MMC and MD simulations. → Finding the most stable configurations of defect clusters. → Energetics of clusters, formation and binding energies. → Size dependence of monomer binding energy formula as input for OKMC methods. - Abstract: The most stable atomic configuration of coherent nanoclusters in bcc-Fe formed by vacancies, Cu and Ni as well as the corresponding energetics are determined by on-lattice simulated annealing and subsequent off-lattice relaxation. An interatomic potential recently designed for investigations of radiation-induced effects in the ternary Fe-Cu-Ni system is used in the atomistic simulations. Ternary v l Cu m Ni n clusters show a core-shell structure with vacancies in the core coated by a shell of Cu atoms, followed by a shell of Ni atoms. In binary Cu m Ni n clusters the Cu core is covered by a shell of Ni atoms. On the contrary, binary v l Ni n clusters consist of a pure vacancy cluster surrounded by an agglomeration of Ni atoms. The latter is similar to a pure Ni cluster (Ni n ) and consists of Ni atoms at the second nearest neighbor distance. Because of this special arrangement of atoms v l Ni n and Ni n are also called quasi-clusters. In all clusters investigated Ni atoms may be nearest neighbors of Cu atoms but never nearest neighbors of vacancies or other Ni atoms. The atomic configurations found can be understood by the peculiarities of the binding between vacancies, Cu, Ni and Fe atoms. The structure obtained for Cu m Ni n clusters is in agreement with previous theoretical results and with indications from measurements while for the other clusters reference data are not available. It is shown that the presence of Ni atoms promotes the nucleation of clusters containing vacancies and Cu. This is in agreement with experimental observations and with recent results of atomic kinetic Monte Carlo simulations. Based on the specific atomic structure

Thermodynamic properties of water in confined environments: a Monte Carlo study

Science.gov (United States)

Gladovic, Martin; Bren, Urban; Urbic, Tomaž

2018-05-01

Monte Carlo simulations of Mercedes-Benz water in a crowded environment were performed. The simulated systems are representative of both composite, porous or sintered materials and living cells with typical matrix packings. We studied the influence of overall temperature as well as the density and size of matrix particles on water density, particle distributions, hydrogen bond formation and thermodynamic quantities. Interestingly, temperature and space occupancy of matrix exhibit a similar effect on water properties following the competition between the kinetic and the potential energy of the system, whereby temperature increases the kinetic and matrix packing decreases the potential contribution. A novel thermodynamic decomposition approach was applied to gain insight into individual contributions of different types of inter-particle interactions. This decomposition proved to be useful and in good agreement with the total thermodynamic quantities especially at higher temperatures and matrix packings, where higher-order potential-energy mixing terms lose their importance.

Effect of Pore Geometry on Gas Adsorption: Grand Canonical Monte Carlo Simulation Studies

International Nuclear Information System (INIS)

Lee, Eon Ji; Chang, Rak Woo; Han, Ji Hyung; Chung, Taek Dong

2012-01-01

In this study, we investigated the pure geometrical effect of porous materials in gas adsorption using the grand canonical Monte Carlo simulations of primitive gas-pore models with various pore geometries such as planar, cylindrical, and random pore geometries. Although the model does not possess atomistic level details of porous materials, our simulation results provided many insightful information in the effect of pore geometry on the adsorption behavior of gas molecules. First, the surface curvature of porous materials plays a significant role in the amount of adsorbed gas molecules: the concave surface such as in cylindrical pores induces more attraction between gas molecules and pore, which results in the enhanced gas adsorption. On the contrary, the convex surface of random pores gives the opposite effect. Second, this geometrical effect shows a nonmonotonic dependence on the gas-pore interaction strength and length. Third, as the external gas pressure is increased, the change in the gas adsorption due to pore geometry is reduced. Finally, the pore geometry also affects the collision dynamics of gas molecules. Since our model is based on primitive description of fluid molecules, our conclusion can be applied to any fluidic systems including reactant-electrode systems

Kinetics of heterogeneous catalysis oxidation of carbon monoxide

International Nuclear Information System (INIS)

Khawaja, Y.; Sadiq, A.

1987-10-01

An irreversible kinetic surface-reaction model, based upon the reaction of carbon monoxide nd oxygen on a catalyst surface is investigated by means of Monte Carlo simulation. The adsorbed molecules/atoms on the surface undergo both first and second order kinetic phase transitions. The first order transition is found to occur at x/sub/co=x/sub/2=0.5255 with an error bar of 0.0003, where x/sub/co is the concentration of carbon monoxide in the gas phase. The time evolution of this catalytic reaction is studied both analytically and by computer simulation. Slightly above x/sub/2, the oxygen coverage relaxation time for the oxygen is found to diverage as the inverse of 3.54 times the absolute of the difference of x/sub/2 and x/sub/co. (orig./A.B.)

The application of polynomial chaos methods to a point kinetics model of MIPR: An Aqueous Homogeneous Reactor

International Nuclear Information System (INIS)

Cooling, C.M.; Williams, M.M.R.; Nygaard, E.T.; Eaton, M.D.

2013-01-01

Highlights: • A point kinetics model for the Medical Isotope Production Reactor is formulated. • Reactivity insertions are simulated using this model. • Polynomial chaos is used to simulate uncertainty in reactor parameters. • The computational efficiency of polynomial chaos is compared to that of Monte Carlo. -- Abstract: This paper models a conceptual Medical Isotope Production Reactor (MIPR) using a point kinetics model which is used to explore power excursions in the event of a reactivity insertion. The effect of uncertainty of key parameters is modelled using intrusive polynomial chaos. It is found that the system is stable against reactivity insertions and power excursions are all bounded and tend towards a new equilibrium state due to the negative feedbacks inherent in Aqueous Homogeneous Reactors (AHRs). The Polynomial Chaos Expansion (PCE) method is found to be much more computationally efficient than that of Monte Carlo simulation in this application

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.

Monte Carlo simulation of atomic short range order and cluster formation in two dimensional model alloys

International Nuclear Information System (INIS)

Rojas T, J.; Instituto Peruano de Energia Nuclear, Lima; Manrique C, E.; Torres T, E.

2002-01-01

Using monte Carlo simulation have been carried out an atomistic description of the structure and ordering processes in the system Cu-Au in a two-dimensional model. The ABV model of the alloy is a system of N atoms A and B, located in rigid lattice with some vacant sites. In the model we assume pair wise interactions between nearest neighbors with constant ordering energy J = 0,03 eV. The dynamics was introduced by means of a vacancy that exchanges of place with any atom of its neighbors. The simulations were carried out in a square lattice with 1024 and 4096 particles, using periodic boundary conditions to avoid border effects. We calculate the first two parameters of short range order of Warren-Cowley as function of the concentration and temperature. It was also studied the probabilities of formation of different atomic clusters that consist of 9 atoms as function of the concentration of the alloy and temperatures in a wide range of values. In some regions of temperature and concentration it was observed compositional and thermal polymorphism

Atomistic simulations of dislocation-precipitate interactions emphasize importance of cross-slip

International Nuclear Information System (INIS)

Singh, C.V.; Mateos, A.J.; Warner, D.H.

2011-01-01

This work examines the interaction of screw dislocations with Guinier-Preston (GP) zones using atomistic simulations. Both Orowan looping and cross-slip mechanisms are found to control the interactions. Cross-slip, occurring both at zero and finite temperatures, is found to either significantly reduce or enhance precipitate strengthening, depending upon the orientation of the dislocation-GP zone interaction. The orientation dependence, and its dependence on temperature, provides a micromechanical explanation for the experiments of Muraishi et al. (Philos. Mag. A 82 (2002) 2755).

Progress on RMC: a Monte Carlo neutron transport code for reactor analysis

International Nuclear Information System (INIS)

Wang, Kan; Li, Zeguang; She, Ding; Liu, Yuxuan; Xu, Qi; Shen, Huayun; Yu, Ganglin

2011-01-01

This paper presents a new 3-D Monte Carlo neutron transport code named RMC (Reactor Monte Carlo code), specifically intended for reactor physics analysis. This code is being developed by Department of Engineering Physics in Tsinghua University and written in C++ and Fortran 90 language with the latest version of RMC 2.5.0. The RMC code uses the method known as the delta-tracking method to simulate neutron transport, the advantages of which include fast simulation in complex geometries and relatively simple handling of complicated geometrical objects. Some other techniques such as computational-expense oriented method and hash-table method have been developed and implemented in RMC to speedup the calculation. To meet the requirements of reactor analysis, the RMC code has the calculational functions including criticality calculation, burnup calculation and also kinetics simulation. In this paper, comparison calculations of criticality problems, burnup problems and transient problems are carried out using RMC code and other Monte Carlo codes, and the results show that RMC performs quite well in these kinds of problems. Based on MPI, RMC succeeds in parallel computation and represents a high speed-up. This code is still under intensive development and the further work directions are mentioned at the end of this paper. (author)

Resolution of the diffusional paradox predicting infinitely fast kinetics on the nanoscale

Science.gov (United States)

Beke, D. L.; Erdélyi, Z.

2006-01-01

In our paper, we offer a natural resolution for a long-standing paradox in diffusion. We show that the growth rate of the diffusion zone (reaction layer) should not go to infinity with decreasing time (as 1/t ), just because the diffusion permeability of the interface is finite. Expression for the changeover thickness X* between the linear and parabolic regimes of the interface shift in phase separating binary A(B) systems is derived in the framework of a deterministic atomistic model for diffusion. X* lies typically between 0.01 and 300nm , depending on the composition dependence of the diffusion coefficient and the phase separation tendency of the alloy. While in ideal binary alloys with composition independent diffusivity, the deviation from the parabolic law practically cannot be observed, in real systems (where the diffusion coefficient can change several orders of magnitude with the composition), measurable deviations are expected as it was experimentally observed very recently in the Ni/Cu and Au/Ni systems. We also offer an atomistic explanation for the phenomenological interface transfer coefficient K . It measures the finite interface permeability (proportional to the jump frequency across the interface) and thus it controls the shift of the interface at short times (diffusion distances). Although it is almost exclusively accepted in the literature that linear growth kinetics are the result of interface reaction control, our results suggest that the linear or nonparabolic growth of a reaction layer on the nanoscale cannot be automatically interpreted by an interface reaction.

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

Science.gov (United States)

Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas

2018-01-01

We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

A kinetic theory for nonanalog Monte Carlo particle transport algorithms: Exponential transform with angular biasing in planar-geometry anisotropically scattering media

International Nuclear Information System (INIS)

Ueki, T.; Larsen, E.W.

1998-01-01

The authors show that Monte Carlo simulations of neutral particle transport in planargeometry anisotropically scattering media, using the exponential transform with angular biasing as a variance reduction device, are governed by a new Boltzman Monte Carlo (BMC) equation, which includes particle weight as an extra independent variable. The weight moments of the solution of the BMC equation determine the moments of the score and the mean number of collisions per history in the nonanalog Monte Carlo simulations. Therefore, the solution of the BMC equation predicts the variance of the score and the figure of merit in the simulation. Also, by (1) using an angular biasing function that is closely related to the ''asymptotic'' solution of the linear Boltzman equation and (2) requiring isotropic weight changes as collisions, they derive a new angular biasing scheme. Using the BMC equation, they propose a universal ''safe'' upper limit of the transform parameter, valid for any type of exponential transform. In numerical calculations, they demonstrate that the behavior of the Monte Carlo simulations and the performance predicted by deterministically solving the BMC equation agree well, and that the new angular biasing scheme is always advantageous

Atomistic Modeling of Ion Conduction through the Voltage-Sensing Domain of the Shaker K+ Ion Channel.

Science.gov (United States)

Wood, Mona L; Freites, J Alfredo; Tombola, Francesco; Tobias, Douglas J

2017-04-20

Voltage-sensing domains (VSDs) sense changes in the membrane electrostatic potential and, through conformational changes, regulate a specific function. The VSDs of wild-type voltage-dependent K + , Na + , and Ca 2+ channels do not conduct ions, but they can become ion-permeable through pathological mutations in the VSD. Relatively little is known about the underlying mechanisms of conduction through VSDs. The most detailed studies have been performed on Shaker K + channel variants in which ion conduction through the VSD is manifested in electrophysiology experiments as a voltage-dependent inward current, the so-called omega current, which appears when the VSDs are in their resting state conformation. Only monovalent cations appear to permeate the Shaker VSD via a pathway that is believed to be, at least in part, the same as that followed by the S4 basic side chains during voltage-dependent activation. We performed μs-time scale atomistic molecular dynamics simulations of a cation-conducting variant of the Shaker VSD under applied electric fields in an experimentally validated resting-state conformation, embedded in a lipid bilayer surrounded by solutions containing guanidinium chloride or potassium chloride. Our simulations provide insights into the Shaker VSD permeation pathway, the protein-ion interactions that control permeation kinetics, and the mechanism of voltage-dependent activation of voltage-gated ion channels.

NanoPSE: Nanoscience Problem Solving Environment for atomistic electronic structure of semiconductor nanostructures

International Nuclear Information System (INIS)

Jones, Wesley B; Bester, Gabriel; Canning, Andrew; Franceschetti, Alberto; Graf, Peter A; Kim, Kwiseon; Langou, Julien; Wang Linwang; Dongarra, Jack; Zunger, Alex

2005-01-01

Researchers at the National Renewable Energy Laboratory and their collaborators have developed over the past ∼10 years a set of algorithms for an atomistic description of the electronic structure of nanostructures, based on plane-wave pseudopotentials and configurationinteraction. The present contribution describes the first step in assembling these various codes into a single, portable, integrated set of software packages. This package is part of an ongoing research project in the development stage. Components of NanoPSE include codes for atomistic nanostructure generation and passivation, valence force field model for atomic relaxation, code for potential field generation, empirical pseudopotential method solver, strained linear combination of bulk bands method solver, configuration interaction solver for excited states, selection of linear algebra methods, and several inverse band structure solvers. Although not available for general distribution at this time as it is being developed and tested, the design goal of the NanoPSE software is to provide a software context for collaboration. The software package is enabled by fcdev, an integrated collection of best practice GNU software for open source development and distribution augmented to better support FORTRAN

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

OpenAIRE

S.V. Kryuchkov; E.I. Kukhar’; D.V. Zav’yalov

2015-01-01

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...

Kinetics of physical adsorption of ethane on Ir(110)-(1×2): Molecular beam reflectivity measurements and Monte Carlo simulations

OpenAIRE

Kang, H. C.; Mullins, C. B.; Weinberg, W. H.

1990-01-01

Experimental results, obtained using a reflectivity method, for the probability of physical adsorption of ethane on the Ir(110)-(1×2) surface are presented. We analyze these results using Monte Carlo simulations and show that physical adsorption can occur either directly or through a precursor state in which an ethane molecule is trapped in a second layer above a first layer of physically adsorbed ethane. From the Monte Carlo simulations, we are able to establish that the energy barrier for d...

Multiscale methods coupling atomistic and continuum mechanics: analysis of a simple case

OpenAIRE

Blanc , Xavier; Le Bris , Claude; Legoll , Frédéric

2007-01-01

International audience; The description and computation of fine scale localized phenomena arising in a material (during nanoindentation, for instance) is a challenging problem that has given birth to many multiscale methods. In this work, we propose an analysis of a simple one-dimensional method that couples two scales, the atomistic one and the continuum mechanics one. The method includes an adaptive criterion in order to split the computational domain into two subdomains, that are described...

Long-term behaviour of irradiated hcp Zr using Monte Carlo simulations

International Nuclear Information System (INIS)

Arevalo, C.; Caturla, M.J.; Perlado, J.M.

2005-01-01

Kinetic Monte Carlo (kMC) modelling has been used to study the diffusion of defects produced under irradiation in alpha-zirconiun. Database of displacement cascades created by recoils from 10 to 25 keV obtained by molecular dynamics (MD) simulations have been used as initial damage state in the metal. These cascades have been annealed for times of hours at a fixed temperature of 600 K. The number of freely migrating defects, the recombination ratio between vacancies and interstitials, the surviving defects in the bulk as well as the average cluster size for these remaining defects have been obtained

Dissociative double ionization of H2 and D2: Comparison between experiment and Monte Carlo wave packet calculations

DEFF Research Database (Denmark)

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

2010-01-01

Theoretical calculations on dissociative double ionization of H2 and D2 in short intense laser pulses using the Monte Carlo wave packet technique are presented for several different field intensities, wavelengths, and pulse durations. We find convincing agreement between theory and experimental...... results for the kinetic energy release spectra of the nuclei. Besides the correctly predicted spectra the Monte Carlo wave packet method offers insight into the nuclear dynamics during the pulse and makes it possible to address the origin of different structures observed in the spectra. Three......-photon resonances in the singly ionized molecule and charge-resonance-enhanced ionization are shown to be the main processes responsible for the observed nuclear energy distributions....

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

Science.gov (United States)

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

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

Supermolecular structure and charge carriers mobilities of perylene diimides

Energy Technology Data Exchange (ETDEWEB)

Marcon, Valentina; Pisula, Wojtek; Andrienko, Denis [Max-Planck-Institut fuer Polymerforschung, Mainz (Germany); Kirkpatrick, James [Max-Planck-Institut fuer Polymerforschung, Mainz (Germany); Department of Physics, Imperial College London, London (United Kingdom)

2008-07-01

Perylene diimides form columnar phases, where the molecules stack on top of each other and the columns arrange in a regular lattice. The self-organization into well-ordered columns results in the one-dimensional charge transport along the stack of the aromatic cores of the molecules. Most of the discotic molecules which organize in columns are p-type semiconductors, while the class of rylene diimide molecules, to which perylene belongs, forms n-type organic semiconductors. Using atomistic molecular dynamics (MD) simulations we study the columnar phases of perylene diimides and establish correlations between the molecular structure, packing, and dynamical properties of these materials. By using a scheme which combines electronic structure calculations, MD and kinetic Monte Carlo simulations, a correlation is then established between the molecular structure and charge mobility of perylenes columnar mesophases.

FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

KAUST Repository

Harmandaris, Vagelis

2017-10-03

The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

Near-ideal strength in metal nanotubes revealed by atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Sun, Mingfei; Xiao, Fei [Department of Materials Science, Fudan University, 220 Handan Road, Shanghai 200433 (China); Deng, Chuang, E-mail: dengc@ad.umanitoba.ca [Department of Mechanical and Manufacturing Engineering, The University of Manitoba, 15Gillson Street, Winnipeg, Manitoba R3T 5V6 (Canada)

2013-12-02

Here we report extraordinary mechanical properties revealed by atomistic simulations in metal nanotubes with hollow interior that have been long overlooked. Particularly, the yield strength in [1 1 1] Au nanotubes is found to be up to 60% higher than the corresponding solid Au nanowire, which approaches the theoretical ideal strength in Au. Furthermore, a remarkable transition from sharp to smooth yielding is observed in Au nanotubes with decreasing wall thickness. The ultrahigh tensile strength in [1 1 1] Au nanotube might originate from the repulsive image force exerted by the interior surface against dislocation nucleation from the outer surface.

Quantum-based Atomistic Simulation of Transition Metals

International Nuclear Information System (INIS)

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

2005-01-01

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

Interwell Connectivity Evaluation Using Injection and Production Fluctuation Data

Science.gov (United States)

Shang, Barry Zhongqi

The development of multiscale methods for computational simulation of biophysical systems represents a significant challenge. Effective computational models that bridge physical insights obtained from atomistic simulations and experimental findings are lacking. An accurate passing of information between these scales would enable: (1) an improved physical understanding of structure-function relationships, and (2) enhanced rational strategies for molecular engineering and materials design. Two approaches are described in this dissertation to facilitate these multiscale goals. In Part I, we develop a lattice kinetic Monte Carlo model to simulate cellulose decomposition by cellulase enzymes and to understand the effects of spatial confinement on enzyme kinetics. An enhanced mechanistic understanding of this reaction system could enhance the design of cellulose bioconversion technologies for renewable and sustainable energy. Using our model, we simulate the reaction up to experimental conversion times of days, while simultaneously capturing the microscopic kinetic behaviors. Therefore, the influence of molecular-scale kinetics on the macroscopic conversion rate is made transparent. The inclusion of spatial constraints in the kinetic model represents a significant advance over classical mass-action models commonly used to describe this reaction system. We find that restrictions due to enzyme jamming and substrate heterogeneity at the molecular level play a dominate role in limiting cellulose conversion. We identify that the key rate limitations are the slow rates of enzyme complexation with glucan chains and the competition between enzyme processivity and jamming. We show that the kinetics of complexation, which involves extraction of a glucan chain end from the cellulose surface and threading through the enzyme active site, occurs slowly on the order of hours, while intrinsic hydrolytic bond cleavage occurs on the order of seconds. We also elucidate the subtle trade

Neutral particle kinetics in fusion devices

International Nuclear Information System (INIS)

Tendler, M.; Heifetz, D.

1986-05-01

The theory of neutral particle kinetics treats the transport of mass, momentum, and energy in a plasma due to neutral particles which themselves are unaffected by magnetic fields. This transport affects the global power and particle balances in fusion devices, as well as profile control and plasma confinement quality, particle and energy fluxes onto device components, performance of pumping systems, and the design of diagnostics and the interpretation of their measurements. This paper reviews the development of analytic, numerical, and Monte Carlo methods of solving the time-independent Boltzmann equation describing neutral kinetics. These models for neutral particle behavior typically use adaptations of techniques developed originally for computing neutron transport, due to the analogy between the two phenomena, where charge-exchange corresponds to scattering and ionization to absorption. Progress in the field depends on developing multidimensional analytic methods, and obtaining experimental data for the physical processes of wall reflection, the neutral/plasma interaction, and for processes in fusion devices which are directly related to neutral transport, such as H/sub α/ emission rates, plenum pressures, and charge-exchange emission spectra

Neutral particle kinetics in fusion devices

Energy Technology Data Exchange (ETDEWEB)

Tendler, M.; Heifetz, D.

1986-05-01

The theory of neutral particle kinetics treats the transport of mass, momentum, and energy in a plasma due to neutral particles which themselves are unaffected by magnetic fields. This transport affects the global power and particle balances in fusion devices, as well as profile control and plasma confinement quality, particle and energy fluxes onto device components, performance of pumping systems, and the design of diagnostics and the interpretation of their measurements. This paper reviews the development of analytic, numerical, and Monte Carlo methods of solving the time-independent Boltzmann equation describing neutral kinetics. These models for neutral particle behavior typically use adaptations of techniques developed originally for computing neutron transport, due to the analogy between the two phenomena, where charge-exchange corresponds to scattering and ionization to absorption. Progress in the field depends on developing multidimensional analytic methods, and obtaining experimental data for the physical processes of wall reflection, the neutral/plasma interaction, and for processes in fusion devices which are directly related to neutral transport, such as H/sub ..cap alpha../ emission rates, plenum pressures, and charge-exchange emission spectra.

Work fluctuation theorems and free energy from kinetic theory

Science.gov (United States)

Brey, J. Javier; Ruiz-Montero, M. J.; Domínguez, Álvaro

2018-01-01

The formulation of the first and second principles of thermodynamics for a particle in contact with a heat bath and submitted to an external force is analyzed, by means of the Boltzmann-Lorentz kinetic equation. The possible definitions of the thermodynamic quantities are discussed in the light of the H theorem verified by the distribution of the particle. The work fluctuation relations formulated by Bochkov and Kuzovlev, and by Jarzynski, respectively, are derived from the kinetic equation. In addition, particle simulations using both the direct simulation Monte Carlo method and molecular dynamics, are used to investigate the practical accuracy of the results. Work distributions are also measured, and they turn out to be rather complex. On the other hand, they seem to depend very little, if any, on the interaction potential between the intruder and the bath.

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

Specialized Monte Carlo codes versus general-purpose Monte Carlo codes

International Nuclear Information System (INIS)

Moskvin, Vadim; DesRosiers, Colleen; Papiez, Lech; Lu, Xiaoyi

2002-01-01

The possibilities of Monte Carlo modeling for dose calculations and optimization treatment are quite limited in radiation oncology applications. The main reason is that the Monte Carlo technique for dose calculations is time consuming while treatment planning may require hundreds of possible cases of dose simulations to be evaluated for dose optimization. The second reason is that general-purpose codes widely used in practice, require an experienced user to customize them for calculations. This paper discusses the concept of Monte Carlo code design that can avoid the main problems that are preventing wide spread use of this simulation technique in medical physics. (authors)

Fully Atomistic Understanding of the Electronic and Optical Properties of a Prototypical Doped Charge-Transfer Interface

DEFF Research Database (Denmark)

Brivio, Gian Paolo; Baby, Anu; Gruenewald, Marco

2017-01-01

The current study generates profound atomistic insights into doping-induced changes of the optical and electronic properties of the prototypical PTCDA/Ag(111) interface. For doping K atoms are used, as KxPTCDA/Ag(111) has the distinct advantage of forming well-defined stoichiometric phases...

Simulation with Phast of the pore water chemistry experiment results (Mont Terri Url, Switzerland), including transport, thermodynamics, kinetics, and biological activity

International Nuclear Information System (INIS)

Tournassat, C.; Gaucher, E.; Pearson, F.J.; Mettler, S.; Wersin, P.

2005-01-01

Full text of publication follows: The Pore water Chemistry (PC-)experiment was initially designed to determine the processes that control the redox properties of pore water in the Opalinus Clay at the Mont Terri URL. However, changes in isotopic data and chemical parameters such as pH, alkalinity, dissolved methane, acetate and sulphate concentrations indicated unexpected microbial activity. The origin of the bacteria is not clear. In the light of published data, an indigenous origin cannot be ruled out. A combined biological and reactive transport model has been developed with the parallel PHAST software to simulate the processes that determine pore water chemistry. The influence of bacterial activity on the system is successfully modelled by considering different reaction pathways scenarios including aceto-genesis, methano-genesis, and methane/acetate oxidation coupled to sulphate reduction. Several conclusions can be clearly stated in the light of the simulation results: - The measured redox potentials (redox electrode) are in line with the S(-II)/S(+VI) redox system. - In the undisturbed pore water, S(-II) and S(+VI) activities are controlled by a mineral assemblage containing pyrite and a Fe carbonate (siderite or ankerite). pH is buffered by mineral phases and SO 4 2- concentration is inherited from the marine sedimentary rock. - Some local redox potentials in the sedimentary rock do not correspond to the measured redox potential; for instance, organic matter/HCO 3 - and CH 4 /HCO 3 - systems are not at equilibrium with the measured redox potential. - Redox disequilibrium can be exploited by micro-organisms as a source of energy for their metabolism. In this experiment CH 4 , acetate and other organic acids were produced and SO 4 2- was reduced to HS - . The redox properties of the system are then governed by kinetics rather than by thermodynamic equilibrium. The unexpected persistence of acetate in the borehole water is one of the consequences of these

Physically representative atomistic modeling of atomic-scale friction

Science.gov (United States)

Dong, Yalin

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

Monte Carlo principles and applications

Energy Technology Data Exchange (ETDEWEB)

Raeside, D E [Oklahoma Univ., Oklahoma City (USA). Health Sciences Center

1976-03-01

The principles underlying the use of Monte Carlo methods are explained, for readers who may not be familiar with the approach. The generation of random numbers is discussed, and the connection between Monte Carlo methods and random numbers is indicated. Outlines of two well established Monte Carlo sampling techniques are given, together with examples illustrating their use. The general techniques for improving the efficiency of Monte Carlo calculations are considered. The literature relevant to the applications of Monte Carlo calculations in medical physics is reviewed.

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)

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

with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force...... is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity...

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.

Mass and heat transfer between evaporation and condensation surfaces: Atomistic simulation and solution of Boltzmann kinetic equation.

Science.gov (United States)

Zhakhovsky, Vasily V; Kryukov, Alexei P; Levashov, Vladimir Yu; Shishkova, Irina N; Anisimov, Sergey I

2018-04-16

Boundary conditions required for numerical solution of the Boltzmann kinetic equation (BKE) for mass/heat transfer between evaporation and condensation surfaces are analyzed by comparison of BKE results with molecular dynamics (MD) simulations. Lennard-Jones potential with parameters corresponding to solid argon is used to simulate evaporation from the hot side, nonequilibrium vapor flow with a Knudsen number of about 0.02, and condensation on the cold side of the condensed phase. The equilibrium density of vapor obtained in MD simulation of phase coexistence is used in BKE calculations for consistency of BKE results with MD data. The collision cross-section is also adjusted to provide a thermal flux in vapor identical to that in MD. Our MD simulations of evaporation toward a nonreflective absorbing boundary show that the velocity distribution function (VDF) of evaporated atoms has the nearly semi-Maxwellian shape because the binding energy of atoms evaporated from the interphase layer between bulk phase and vapor is much smaller than the cohesive energy in the condensed phase. Indeed, the calculated temperature and density profiles within the interphase layer indicate that the averaged kinetic energy of atoms remains near-constant with decreasing density almost until the interphase edge. Using consistent BKE and MD methods, the profiles of gas density, mass velocity, and temperatures together with VDFs in a gap of many mean free paths between the evaporation and condensation surfaces are obtained and compared. We demonstrate that the best fit of BKE results with MD simulations can be achieved with the evaporation and condensation coefficients both close to unity.

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.

Precipitation kinetics in binary Fe–Cu and ternary Fe–Cu–Ni alloys via kMC method

Directory of Open Access Journals (Sweden)

Yi Wang

2017-08-01

Full Text Available The precipitation kinetics of coherent Cu rich precipitates (CRPs in binary Fe–Cu and ternary Fe–Cu–Ni alloys during thermal aging was modelled by the kinetic Monte Carlo method (kMC. A good agreement of the precipitation kinetics of Fe–Cu was found between the simulation and experimental results, as observed by means of advancement factor and cluster number density. This agreement was obtained owing to the correct description of the fast cluster mobility. The simulation results indicate that the effects of Ni are two-fold: Ni promotes the nucleation of Cu clusters; while the precipitation kinetics appears to be delayed by Ni addition during the coarsening stage. The apparent delayed precipitation kinetics is revealed to be related with the cluster mobility, which are reduced by Ni addition. The reduction effect of the cluster mobility weakens when the CRPs sizes increase. The results provide a view angle on the effects of solute elements upon Cu precipitation kinetics through the consideration of the non-conventional cluster growth mechanism, and kMC is verified to be a powerful approach on that.

Dynamic characteristics of nanoindentation using atomistic simulation

International Nuclear Information System (INIS)

Fang, Te-Hua; Chang, Wen-Yang; Huang, Jian-Jin

2009-01-01

Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0 o , is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

Dynamic characteristics of nanoindentation using atomistic simulation

Energy Technology Data Exchange (ETDEWEB)

Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China); Chang, Wen-Yang [Microsystems Technology Center, Industrial Technology Research Institute, Tainan 709, Taiwan (China); Huang, Jian-Jin [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China)

2009-06-15

Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0{sup o}, is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

Accelerated procedure to solve kinetic equation for neutral atoms in a hot plasma

Science.gov (United States)

Tokar, Mikhail Z.

2017-12-01

The recombination of plasma charged components, electrons and ions of hydrogen isotopes, on the wall of a fusion reactor is a source of neutral molecules and atoms, recycling back into the plasma volume. Here neutral species participate, in particular, in charge-exchange (c-x) collisions with the plasma ions and, as a result, atoms of high energies with chaotically directed velocities are generated. Some fraction of these hot atoms hit the wall. Statistical Monte Carlo methods normally used to model c-x atoms are too time consuming for reasonably small level of accident errors and extensive parameter studies are problematic. By applying pass method to evaluate integrals from functions, including the ion velocity distribution, an iteration approach to solve one-dimensional kinetic equation [1], being alternative to Monte Carlo procedure, has been tremendously accelerated, at least by a factor of 30-50 [2]. Here this approach is developed further to solve the 2-D kinetic equation, applied to model the transport of c-x atoms in the vicinity of an opening in the wall, e.g., the entrance of the duct guiding to a diagnostic installation. This is necessary to determine firmly the energy spectrum of c-x atoms penetrating into the duct and to assess the erosion of the installation there. The results of kinetic modeling are compared with those obtained with the diffusion description for c-x atoms, being strictly relevant under plasma conditions of low temperature and high density, where the mean free path length between c-x collisions is much smaller than that till the atom ionization by electrons. It is demonstrated that the previous calculations [3], done with the diffusion approximation for c-x atoms, overestimate the erosion rate of Mo mirrors in a reactor by a factor of 3 compared to the result of the present kinetic study.

Atomistic Simulation of the Rate-Dependent Ductile-to-Brittle Failure Transition in Bicrystalline Metal Nanowires.

Science.gov (United States)

Tao, Weiwei; Cao, Penghui; Park, Harold S

2018-02-14

The mechanical properties and plastic deformation mechanisms of metal nanowires have been studied intensely for many years. One of the important yet unresolved challenges in this field is to bridge the gap in properties and deformation mechanisms reported for slow strain rate experiments (∼10 -2 s -1 ), and high strain rate molecular dynamics (MD) simulations (∼10 8 s -1 ) such that a complete understanding of strain rate effects on mechanical deformation and plasticity can be obtained. In this work, we use long time scale atomistic modeling based on potential energy surface exploration to elucidate the atomistic mechanisms governing a strain-rate-dependent incipient plasticity and yielding transition for face centered cubic (FCC) copper and silver nanowires. The transition occurs for both metals with both pristine and rough surfaces for all computationally accessible diameters (ductile-to-brittle transition in failure mode similar to previous experimental studies on bicrystalline silver nanowires is observed, which is driven by differences in dislocation activity and grain boundary mobility as compared to the high strain rate case.

An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

Directory of Open Access Journals (Sweden)

Matthew W. Thompson

2017-10-01

Full Text Available We report a novel atomistic model of carbide-derived carbons (CDCs, which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors.

Plasma flow to a surface using the iterative Monte Carlo method

International Nuclear Information System (INIS)

Pitcher, C.S.

1994-01-01

The iterative Monte Carlo (IMC) method is applied to a number of one-dimensional plasma flow problems, which encompass a wide range of conditions typical of those present in the boundary of magnetic fusion devices. The kinetic IMC method of solving plasma flow to a surface consists of launching and following particles within a grid of 'bins' into which weights are left according to the time a particle spends within a bin. The density and potential distributions within the plasma are iterated until the final solution is arrived at. The IMC results are compared with analytical treatments of these problems and, in general, good agreement is obtained. (author)

New kinetic insight into the spontaneous oxidation process of lithium in air by EPMA

Energy Technology Data Exchange (ETDEWEB)

Otero, Manuel [IFEG, Facultad de Matemáticas, Astronomía y Física, Universidad Nacional de Córdoba, Córdoba (Argentina); INFICQ, Departamento de Matemáticas y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba (Argentina); Lener, German [INFAP, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, San Luis (Argentina); Trincavelli, Jorge, E-mail: trincavelli@famaf.unc.edu.ar [IFEG, Facultad de Matemáticas, Astronomía y Física, Universidad Nacional de Córdoba, Córdoba (Argentina); Barraco, Daniel [IFEG, Facultad de Matemáticas, Astronomía y Física, Universidad Nacional de Córdoba, Córdoba (Argentina); Nazzarro, Marcelo Sandro; Furlong, Octavio [INFAP, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, San Luis (Argentina); Leiva, Ezequiel Pedro Marcos [INFICQ, Departamento de Matemáticas y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba (Argentina)

2016-10-15

Highlights: • EPMA measurements and Monte Carlo simulations were applied to study the corrosion process of Li in air. • The kinetic mechanism of corrosion was discussed. • A diffusion process of water through LiOH was found and quantitatively studied. - Abstract: The exposure of metallic lithium to ambient air produces a fast corrosion reaction of the surface that continues to the bulk of the material. This spontaneous process was explored by means of X-ray Photoelectron Spectroscopy (XPS) and Electron Probe Micro-Analysis (EPMA). The combination of these techniques and Monte Carlo simulations allowed observing the formation of a film of lithium hydroxide (LiOH) and studying the growth within the material during the first 300 s. The corrosion is mainly due to the reaction of lithium with water and the diffusion of water through the growing LiOH film is the rate determining step. On the basis of a kinetic analysis we studied the mechanism of reaction and inferred a diffusion coefficient of D = (5.1 ± 0.4) × 10{sup −12} cm{sup 2}/s in agreement with results from the literature obtained using different techniques.

Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

Science.gov (United States)

Xiao, HuiFang; Huang, Bin; Yao, Ge; Kang, WenBin; Gong, Sheng; Pan, Hai; Cao, Yi; Wang, Jun; Zhang, Jian; Wang, Wei

2018-03-01

Understanding the processes of protein adsorption/desorption on nanoparticles' surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for these processes and for the simultaneous protein conformational change is missing. Here, we report the adsorption of protein GB1 on a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states, each involving both the adsorbed and desorbed modes. We also studied the change of the secondary and tertiary structures of GB1 during adsorption and the dominant interactions between the protein and surface in different adsorption stages. The results we obtained from simulation were found to be more adequate and complete than the previous one. We believe the model presented in this paper, in comparison with the previous ones, is a better theoretical model to understand and explain the experimental results.

Monte Carlo simulations of magnetic order in Fe-doped manganites

International Nuclear Information System (INIS)

Alonso, J.; Gutierrez, J.; Barandiaran, J.M.; Bermejo, F.J.; Brey, L.

2008-01-01

The effect of Fe doping on the magnetic properties of La 0.7 Pb 0.3 Mn 1-x Fe x O 3 (x=0, 0.05, 0.1, 0.15 and 0.2) manganites is studied by the Monte Carlo simulation technique. As a first approximation, by means of a simple Heisenberg Hamiltonian, experimental normalized magnetizations at low temperatures have been reproduced for concentrations of Fe (x<0.2), but the calculated order temperatures show a large deviation from the measured ones. This shortcoming can be corrected by using a one electron effective hopping semi-classical Hamiltonian, with a simplified expression for the kinetic energy of the free electrons, which also avoids time-consuming diagonalizations

Shock wave, fluid instability and implosion studies with a kinetic particle approach

Science.gov (United States)

Sagert, Irina; Even, Wesley P.; Strother, Terrance T.

2016-10-01

Many problems in laboratory plasma physics are subject to flows that move between the continuum and the kinetic regime. The correct description of these flows is crucial in order to capture their impact on the system's dynamical evolution. Examples are capsule implosions in inertial confinement fusion (ICF). Although their dynamics is predominantly shaped by shock waves and fluid instabilities, non-equilibrium flows in form of deuterium/tritium ions have been shown to play a significant role. We present recent studies with our Monte Carlo kinetic particle code that is designed to capture continuum and kinetic flows in large physical systems with possible applications in ICF studies. Discussed results will include standard shock wave and fluid instability tests and simulations that are adapted towards future ICF studies with comparisons to hydrodynamic simulations. This work used the Wolf TriLAB Capacity Cluster at LANL. I.S. acknowledges support through a Director's fellowship (20150741PRD3) from Los Alamos National Laboratory.

Interplay of bistable kinetics of gene expression during cellular growth

International Nuclear Information System (INIS)

Zhdanov, Vladimir P

2009-01-01

In cells, the bistable kinetics of gene expression can be observed on the level of (i) one gene with positive feedback between protein and mRNA production, (ii) two genes with negative mutual feedback between protein and mRNA production, or (iii) in more complex cases. We analyse the interplay of two genes of type (ii) governed by a gene of type (i) during cellular growth. In particular, using kinetic Monte Carlo simulations, we show that in the case where gene 1, operating in the bistable regime, regulates mutually inhibiting genes 2 and 3, also operating in the bistable regime, the latter genes may eventually be trapped either to the state with high transcriptional activity of gene 2 and low activity of gene 3 or to the state with high transcriptional activity of gene 3 and low activity of gene 2. The probability to get to one of these states depends on the values of the model parameters. If genes 2 and 3 are kinetically equivalent, the probability is equal to 0.5. Thus, our model illustrates how different intracellular states can be chosen at random with predetermined probabilities. This type of kinetics of gene expression may be behind complex processes occurring in cells, e.g., behind the choice of the fate by stem cells

Time-dependent integral equations of neutron transport for calculating the kinetics of nuclear reactors by the Monte Carlo method

Energy Technology Data Exchange (ETDEWEB)

Davidenko, V. D., E-mail: Davidenko-VD@nrcki.ru; Zinchenko, A. S., E-mail: zin-sn@mail.ru; Harchenko, I. K. [National Research Centre Kurchatov Institute (Russian Federation)

2016-12-15

Integral equations for the shape functions in the adiabatic, quasi-static, and improved quasi-static approximations are presented. The approach to solving these equations by the Monte Carlo method is described.

An atomistic methodology of energy release rate for graphene at nanoscale

International Nuclear Information System (INIS)

Zhang, Zhen; Lee, James D.; Wang, Xianqiao

2014-01-01

Graphene is a single layer of carbon atoms packed into a honeycomb architecture, serving as a fundamental building block for electric devices. Understanding the fracture mechanism of graphene under various conditions is crucial for tailoring the electrical and mechanical properties of graphene-based devices at atomic scale. Although most of the fracture mechanics concepts, such as stress intensity factors, are not applicable in molecular dynamics simulation, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at nanoscale. This work introduces an atomistic simulation methodology, based on the energy release rate, as a tool to unveil the fracture mechanism of graphene at nanoscale. This methodology can be easily extended to any atomistic material system. We have investigated both opening mode and mixed mode at different temperatures. Simulation results show that the critical energy release rate of graphene is independent of initial crack length at low temperature. Graphene with inclined pre-crack possesses higher fracture strength and fracture deformation but smaller critical energy release rate compared with the graphene with vertical pre-crack. Owing to its anisotropy, graphene with armchair chirality always has greater critical energy release rate than graphene with zigzag chirality. The increase of temperature leads to the reduction of fracture strength, fracture deformation, and the critical energy release rate of graphene. Also, higher temperature brings higher randomness of energy release rate of graphene under a variety of predefined crack lengths. The energy release rate is independent of the strain rate as long as the strain rate is small enough

Bayesian inference of chemical kinetic models from proposed reactions

KAUST Repository

Galagali, Nikhil

2015-02-01

© 2014 Elsevier Ltd. Bayesian inference provides a natural framework for combining experimental data with prior knowledge to develop chemical kinetic models and quantify the associated uncertainties, not only in parameter values but also in model structure. Most existing applications of Bayesian model selection methods to chemical kinetics have been limited to comparisons among a small set of models, however. The significant computational cost of evaluating posterior model probabilities renders traditional Bayesian methods infeasible when the model space becomes large. We present a new framework for tractable Bayesian model inference and uncertainty quantification using a large number of systematically generated model hypotheses. The approach involves imposing point-mass mixture priors over rate constants and exploring the resulting posterior distribution using an adaptive Markov chain Monte Carlo method. The posterior samples are used to identify plausible models, to quantify rate constant uncertainties, and to extract key diagnostic information about model structure-such as the reactions and operating pathways most strongly supported by the data. We provide numerical demonstrations of the proposed framework by inferring kinetic models for catalytic steam and dry reforming of methane using available experimental data.

Development of a generalized stochastic model for the analysis of monoenergetic space-time nuclear factor Kinetics

International Nuclear Information System (INIS)

Pham, Nhu Viet Ha

2011-02-01

(SSKM), which can be considered as a generalization of the stochastic point-kinetics equations, was then validated by testing against analog Monte Carlo calculations for cases of slab reactors. The comparative results showed that the SSKM agrees well within about 5% with the Monte Carlo method. Also, the SSKM was confirmed to provide a fast calculation method in comparison with the Monte Carlo computations. Finally, an additional numerical investigation was conducted using the SSKM in order to observe the random fluctuations in population dynamics under various reactor transients. The numerical results, which appear plausible on a physical basis, demonstrate that the behavior of the stochastic neutron and precursor distributions within a reactor can be explicitly induced by using the SSKM. Thus, it is realized that the SSKM can be applied to reactor transient and safety analysis with possibility of predicting the trends in variances of the interacting populations in advance

Electrostatic Screening and Charge Correlation Effects in Micellization of Ionic Surfactants

KAUST Repository

Jusufi, Arben; Hynninen, Antti-Pekka; Haataja, Mikko; Panagiotopoulos, Athanassios Z.

2009-01-01

We have used atomistic simulations to study the role of electrostatic screening and charge correlation effects in self-assembly processes of ionic surfactants into micelles. Specifically, we employed grand canonical Monte Carlo simulations

Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

Science.gov (United States)

Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

2016-10-01

Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations.

Science.gov (United States)

Casasnovas, Rodrigo; Limongelli, Vittorio; Tiwary, Pratyush; Carloni, Paolo; Parrinello, Michele

2017-04-05

Understanding the structural and energetic requisites of ligand binding toward its molecular target is of paramount relevance in drug design. In recent years, atomistic free energy calculations have proven to be a valid tool to complement experiments in characterizing the thermodynamic and kinetic properties of protein/ligand interaction. Here, we investigate, through a recently developed metadynamics-based protocol, the unbinding mechanism of an inhibitor of the pharmacologically relevant target p38 MAP kinase. We provide a thorough description of the ligand unbinding pathway identifying the most stable binding mode and other thermodynamically relevant poses. From our simulations, we estimated the unbinding rate as k off = 0.020 ± 0.011 s -1 . This is in good agreement with the experimental value (k off = 0.14 s -1 ). Next, we developed a Markov state model that allowed identifying the rate-limiting step of the ligand unbinding process. Our calculations further show that the solvation of the ligand and that of the active site play crucial roles in the unbinding process. This study paves the way to investigations on the unbinding dynamics of more complex p38 inhibitors and other pharmacologically relevant inhibitors in general, demonstrating that metadynamics can be a powerful tool in designing new drugs with engineered binding/unbinding kinetics.

Efficient kinetic Monte Carlo method for reaction-diffusion problems with spatially varying annihilation rates

Science.gov (United States)

Schwarz, Karsten; Rieger, Heiko

2013-03-01

We present an efficient Monte Carlo method to simulate reaction-diffusion processes with spatially varying particle annihilation or transformation rates as it occurs for instance in the context of motor-driven intracellular transport. Like Green's function reaction dynamics and first-passage time methods, our algorithm avoids small diffusive hops by propagating sufficiently distant particles in large hops to the boundaries of protective domains. Since for spatially varying annihilation or transformation rates the single particle diffusion propagator is not known analytically, we present an algorithm that generates efficiently either particle displacements or annihilations with the correct statistics, as we prove rigorously. The numerical efficiency of the algorithm is demonstrated with an illustrative example.

A Monte Carlo model for 3D grain evolution during welding

Science.gov (United States)

Rodgers, Theron M.; Mitchell, John A.; Tikare, Veena

2017-09-01

Welding is one of the most wide-spread processes used in metal joining. However, there are currently no open-source software implementations for the simulation of microstructural evolution during a weld pass. Here we describe a Potts Monte Carlo based model implemented in the SPPARKS kinetic Monte Carlo computational framework. The model simulates melting, solidification and solid-state microstructural evolution of material in the fusion and heat-affected zones of a weld. The model does not simulate thermal behavior, but rather utilizes user input parameters to specify weld pool and heat-affect zone properties. Weld pool shapes are specified by Bézier curves, which allow for the specification of a wide range of pool shapes. Pool shapes can range from narrow and deep to wide and shallow representing different fluid flow conditions within the pool. Surrounding temperature gradients are calculated with the aide of a closest point projection algorithm. The model also allows simulation of pulsed power welding through time-dependent variation of the weld pool size. Example simulation results and comparisons with laboratory weld observations demonstrate microstructural variation with weld speed, pool shape, and pulsed-power.

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.

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

KAUST Repository

Liang, Faming

2009-01-01

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

Stability and mobility of Cu-vacancy clusters in Fe-Cu alloys: A computational study based on the use of artificial neural networks for energy barrier calculations

Science.gov (United States)

Pascuet, M. I.; Castin, N.; Becquart, C. S.; Malerba, L.

2011-05-01

An atomistic kinetic Monte Carlo (AKMC) method has been applied to study the stability and mobility of copper-vacancy clusters in Fe. This information, which cannot be obtained directly from experimental measurements, is needed to parameterise models describing the nanostructure evolution under irradiation of Fe alloys (e.g. model alloys for reactor pressure vessel steels). The physical reliability of the AKMC method has been improved by employing artificial intelligence techniques for the regression of the activation energies required by the model as input. These energies are calculated allowing for the effects of local chemistry and relaxation, using an interatomic potential fitted to reproduce them as accurately as possible and the nudged-elastic-band method. The model validation was based on comparison with available ab initio calculations for verification of the used cohesive model, as well as with other models and theories.

Stability and mobility of Cu-vacancy clusters in Fe-Cu alloys: A computational study based on the use of artificial neural networks for energy barrier calculations

International Nuclear Information System (INIS)

Pascuet, M.I.; Castin, N.; Becquart, C.S.; Malerba, L.

2011-01-01

An atomistic kinetic Monte Carlo (AKMC) method has been applied to study the stability and mobility of copper-vacancy clusters in Fe. This information, which cannot be obtained directly from experimental measurements, is needed to parameterise models describing the nanostructure evolution under irradiation of Fe alloys (e.g. model alloys for reactor pressure vessel steels). The physical reliability of the AKMC method has been improved by employing artificial intelligence techniques for the regression of the activation energies required by the model as input. These energies are calculated allowing for the effects of local chemistry and relaxation, using an interatomic potential fitted to reproduce them as accurately as possible and the nudged-elastic-band method. The model validation was based on comparison with available ab initio calculations for verification of the used cohesive model, as well as with other models and theories.

Emergence of linear elasticity from the atomistic description of matter

Energy Technology Data Exchange (ETDEWEB)

Cakir, Abdullah, E-mail: acakir@ntu.edu.sg [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Pica Ciamarra, Massimo [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Dipartimento di Scienze Fisiche, CNR–SPIN, Università di Napoli Federico II, I-80126 Napoli (Italy)

2016-08-07

We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

Emergence of linear elasticity from the atomistic description of matter

International Nuclear Information System (INIS)

Cakir, Abdullah; Pica Ciamarra, Massimo

2016-01-01

We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

Science.gov (United States)

Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

2011-06-09

Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

DEFF Research Database (Denmark)

Euro, Liliya; Haapanen, Outi; Róg, Tomasz

2017-01-01

of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

Redox reactions with empirical potentials: atomistic battery discharge simulations.

Science.gov (United States)

Dapp, Wolf B; Müser, Martin H

2013-08-14

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 atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

Vectorized Monte Carlo

International Nuclear Information System (INIS)

Brown, F.B.

1981-01-01

Examination of the global algorithms and local kernels of conventional general-purpose Monte Carlo codes shows that multigroup Monte Carlo methods have sufficient structure to permit efficient vectorization. A structured multigroup Monte Carlo algorithm for vector computers is developed in which many particle events are treated at once on a cell-by-cell basis. Vectorization of kernels for tracking and variance reduction is described, and a new method for discrete sampling is developed to facilitate the vectorization of collision analysis. To demonstrate the potential of the new method, a vectorized Monte Carlo code for multigroup radiation transport analysis was developed. This code incorporates many features of conventional general-purpose production codes, including general geometry, splitting and Russian roulette, survival biasing, variance estimation via batching, a number of cutoffs, and generalized tallies of collision, tracklength, and surface crossing estimators with response functions. Predictions of vectorized performance characteristics for the CYBER-205 were made using emulated coding and a dynamic model of vector instruction timing. Computation rates were examined for a variety of test problems to determine sensitivities to batch size and vector lengths. Significant speedups are predicted for even a few hundred particles per batch, and asymptotic speedups by about 40 over equivalent Amdahl 470V/8 scalar codes arepredicted for a few thousand particles per batch. The principal conclusion is that vectorization of a general-purpose multigroup Monte Carlo code is well worth the significant effort required for stylized coding and major algorithmic changes

Theoretical modeling of zircon's crystal morphology according to data of atomistic calculations

Science.gov (United States)

Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

2017-04-01

Zircon is an essential mineral that is used in the U-Pb dating. Moreover, zircon is highly resistant to radioactive exposure. It is of great interest in solving both fundamental and applied problems associated with the isolation of high-level radioactive waste. There is significant progress in forecasting of the most energetically favorable crystal structures at the present time. Unfortunately, the theoretical forecast of crystal morphology at high technological level is under-explored nowadays, though the estimation of crystal equilibrium habit is extremely important in studying the physical and chemical properties of new materials. For the first time, the thesis about relation of the equilibrium shape of a crystal with its crystal structure was put forward in the works by O.Brave. According to it, the idealized habit is determined in the simplest case by a correspondence with the reticular densities Rhkl of individual faces. This approach, along with all subsequent corrections, does not take into account the nature of atoms and the specific features of the chemical bond in crystals. The atomistic calculations of crystal surfaces are commonly performed using the energetic characteristics of faces, namely, the surface energy (Esurf), which is a measure of the thermodynamic stability of the crystal face. The stable crystal faces are characterized by small positive values of Esurf. As we know from our previous research (Gromalova et al.,2015) one of the constitutive factors affecting the value of the surface energy in calculations is a choice of potentials model. In this regard, we studied several sets of parameters of atomistic interatomic potentials optimized previously. As the first test model («Zircon 1») were used sets of interatomic potentials of interaction Zr-O, Si-O and O-O in the form of Buckingham potentials. To improve playback properties of zircon additionally used Morse potential for a couple of Zr-Si, as well as the three-particle angular harmonic

Adjoint electron Monte Carlo calculations

International Nuclear Information System (INIS)

Jordan, T.M.

1986-01-01

Adjoint Monte Carlo is the most efficient method for accurate analysis of space systems exposed to natural and artificially enhanced electron environments. Recent adjoint calculations for isotropic electron environments include: comparative data for experimental measurements on electronics boxes; benchmark problem solutions for comparing total dose prediction methodologies; preliminary assessment of sectoring methods used during space system design; and total dose predictions on an electronics package. Adjoint Monte Carlo, forward Monte Carlo, and experiment are in excellent agreement for electron sources that simulate space environments. For electron space environments, adjoint Monte Carlo is clearly superior to forward Monte Carlo, requiring one to two orders of magnitude less computer time for relatively simple geometries. The solid-angle sectoring approximations used for routine design calculations can err by more than a factor of 2 on dose in simple shield geometries. For critical space systems exposed to severe electron environments, these potential sectoring errors demand the establishment of large design margins and/or verification of shield design by adjoint Monte Carlo/experiment

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

Seeking kinetic pathways relevant to the structural evolution of metal nanoparticles

International Nuclear Information System (INIS)

Haldar, Paramita; Chatterjee, Abhijit

2015-01-01

Understanding the kinetic pathways that cause metal nanoparticles to structurally evolve over time is essential for predicting their shape and size distributions and catalytic properties. Consequently, we need detailed kinetic models that can provide such information. Most kinetic Monte Carlo models used for metal systems contain a fixed catalogue of atomic moves; the catalogue is largely constructed based on our physical understanding of the material. In some situations, it is possible that an incorrect picture of the overall dynamics is obtained when kinetic pathways that are relevant to the dynamics are missing from the catalogue. Hence, a computational framework that can systematically determine the relevant pathways is required. This work intends to fulfil this requirement. Examples involving an Ag nanoparticle are studied to illustrate how molecular dynamics (MD) calculations can be employed to find the relevant pathways in a system. Since pathways that are unlikely to be selected at short timescales can become relevant at longer times, the accuracy of the catalogue is maintained by continually seeking these pathways using MD. We discuss various aspects of our approach, namely, defining the relevance of atomic moves to the dynamics and determining when additional MD is required to ensure the desired accuracy, as well as physical insights into the Ag nanoparticle. (paper)

Monte Carlo: Basics

OpenAIRE

Murthy, K. P. N.

2001-01-01

An introduction to the basics of Monte Carlo is given. The topics covered include, sample space, events, probabilities, random variables, mean, variance, covariance, characteristic function, chebyshev inequality, law of large numbers, central limit theorem (stable distribution, Levy distribution), random numbers (generation and testing), random sampling techniques (inversion, rejection, sampling from a Gaussian, Metropolis sampling), analogue Monte Carlo and Importance sampling (exponential b...

Atomistic calculation of size effects on elastic coefficients in nanometre-sized tungsten layers and wires

International Nuclear Information System (INIS)

Villain, P.; Beauchamp, P.; Badawi, K.F.; Goudeau, P.; Renault, P.-O.

2004-01-01

Equilibrium state and elastic coefficients of nanometre-sized single crystal tungsten layers and wires are investigated by atomistic simulations. The variations of the equilibrium distances as a function of the layer thickness or wire cross-section are mainly due to elastic effects of surface tension forces. A strong decrease of the Young's modulus is observed when the transverse dimensions are reduced below 2-3 nm

Atomistic simulation of dislocation nucleation barriers from cracktips in α-Fe

International Nuclear Information System (INIS)

Gordon, Peter A; Neeraj, T; Luton, Michael J

2008-01-01

In this work, we demonstrate that activation pathways for dislocation loop nucleation from cracktips can be explored with full atomistic detail using an efficient form of the nudged elastic band method. The approach is demonstrated in detail with an example of edge emission from an Fe crack under mode II loading, wherein activation energy barriers are obtained as a function of sub-critical stress intensity and the energy barriers for loop formation are compared with 2D calculations. Activation energy barriers are also computed for an intrinsically ductile cracktip orientation under mode I loading, from which we can infer the frequency of nucleation from the cracktip

Microstructural evolution under high flux irradiation of dilute Fe-CuNiMnSi alloys studied by an atomic kinetic Monte Carlo model accounting for both vacancies and self interstitials

International Nuclear Information System (INIS)

Vincent, E.; Becquart, C.S.; Domain, C.

2008-01-01

Under neutron irradiation, a large amount of point defects (vacancies and interstitials) are created. In the irradiated pressure vessel steels, weakly alloyed, these point defects are responsible for the diffusion of the solute atoms, leading to the formation of solute rich precipitates within the matrix. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si). For Mn, the results of these calculations lead to think that solute transport in α-Fe can very likely take place through an interstitial mechanism as well as via vacancies while the other solutes (Cu, Ni and Si) which establish strong bonds with vacancies diffuse more likely via vacancies only. The database thus created has been used to parameterize an atomic kinetic Monte Carlo model taking into account both vacancies and interstitials. Some results of irradiation damage in dilute Fe-CuNiMnSi alloys obtained with this model will be presented

Microstructural evolution under high flux irradiation of dilute Fe CuNiMnSi alloys studied by an atomic kinetic Monte Carlo model accounting for both vacancies and self interstitials

Science.gov (United States)

Vincent, E.; Becquart, C. S.; Domain, C.

2008-12-01

Under neutron irradiation, a large amount of point defects (vacancies and interstitials) are created. In the irradiated pressure vessel steels, weakly alloyed, these point defects are responsible for the diffusion of the solute atoms, leading to the formation of solute rich precipitates within the matrix. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si). For Mn, the results of these calculations lead to think that solute transport in α-Fe can very likely take place through an interstitial mechanism as well as via vacancies while the other solutes (Cu, Ni and Si) which establish strong bonds with vacancies diffuse more likely via vacancies only. The database thus created has been used to parameterize an atomic kinetic Monte Carlo model taking into account both vacancies and interstitials. Some results of irradiation damage in dilute Fe-CuNiMnSi alloys obtained with this model will be presented.

MORSE Monte Carlo code

International Nuclear Information System (INIS)

Cramer, S.N.

1984-01-01

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

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)

Ghiass, M.; Dabir, B.; Nikazar, M.; Rey, A.D.; Mirzadeh, H.

2001-01-01

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

Alternative definitions of kinetic parameters for accelerator driven systems

International Nuclear Information System (INIS)

Talamo, Alberto; Gohar, Yousry; Dulla, Sandra; Ravetto, Piero

2012-01-01

Highlights: ► New definition of kinetic parameters for accelerator driven systems. ► Difference between effective and average delayed neutron fraction. ► Difference between effective and average prompt neutron lifetime. ► Effect of the neutron source (Cf, D–D, D–T) on k src . ► Effect of the (n, xn) reactions and source energy-angle distribution on k src . - Abstract: This study introduces a new formulation of kinetic parameters for accelerator driven systems and it is structured into two parts. The first part is dedicated to the classic definition of the kinetic parameters and compares different calculation methodologies. The second part considers a new definition of the kinetic parameters for subcritical assemblies, with particular emphasis on the delayed neutron fraction and the prompt neutron lifetime. This new definition takes into account neutrons from the external neutron source and (n, xn) reactions, which increase the fraction of prompt neutrons. The developed theoretical framework has been applied by Monte Carlo and deterministic calculations to the YALINA Thermal subcritical assembly located in Belarus. This facility can be driven by californium, deuterium–deuterium (D–D), or deuterium–tritium (D–T) external neutron sources. For the D–T neutron source, (n, xn) reactions must be taken into account in order to produce accurate results because the average energy of D–T source neutrons is 14.1 MeV, a value which is much higher than the threshold energy of the (n, 2n) cross section of uranium isotopes.

Monte Carlo theory and practice

International Nuclear Information System (INIS)

James, F.

1987-01-01

Historically, the first large-scale calculations to make use of the Monte Carlo method were studies of neutron scattering and absorption, random processes for which it is quite natural to employ random numbers. Such calculations, a subset of Monte Carlo calculations, are known as direct simulation, since the 'hypothetical population' of the narrower definition above corresponds directly to the real population being studied. The Monte Carlo method may be applied wherever it is possible to establish equivalence between the desired result and the expected behaviour of a stochastic system. The problem to be solved may already be of a probabilistic or statistical nature, in which case its Monte Carlo formulation will usually be a straightforward simulation, or it may be of a deterministic or analytic nature, in which case an appropriate Monte Carlo formulation may require some imagination and may appear contrived or artificial. In any case, the suitability of the method chosen will depend on its mathematical properties and not on its superficial resemblance to the problem to be solved. The authors show how Monte Carlo techniques may be compared with other methods of solution of the same physical problem

Molecular modeling and simulation of atactic polystyrene/amorphous silica nanocomposites

International Nuclear Information System (INIS)

Mathioudakis, I; Vogiatzis, G G; Tzoumanekas, C; Theodorou, D N

2016-01-01

The local structure, segmental dynamics, topological analysis of entanglement networks and mechanical properties of atactic polystyrene - amorphous silica nanocomposites are studied via molecular simulations using two interconnected levels of representation: (a) A coarse - grained level. Equilibration at all length scales at this level is achieved via connectivity - altering Monte Carlo simulations. (b) An atomistic level. Initial configurations for atomistic Molecular Dynamics (MD) simulations are obtained by reverse mapping well- equilibrated coarse-grained configurations. By analyzing atomistic MD trajectories, the polymer density profile is found to exhibit layering in the vicinity of the nanoparticle surface. The dynamics of polystyrene (in neat and filled melt systems) is characterized in terms of bond orientation. Well-equilibrated coarse-grained long-chain configurations are reduced to entanglement networks via topological analysis with the CReTA algorithm. Atomistic simulation results for the mechanical properties are compared to the experimental measurements and other computational works. (paper)

Ordering kinetics in quasi-one-dimensional Ising-like systems

International Nuclear Information System (INIS)

Mueller, M.; Paul, W.

1993-01-01

Results are presented of a Monte Carlo simulation of the kinetics of ordering in the two-dimensional nearest-neighbor Ising model in an L x M geometry with two free boundaries of length M much-gt L. This model can be viewed as representing an adsorbant on a stepped surface with mean terrace width L. The authors follow the ordering kinetics after quenches to temperatures 0.25 ≤T/T c ≤1 starting from a random initial configuration at a coverage of Θ=0.5 in the corresponding lattice gas picture. The systems evolve in time according to a Glauber kinetics with nonconserved order parameter. The equilibrium structure is given by a one-dimensional sequence of ordered domains. The ordering process evolves from a short initial two-dimensional ordering process through a crossover region to a quasi-one-dimensional behavior. The whole process is diffusive (inverse half-width of the structure factor peak 1/Δq parallel ∝ √t), in contrast to a model proposed by Kawasaki et al., where an intermediate logarithmic growth law is expected. All results are completely describable in the picture of an annihilating random walk (ARW) of domain walls. 36 refs., 16 figs

Basic physical and chemical information needed for development of Monte Carlo codes

International Nuclear Information System (INIS)

Inokuti, M.

1993-01-01

It is important to view track structure analysis as an application of a branch of theoretical physics (i.e., statistical physics and physical kinetics in the language of the Landau school). Monte Carlo methods and transport equation methods represent two major approaches. In either approach, it is of paramount importance to use as input the cross section data that best represent the elementary microscopic processes. Transport analysis based on unrealistic input data must be viewed with caution, because results can be misleading. Work toward establishing the cross section data, which demands a wide scope of knowledge and expertise, is being carried out through extensive international collaborations. In track structure analysis for radiation biology, the need for cross sections for the interactions of electrons with DNA and neighboring protein molecules seems to be especially urgent. Finally, it is important to interpret results of Monte Carlo calculations fully and adequately. To this end, workers should document input data as thoroughly as possible and report their results in detail in many ways. Workers in analytic transport theory are then likely to contribute to the interpretation of the results

A benchmark study of the Signed-particle Monte Carlo algorithm for the Wigner equation

Directory of Open Access Journals (Sweden)

Muscato Orazio

2017-12-01

Full Text Available The Wigner equation represents a promising model for the simulation of electronic nanodevices, which allows the comprehension and prediction of quantum mechanical phenomena in terms of quasi-distribution functions. During these years, a Monte Carlo technique for the solution of this kinetic equation has been developed, based on the generation and annihilation of signed particles. This technique can be deeply understood in terms of the theory of pure jump processes with a general state space, producing a class of stochastic algorithms. One of these algorithms has been validated successfully by numerical experiments on a benchmark test case.

Atomistic switch of giant magnetoresistance and spin thermopower in graphene-like nanoribbons

Science.gov (United States)

Zhai, Ming-Xing; Wang, Xue-Feng

2016-01-01

We demonstrate that the giant magnetoresistance can be switched off (on) in even- (odd-) width zigzag graphene-like nanoribbons by an atomistic gate potential or edge disorder inside the domain wall in the antiparallel (ap) magnetic configuration. A strong magneto-thermopower effect is also predicted that the spin thermopower can be greatly enhanced in the ap configuration while the charge thermopower remains low. The results extracted from the tight-binding model agree well with those obtained by first-principles simulations for edge doped graphene nanoribbons. Analytical expressions in the simplest case are obtained to facilitate qualitative analyses in general contexts. PMID:27857156

MVP/GMVP version 3. General purpose Monte Carlo codes for neutron and photon transport calculations based on continuous energy and multigroup methods

International Nuclear Information System (INIS)

Nagaya, Yasunobu; Okumura, Keisuke; Sakurai, Takeshi; Mori, Takamasa

2017-03-01

In order to realize fast and accurate Monte Carlo simulation of neutron and photon transport problems, two Monte Carlo codes MVP (continuous-energy method) and GMVP (multigroup method) have been developed at Japan Atomic Energy Agency. The codes have adopted a vectorized algorithm and have been developed for vector-type supercomputers. They also support parallel processing with a standard parallelization library MPI and thus a speed-up of Monte Carlo calculations can be achieved on general computing platforms. The first and second versions of the codes were released in 1994 and 2005, respectively. They have been extensively improved and new capabilities have been implemented. The major improvements and new capabilities are as follows: (1) perturbation calculation for effective multiplication factor, (2) exact resonant elastic scattering model, (3) calculation of reactor kinetics parameters, (4) photo-nuclear model, (5) simulation of delayed neutrons, (6) generation of group constants. This report describes the physical model, geometry description method used in the codes, new capabilities and input instructions. (author)

Studies of the kinetics of radiation induced spurs

International Nuclear Information System (INIS)

Green, N.J.B.

1982-12-01

This thesis addresses two major unresolved problems of diffusion-controlled reaction kinetics: diffusion and reaction in a system containing a small number of particles and the geminate recombination of ions. The few particle system is approached from the assumption that all pair distances evolve independently. From this assumption a Master equation is set up with which the discrete nature of the reaction process in removing particles in pairs is described. The independent pairs assumption gives an expression for the time-dependent rate of transition between states of the process. The model is compared with direct Monte Carlo simulations of the diffusion-reaction process for systems where the initial distribution of particles is Gaussian. Several gross effects are accounted for quantitatively. Minor discrepancies are resolved by further comparison with a Monte Carlo formulation of the independent pairs model which accounts for all initial correlations. Several extensions of the model are discussed, in particular the extensions to systems of charged particles and scavenging reactions. In order to make the extension to account for Coulomb forces, the recombination of a geminate charged pair must be analysed. The analysis is made in terms of the mathematical theory of diffusion. (author)

Monte Carlo Methods in Physics

International Nuclear Information System (INIS)

Santoso, B.

1997-01-01

Method of Monte Carlo integration is reviewed briefly and some of its applications in physics are explained. A numerical experiment on random generators used in the monte Carlo techniques is carried out to show the behavior of the randomness of various methods in generating them. To account for the weight function involved in the Monte Carlo, the metropolis method is used. From the results of the experiment, one can see that there is no regular patterns of the numbers generated, showing that the program generators are reasonably good, while the experimental results, shows a statistical distribution obeying statistical distribution law. Further some applications of the Monte Carlo methods in physics are given. The choice of physical problems are such that the models have available solutions either in exact or approximate values, in which comparisons can be mode, with the calculations using the Monte Carlo method. Comparison show that for the models to be considered, good agreement have been obtained

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...

Statistical implications in Monte Carlo depletions - 051

International Nuclear Information System (INIS)

Zhiwen, Xu; Rhodes, J.; Smith, K.

2010-01-01

As a result of steady advances of computer power, continuous-energy Monte Carlo depletion analysis is attracting considerable attention for reactor burnup calculations. The typical Monte Carlo analysis is set up as a combination of a Monte Carlo neutron transport solver and a fuel burnup solver. Note that the burnup solver is a deterministic module. The statistical errors in Monte Carlo solutions are introduced into nuclide number densities and propagated along fuel burnup. This paper is towards the understanding of the statistical implications in Monte Carlo depletions, including both statistical bias and statistical variations in depleted fuel number densities. The deterministic Studsvik lattice physics code, CASMO-5, is modified to model the Monte Carlo depletion. The statistical bias in depleted number densities is found to be negligible compared to its statistical variations, which, in turn, demonstrates the correctness of the Monte Carlo depletion method. Meanwhile, the statistical variation in number densities generally increases with burnup. Several possible ways of reducing the statistical errors are discussed: 1) to increase the number of individual Monte Carlo histories; 2) to increase the number of time steps; 3) to run additional independent Monte Carlo depletion cases. Finally, a new Monte Carlo depletion methodology, called the batch depletion method, is proposed, which consists of performing a set of independent Monte Carlo depletions and is thus capable of estimating the overall statistical errors including both the local statistical error and the propagated statistical error. (authors)

Optimal Bayesian Experimental Design for Combustion Kinetics

KAUST Repository

Huan, Xun

2011-01-04

Experimental diagnostics play an essential role in the development and refinement of chemical kinetic models, whether for the combustion of common complex hydrocarbons or of emerging alternative fuels. Questions of experimental design—e.g., which variables or species to interrogate, at what resolution and under what conditions—are extremely important in this context, particularly when experimental resources are limited. This paper attempts to answer such questions in a rigorous and systematic way. We propose a Bayesian framework for optimal experimental design with nonlinear simulation-based models. While the framework is broadly applicable, we use it to infer rate parameters in a combustion system with detailed kinetics. The framework introduces a utility function that reflects the expected information gain from a particular experiment. Straightforward evaluation (and maximization) of this utility function requires Monte Carlo sampling, which is infeasible with computationally intensive models. Instead, we construct a polynomial surrogate for the dependence of experimental observables on model parameters and design conditions, with the help of dimension-adaptive sparse quadrature. Results demonstrate the efficiency and accuracy of the surrogate, as well as the considerable effectiveness of the experimental design framework in choosing informative experimental conditions.

Direct Simulation Monte Carlo (DSMC) on the Connection Machine

International Nuclear Information System (INIS)

Wong, B.C.; Long, L.N.

1992-01-01

The massively parallel computer Connection Machine is utilized to map an improved version of the direct simulation Monte Carlo (DSMC) method for solving flows with the Boltzmann equation. The kinetic theory is required for analyzing hypersonic aerospace applications, and the features and capabilities of the DSMC particle-simulation technique are discussed. The DSMC is shown to be inherently massively parallel and data parallel, and the algorithm is based on molecule movements, cross-referencing their locations, locating collisions within cells, and sampling macroscopic quantities in each cell. The serial DSMC code is compared to the present parallel DSMC code, and timing results show that the speedup of the parallel version is approximately linear. The correct physics can be resolved from the results of the complete DSMC method implemented on the connection machine using the data-parallel approach. 41 refs

Charge transport in amorphous organic semiconductors

Energy Technology Data Exchange (ETDEWEB)

Lukyanov, Alexander

2011-03-15

Organic semiconductors with the unique combination of electronic and mechanical properties may offer cost-effective ways of realizing many electronic applications, e. g. large-area flexible displays, printed integrated circuits and plastic solar cells. In order to facilitate the rational compound design of organic semiconductors, it is essential to understand relevant physical properties e. g. charge transport. This, however, is not straightforward, since physical models operating on different time and length scales need to be combined. First, the material morphology has to be known at an atomistic scale. For this atomistic molecular dynamics simulations can be employed, provided that an atomistic force field is available. Otherwise it has to be developed based on the existing force fields and first principle calculations. However, atomistic simulations are typically limited to the nanometer length- and nanosecond time-scales. To overcome these limitations, systematic coarse-graining techniques can be used. In the first part of this thesis, it is demonstrated how a force field can be parameterized for a typical organic molecule. Then different coarse-graining approaches are introduced together with the analysis of their advantages and problems. When atomistic morphology is available, charge transport can be studied by combining the high-temperature Marcus theory with kinetic Monte Carlo simulations. The approach is applied to the hole transport in amorphous films of tris(8- hydroxyquinoline)aluminium (Alq{sub 3}). First the influence of the force field parameters and the corresponding morphological changes on charge transport is studied. It is shown that the energetic disorder plays an important role for amorphous Alq{sub 3}, defining charge carrier dynamics. Its spatial correlations govern the Poole-Frenkel behavior of the charge carrier mobility. It is found that hole transport is dispersive for system sizes accessible to simulations, meaning that calculated

Monte Carlo simulation for IRRMA

International Nuclear Information System (INIS)

Gardner, R.P.; Liu Lianyan

2000-01-01

Monte Carlo simulation is fast becoming a standard approach for many radiation applications that were previously treated almost entirely by experimental techniques. This is certainly true for Industrial Radiation and Radioisotope Measurement Applications - IRRMA. The reasons for this include: (1) the increased cost and inadequacy of experimentation for design and interpretation purposes; (2) the availability of low cost, large memory, and fast personal computers; and (3) the general availability of general purpose Monte Carlo codes that are increasingly user-friendly, efficient, and accurate. This paper discusses the history and present status of Monte Carlo simulation for IRRMA including the general purpose (GP) and specific purpose (SP) Monte Carlo codes and future needs - primarily from the experience of the authors

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

Vortex lattice melting, pinning and kinetics

International Nuclear Information System (INIS)

Doniach, S.; Ryu, S.; Kapitulnik, A.

1994-01-01

The phenomenology of the high T c superconductors is discussed both at the level of the thermodynamics of melting of the Abrikosov flux lattice and in terms of the melting and kinetics of the flux lattice for a pinned system. The authors review results on 3D melting obtained by a Monte Carlo simulation approach in which the 2D open-quotes pancakeclose quotes vortices are treated as statistical variables. The authors discuss pinning in the context of the strong pinning regime in which the vortex density given in terms of the applied field B is small compared to that represented by an effective field B pin measuring the pinning center density. The authors introduce a new criterion for the unfreezing of a vortex glass on increase of magnetic field or temperature, in the strong pinning, small field unit. The authors model this limit in terms of a single flux line interacting with a columnar pin. This model is studied both analytically and by computer simulation. By applying a tilt potential, the authors study the kinetics of the vortex motion in an external current and show that the resulting current-voltage characteristic follows a basic vortex glass-like scaling relation in the vicinity of the depinning transition

Insights into the charge carrier terahertz mobility in polyfluorenes from large-scale atomistic simulations and time-resolved terahertz spectroscopy

Czech Academy of Sciences Publication Activity Database

Vukmirović, N.; Ponseca, C.S.; Němec, Hynek; Yartsev, A.; Sundström, V.

2012-01-01

Roč. 116, č. 37 (2012), s. 19665-1972 ISSN 1932-7447 Institutional research plan: CEZ:AV0Z10100520 Keywords : charge carrier mobility * time-resolved terahertz spectroscopy * multiscale atomistic calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.814, year: 2012

Atomistic modeling of the structural components of the blood-brain barrier

Science.gov (United States)

Glukhova, O. E.; Grishina, O. A.; Slepchenkov, M. M.

2015-03-01

Blood-brain barrier, which is a barrage system between the brain and blood vessels, plays a key role in the "isolation" of the brain of unnecessary information, and reduce the "noise" in the interneuron communication. It is known that the barrier function of the BBB strictly depends on the initial state of the organism and changes significantly with age and, especially in developing the "vascular accidents". Disclosure mechanisms of regulation of the barrier function will develop new ways to deliver neurotrophic drugs to the brain in the newborn. The aim of this work is the construction of atomistic models of structural components of the blood-brain barrier to reveal the mechanisms of regulation of the barrier function.

Microscopic theory for coupled atomistic magnetization and lattice dynamics

Science.gov (United States)

Fransson, J.; Thonig, D.; Bessarab, P. F.; Bhattacharjee, S.; Hellsvik, J.; Nordström, L.

2017-12-01

A coupled atomistic spin and lattice dynamics approach is developed which merges the dynamics of these two degrees of freedom into a single set of coupled equations of motion. The underlying microscopic model comprises local exchange interactions between the electron spin and magnetic moment and the local couplings between the electronic charge and lattice displacements. An effective action for the spin and lattice variables is constructed in which the interactions among the spin and lattice components are determined by the underlying electronic structure. In this way, expressions are obtained for the electronically mediated couplings between the spin and lattice degrees of freedom, besides the well known interatomic force constants and spin-spin interactions. These former susceptibilities provide an atomistic ab initio description for the coupled spin and lattice dynamics. It is important to notice that this theory is strictly bilinear in the spin and lattice variables and provides a minimal model for the coupled dynamics of these subsystems and that the two subsystems are treated on the same footing. Questions concerning time-reversal and inversion symmetry are rigorously addressed and it is shown how these aspects are absorbed in the tensor structure of the interaction fields. By means of these results regarding the spin-lattice coupling, simple explanations of ionic dimerization in double-antiferromagnetic materials, as well as charge density waves induced by a nonuniform spin structure, are given. In the final parts, coupled equations of motion for the combined spin and lattice dynamics are constructed, which subsequently can be reduced to a form which is analogous to the Landau-Lifshitz-Gilbert equations for spin dynamics and a damped driven mechanical oscillator for the ionic motion. It is important to notice, however, that these equations comprise contributions that couple these descriptions into one unified formulation. Finally, Kubo-like expressions for

Geology of Maxwell Montes, Venus

Science.gov (United States)

Head, J. W.; Campbell, D. B.; Peterfreund, A. R.; Zisk, S. A.

1984-01-01

Maxwell Montes represent the most distinctive topography on the surface of Venus, rising some 11 km above mean planetary radius. The multiple data sets of the Pioneer missing and Earth based radar observations to characterize Maxwell Montes are analyzed. Maxwell Montes is a porkchop shaped feature located at the eastern end of Lakshmi Planum. The main massif trends about North 20 deg West for approximately 1000 km and the narrow handle extends several hundred km West South-West WSW from the north end of the main massif, descending down toward Lakshmi Planum. The main massif is rectilinear and approximately 500 km wide. The southern and northern edges of Maxwell Montes coincide with major topographic boundaries defining the edge of Ishtar Terra.

Diffusion in energy materials: Governing dynamics from atomistic modelling

Science.gov (United States)

Parfitt, D.; Kordatos, A.; Filippatos, P. P.; Chroneos, A.

2017-09-01

Understanding diffusion in energy materials is critical to optimising the performance of solid oxide fuel cells (SOFCs) and batteries both of which are of great technological interest as they offer high efficiency for cleaner energy conversion and storage. In the present review, we highlight the insights offered by atomistic modelling of the ionic diffusion mechanisms in SOFCs and batteries and how the growing predictive capability of high-throughput modelling, together with our new ability to control compositions and microstructures, will produce advanced materials that are designed rather than chosen for a given application. The first part of the review focuses on the oxygen diffusion mechanisms in cathode and electrolyte materials for SOFCs and in particular, doped ceria and perovskite-related phases with anisotropic structures. The second part focuses on disordered oxides and two-dimensional materials as these are very promising systems for battery applications.

Mesoscale modeling of amorphous metals by shear transformation zone dynamics

International Nuclear Information System (INIS)

Homer, Eric R.; Schuh, Christopher A.

2009-01-01

A new mesoscale modeling technique for the thermo-mechanical behavior of metallic glasses is proposed. The modeling framework considers the shear transformation zone (STZ) as the fundamental unit of deformation, and coarse-grains an amorphous collection of atoms into an ensemble of STZs on a mesh. By employing finite element analysis and a kinetic Monte Carlo algorithm, the modeling technique is capable of simulating glass processing and deformation on time and length scales greater than those usually attainable by atomistic modeling. A thorough explanation of the framework is presented, along with a specific two-dimensional implementation for a model metallic glass. The model is shown to capture the basic behaviors of metallic glasses, including high-temperature homogeneous flow following the expected constitutive law, and low-temperature strain localization into shear bands. Details of the effects of processing and thermal history on the glass structure and properties are also discussed.

Atomistic simulations of contact area and conductance at nanoscale interfaces.

Science.gov (United States)

Hu, Xiaoli; Martini, Ashlie

2017-11-09

Atomistic simulations were used to study conductance across the interface between a nanoscale gold probe and a graphite surface with a step edge. Conductance on the graphite terrace was observed to increase with load and be approximately proportional to contact area calculated from the positions of atoms in the interface. The relationship between area and conductance was further explored by varying the position of the contact relative to the location of the graphite step edge. These simulations reproduced a previously-reported current dip at step edges measured experimentally and the trend was explained by changes in both contact area and the distribution of distances between atoms in the interface. The novel approach reported here provides a foundation for future studies of the fundamental relationships between conductance, load and surface topography at the atomic scale.

Role of Sink Density in Nonequilibrium Chemical Redistribution in Alloys

Science.gov (United States)

Martínez, Enrique; Senninger, Oriane; Caro, Alfredo; Soisson, Frédéric; Nastar, Maylise; Uberuaga, Blas P.

2018-03-01

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role of interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. This model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.

(U) Introduction to Monte Carlo Methods

Energy Technology Data Exchange (ETDEWEB)

Hungerford, Aimee L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-03-20

Monte Carlo methods are very valuable for representing solutions to particle transport problems. Here we describe a “cook book” approach to handling the terms in a transport equation using Monte Carlo methods. Focus is on the mechanics of a numerical Monte Carlo code, rather than the mathematical foundations of the method.

Displacement cascades and defect annealing in tungsten, Part III: The sensitivity of cascade annealing in tungsten to the values of kinetic parameters

Energy Technology Data Exchange (ETDEWEB)

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

2015-07-01

Object kinetic Monte Carlo (OKMC) simulations have been performed to investigate various aspects of cascade aging in bulk tungsten and to determine the sensitivity of the results to the kinetic parameters. The primary focus is on how the kinetic parameters affect the initial recombination of defects in the first few ns of a simulation. The simulations were carried out using the object kinetic Monte Carlo (OKMC) code KSOME (kinetic simulations of microstructure evolution), using a database of cascades obtained from results of molecular dynamics (MD) simulations at various primary knock-on atom (PKA) energies and directions at temperatures of 300, 1025 and 2050 K. The OKMC model was parameterized using defect migration barriers and binding energies from ab initio calculations. Results indicate that, due to the disparate mobilities of SIA and vacancy clusters in tungsten, annealing is dominated by SIA migration even at temperatures as high as 2050 K. For 100 keV cascades initiated at 300 K recombination is dominated by annihilation of large defect clusters. But for all other PKA energies and temperatures most of the recombination is due to the migration and rotation of small SIA clusters, while all the large SIA clusters escape the cubic simulation cell. The inverse U-shape behavior exhibited by the annealing efficiency as a function of temperature curve, especially for cascades of large PKA energies, is due to asymmetry in SIA and vacancy clustering assisted by the large difference in mobilities of SIAs and vacancies. This annealing behavior is unaffected by the dimensionality of SIA migration persists over a broad range of relative mobilities of SIAs and vacancies.

Atomistic modeling of defect evolution in Si for amorphizing and subamorphizing implants

International Nuclear Information System (INIS)

Lopez, Pedro; Pelaz, Lourdes; Marques, Luis A.; Santos, Ivan; Aboy, Maria; Barbolla, Juan

2004-01-01

Solid phase epitaxial regrowth of pre-amorphizing implants has received significant attention as a method to achieve high dopant activation with minimal diffusion at low implant temperatures and suppress channelling. Therefore, a good understanding of the amorphization and regrowth mechanisms is required in process simulators. We present an atomistic amorphization and recrystallization model that uses the interstitial-vacancy (I-V) pair as a building block to describe the amorphous phase. I-V pairs are locally characterized by the number of neighbouring I-V pairs. This feature captures the damage generation and the dynamical annealing during ion implantation, and also explains the annealing behaviour of amorphous layers and amorphous pockets

Atomistic simulations of screw dislocations in bcc tungsten: From core structures and static properties to interaction with vacancies

Energy Technology Data Exchange (ETDEWEB)

Xu, Ke [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Niu, Liang-Liang [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Department of Nuclear Engineering and Radiological Science, University of Michigan, Ann Arbor, MI 48109 (United States); Jin, Shuo, E-mail: jinshuo@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Shu, Xiaolin [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Xie, Hongxian [School of Mechanical Engineering, Hebei University of Technology, Tianjin 300132 (China); Wang, Lifang; Lu, Guang-Hong [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China)

2017-02-15

Atomistic simulations have been used to investigate the core structures, static properties of isolated 1/2 <1 1 1> screw dislocations, and their interaction with vacancies in bcc tungsten (W) based on three empirical interatomic potentials. Differential displacement maps show that only one embedded atom method potential is able to reproduce the compact non-degenerate core as evidenced by ab initio calculations. The obtained strain energy and stress distribution from atomistic simulations are, in general, consistent with elasticity theory predictions. In particular, one component of the calculated shear stress, which is not present according to elasticity theory, is non-negligible in the core region of our dislocation model. The differences between the results calculated from three interatomic potentials are in details, such as the specific value and the symmetry, but the trend of spatial distributions of static properties in the long range are close to each other. By calculating the binding energies between the dislocations and vacancies, we demonstrate that the dislocations act as vacancy sinks, which may be important for the nucleation and growth of hydrogen bubbles in W under irradiation.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

Science.gov (United States)

Quevillon, Michael J; Whitmer, Jonathan K

2018-01-02

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure-constant temperature ensemble. These materials exhibit a distinct "smectic" liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

MVP/GMVP Version 3. General purpose Monte Carlo codes for neutron and photon transport calculations based on continuous energy and multigroup methods (Translated document)

International Nuclear Information System (INIS)

Nagaya, Yasunobu; Okumura, Keisuke; Sakurai, Takeshi; Mori, Takamasa

2017-03-01

In order to realize fast and accurate Monte Carlo simulation of neutron and photon transport problems, two Monte Carlo codes MVP (continuous-energy method) and GMVP (multigroup method) have been developed at Japan Atomic Energy Agency. The codes have adopted a vectorized algorithm and have been developed for vector-type supercomputers. They also support parallel processing with a standard parallelization library MPI and thus a speed-up of Monte Carlo calculations can be achieved on general computing platforms. The first and second versions of the codes were released in 1994 and 2005, respectively. They have been extensively improved and new capabilities have been implemented. The major improvements and new capabilities are as follows: (1) perturbation calculation for effective multiplication factor, (2) exact resonant elastic scattering model, (3) calculation of reactor kinetics parameters, (4) photo-nuclear model, (5) simulation of delayed neutrons, (6) generation of group constants. This report describes the physical model, geometry description method used in the codes, new capabilities and input instructions. (author)

Cationic Dimyristoylphosphatidylcholine and Dioleoyloxytrimethylammonium Propane Lipid Bilayers: Atomistic Insight for Structure and Dynamics

DEFF Research Database (Denmark)

Zhao, W.; Gurtovenko, A. A.; Vattulainen, I.

2012-01-01

We performed atomistic molecular dynamics simulations of lipid bilayers consisting of a mixture of cationic dioleoyloxytrimethylammonium propane (DOTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) lipids at different DOTAP fractions. Our primary focus was the specific effects...... of unsaturated lipid chains on structural and dynamic properties of mixed cationic bilayers. The bilayer area, as well as the ordering of lipid tails, shows a pronounced nonmonotonic behavior when TAP lipid fraction increases. The minimum in area (maximum in ordering) was observed for a bilayer with TAP fraction...... lipids, which were found to form PC-PC and PC-TAP pairs, and the formation of lipid clusters....

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.

Lectures on Monte Carlo methods

CERN Document Server

Madras, Neal

2001-01-01

Monte Carlo methods form an experimental branch of mathematics that employs simulations driven by random number generators. These methods are often used when others fail, since they are much less sensitive to the "curse of dimensionality", which plagues deterministic methods in problems with a large number of variables. Monte Carlo methods are used in many fields: mathematics, statistics, physics, chemistry, finance, computer science, and biology, for instance. This book is an introduction to Monte Carlo methods for anyone who would like to use these methods to study various kinds of mathemati

Computer code for the atomistic simulation of lattice defects and dynamics

International Nuclear Information System (INIS)

Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

1980-04-01

This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability

Hybrid SN/Monte Carlo research and results

International Nuclear Information System (INIS)

Baker, R.S.

1993-01-01

The neutral particle transport equation is solved by a hybrid method that iteratively couples regions where deterministic (S N ) and stochastic (Monte Carlo) methods are applied. The Monte Carlo and S N regions are fully coupled in the sense that no assumption is made about geometrical separation or decoupling. The hybrid Monte Carlo/S N method provides a new means of solving problems involving both optically thick and optically thin regions that neither Monte Carlo nor S N is well suited for by themselves. The hybrid method has been successfully applied to realistic shielding problems. The vectorized Monte Carlo algorithm in the hybrid method has been ported to the massively parallel architecture of the Connection Machine. Comparisons of performance on a vector machine (Cray Y-MP) and the Connection Machine (CM-2) show that significant speedups are obtainable for vectorized Monte Carlo algorithms on massively parallel machines, even when realistic problems requiring variance reduction are considered. However, the architecture of the Connection Machine does place some limitations on the regime in which the Monte Carlo algorithm may be expected to perform well

Critical assessment of Pt surface energy - An atomistic study

Science.gov (United States)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

Three-dimensional Monte Carlo model of pulsed-laser treatment of cutaneous vascular lesions

Science.gov (United States)

Milanič, Matija; Majaron, Boris

2011-12-01

We present a three-dimensional Monte Carlo model of optical transport in skin with a novel approach to treatment of side boundaries of the volume of interest. This represents an effective way to overcome the inherent limitations of ``escape'' and ``mirror'' boundary conditions and enables high-resolution modeling of skin inclusions with complex geometries and arbitrary irradiation patterns. The optical model correctly reproduces measured values of diffuse reflectance for normal skin. When coupled with a sophisticated model of thermal transport and tissue coagulation kinetics, it also reproduces realistic values of radiant exposure thresholds for epidermal injury and for photocoagulation of port wine stain blood vessels in various skin phototypes, with or without application of cryogen spray cooling.

Benchmark test of drift-kinetic and gyrokinetic codes through neoclassical transport simulations

International Nuclear Information System (INIS)

Satake, S.; Sugama, H.; Watanabe, T.-H.; Idomura, Yasuhiro

2009-09-01

Two simulation codes that solve the drift-kinetic or gyrokinetic equation in toroidal plasmas are benchmarked by comparing the simulation results of neoclassical transport. The two codes are the drift-kinetic δf Monte Carlo code (FORTEC-3D) and the gyrokinetic full- f Vlasov code (GT5D), both of which solve radially-global, five-dimensional kinetic equation with including the linear Fokker-Planck collision operator. In a tokamak configuration, neoclassical radial heat flux and the force balance relation, which relates the parallel mean flow with radial electric field and temperature gradient, are compared between these two codes, and their results are also compared with the local neoclassical transport theory. It is found that the simulation results of the two codes coincide very well in a wide rage of plasma collisionality parameter ν * = 0.01 - 10 and also agree with the theoretical estimations. The time evolution of radial electric field and particle flux, and the radial profile of the geodesic acoustic mode frequency also coincide very well. These facts guarantee the capability of GT5D to simulate plasma turbulence transport with including proper neoclassical effects of collisional diffusion and equilibrium radial electric field. (author)

Monte Carlo simulation in nuclear medicine

International Nuclear Information System (INIS)

Morel, Ch.

2007-01-01

The Monte Carlo method allows for simulating random processes by using series of pseudo-random numbers. It became an important tool in nuclear medicine to assist in the design of new medical imaging devices, optimise their use and analyse their data. Presently, the sophistication of the simulation tools allows the introduction of Monte Carlo predictions in data correction and image reconstruction processes. The availability to simulate time dependent processes opens up new horizons for Monte Carlo simulation in nuclear medicine. In a near future, these developments will allow to tackle simultaneously imaging and dosimetry issues and soon, case system Monte Carlo simulations may become part of the nuclear medicine diagnostic process. This paper describes some Monte Carlo method basics and the sampling methods that were developed for it. It gives a referenced list of different simulation software used in nuclear medicine and enumerates some of their present and prospective applications. (author)

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Science.gov (United States)

Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

2018-05-01

Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Directory of Open Access Journals (Sweden)

Zhiwei Zhang

2018-05-01

Full Text Available Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young’s modulus, ultimate tensile strength (UTS, and strain at fracture is observed.

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)

Dabli, Djamel

2010-01-01

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)

Atomistic tight-binding theory of excitonic splitting energies in CdX(X = Se, S and Te)/ZnS core/shell nanocrystals

Science.gov (United States)

Sukkabot, Worasak; Pinsook, Udomsilp

2017-01-01

Using the atomistic tight-binding theory (TB) and a configuration interaction description (CI), we numerically compute the excitonic splitting of CdX(X = Se, S and Te)/ZnS core/shell nanocrystals with the objective to explain how types of the core materials and growth shell thickness can provide the detailed manipulation of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting, beneficial for the active application of quantum information. To analyze the splitting of the excitonic states, the optical band gaps, ground-state wave function overlaps and atomistic electron-hole interactions tend to be numerically demonstrated. Based on the atomistic computations, the single-particle and excitonic gaps are mainly reduced with the increasing ZnS shell thickness owing to the quantum confinement. In the range of the higher to lower energies, the order of the single-particle gaps is CdSe/ZnS, CdS/ZnS and CdTe/ZnS core/shell nanocrystals, while one of the excitonic gaps is CdS/ZnS, CdSe/ZnS and CdTe/ZnS core/shell nanocrystals because of the atomistic electron-hole interaction. The strongest electron-hole interactions are mainly observed in CdSe/ZnS core/shell nanocrystals. In addition, the computational results underline that the energies of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting are generally reduced with the increasing ZnS growth shell thickness as described by the trend of the electron-hole exchange interaction. The high-to-low splitting of the excitonic states is demonstrated in CdSe/ZnS, CdTe/ZnS and CdS/ZnS core/shell nanocrystals because of the fashion in the electron-hole exchange interaction and overlaps of the electron-hole wave functions. As the resulting calculations, it is expected that CdS/ZnS core/shell nanocrystals are the best candidates to be the source of entangled photons. Finally, the comprehensive information on the excitonic splitting can enable the use of suitable core

Effects of Neutron Emission on Fragment Mass and Kinetic Energy Distribution from Thermal Neutron-Induced Fission of 235U

International Nuclear Information System (INIS)

Montoya, M.; Rojas, J.; Saetone, E.

2007-01-01

The mass and kinetic energy distribution of nuclear fragments from thermal neutron-induced fission of 235 U(n th ,f) have been studied using a Monte-Carlo simulation. Besides reproducing the pronounced broadening in the standard deviation of the kinetic energy at the final fragment mass number around m = 109, our simulation also produces a second broadening around m = 125. These results are in good agreement with the experimental data obtained by Belhafaf et al. and other results on yield of mass. We conclude that the obtained results are a consequence of the characteristics of the neutron emission, the sharp variation in the primary fragment kinetic energy and mass yield curves. We show that because neutron emission is hazardous to make any conclusion on primary quantities distribution of fragments from experimental results on final quantities distributions

Nucleation and growth kinetics of palladium nanoparticles on thin ...

African Journals Online (AJOL)

transmission electron microscopy (TEM), related to the first quantitative study on the ... density of clusters decreases when the substrate temperature increases following Arrhenius law. ... in two terms classical thermodynamics and atomistic.

Belo Monte hydropower project: actual studies; AHE Belo Monte: os estudos atuais

Energy Technology Data Exchange (ETDEWEB)

Figueira Netto, Carlos Alberto de Moya [CNEC Engenharia S.A., Sao Paulo, SP (Brazil); Rezende, Paulo Fernando Vieira Souto [Centrais Eletricas Brasileiras S.A. (ELETROBRAS), Rio de Janeiro, RJ (Brazil)

2008-07-01

This article presents the evolution of the studies of Belo Monte Hydro Power Project (HPP) since the initial inventory studies of the Xingu River in 1979 until the current studies for conclusion of the Technical, Economic and Environmental Feasibility Studies the Belo Monte Hydro Power Project, as authorized by Brazilian National Congress. The current studies characterize the Belo Monte HPP with an installed capacity of 11,181.3 MW (20 units of 550 MW in the main power house and 7 units of 25.9 MW in the additional power house), connected to the Brazilian Interconnected Power Grid, allowing to generate 4,796 mean MW of firm energy, without depending on any flow rate regularization of the upstream Xingu river flooding only 441 k m2, of which approximately 200 k m2, correspond to the normal annual wet season flooding of the Xingu River. (author)

Atomic scale Monte Carlo simulations of BF3 plasma immersion ion implantation in Si

International Nuclear Information System (INIS)

La Magna, Antonino; Fisicaro, Giuseppe; Nicotra, Giuseppe; Spiegel, Yohann; Torregrosa, Frank

2014-01-01

We present a numerical model aimed to accurately simulate the plasma immersion ion implantation (PIII) process in micro and nano-patterned Si samples. The code, based on the Monte Carlo approach, is designed to reproduce all the relevant physical phenomena involved in the process. The particle based simulation technique is fundamental to efficiently compute the material modifications promoted by the plasma implantation at the atomic resolution. The accuracy in the description of the process kinetic is achieved linking (one to one) each virtual Monte Carlo event to each possible atomic phenomenon (e.g. ion penetration, neutral absorption, ion induced surface modification, etc.). The code is designed to be coupled with a generic plasma status, characterized by the particle types (ions and neutrals), their flow rates and their energy/angle distributions. The coupling with a Poisson solver allows the simulation of the correct trajectories of charged particles in the void regions of the micro-structures. The implemented model is able to predict the implantation 2D profiles and significantly support the process design. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Advanced Multilevel Monte Carlo Methods

KAUST Repository

Jasra, Ajay

2017-04-24

This article reviews the application of advanced Monte Carlo techniques in the context of Multilevel Monte Carlo (MLMC). MLMC is a strategy employed to compute expectations which can be biased in some sense, for instance, by using the discretization of a associated probability law. The MLMC approach works with a hierarchy of biased approximations which become progressively more accurate and more expensive. Using a telescoping representation of the most accurate approximation, the method is able to reduce the computational cost for a given level of error versus i.i.d. sampling from this latter approximation. All of these ideas originated for cases where exact sampling from couples in the hierarchy is possible. This article considers the case where such exact sampling is not currently possible. We consider Markov chain Monte Carlo and sequential Monte Carlo methods which have been introduced in the literature and we describe different strategies which facilitate the application of MLMC within these methods.

Advanced Multilevel Monte Carlo Methods

KAUST Repository

Jasra, Ajay; Law, Kody; Suciu, Carina

2017-01-01

This article reviews the application of advanced Monte Carlo techniques in the context of Multilevel Monte Carlo (MLMC). MLMC is a strategy employed to compute expectations which can be biased in some sense, for instance, by using the discretization of a associated probability law. The MLMC approach works with a hierarchy of biased approximations which become progressively more accurate and more expensive. Using a telescoping representation of the most accurate approximation, the method is able to reduce the computational cost for a given level of error versus i.i.d. sampling from this latter approximation. All of these ideas originated for cases where exact sampling from couples in the hierarchy is possible. This article considers the case where such exact sampling is not currently possible. We consider Markov chain Monte Carlo and sequential Monte Carlo methods which have been introduced in the literature and we describe different strategies which facilitate the application of MLMC within these methods.

Atomistic Simulation of Initiation in Hexanitrostilbene

Science.gov (United States)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. 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. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Atomistic mechanism of graphene growth on a SiC substrate: Large-scale molecular dynamics simulations based on a new charge-transfer bond-order type potential

Science.gov (United States)

Takamoto, So; Yamasaki, Takahiro; Nara, Jun; Ohno, Takahisa; Kaneta, Chioko; Hatano, Asuka; Izumi, Satoshi

2018-03-01

Thermal decomposition of silicon carbide is a promising approach for the fabrication of graphene. However, the atomistic growth mechanism of graphene remains unclear. This paper describes the development of a new charge-transfer interatomic potential. Carbon bonds with a wide variety of characteristics can be reproduced by the proposed vectorized bond-order term. A large-scale thermal decomposition simulation enables us to observe the continuous growth process of the multiring carbon structure. The annealing simulation reveals the atomistic process by which the multiring carbon structure is transformed to flat graphene involving only six-membered rings. Also, it is found that the surface atoms of the silicon carbide substrate enhance the homogeneous graphene formation.

A simplified kinetic and mass transfer modelling of the thermal hydrolysis of vegetable oils

DEFF Research Database (Denmark)

Forero-Hernandez, Hector Alexander; Jones, Mark Nicholas; Sarup, Bent

2017-01-01

This work presents a combined modelling approach to investigate the kinetics and masstransfer effects on the hydrolysis of vegetable oils under subcritical conditions. The primary purpose of this simplified model is to interpret experimental data collected from typical batch tests and to estimate...... parameters for the proposed model. Due to its heterogeneous nature, the hydrolysis reaction is affected not only by the chemical kinetics but also by the rate of mass transfer between the oil and water as well as their specific contact area in this two phase emulsion. Considering these properties, a model...... and improvement accompanied by Monte Carlo uncertainty analysis. Since the lack of experimental data is a crucial issue in the hydrolysis of vegetable oils, this model-based analysis of data is of substantial value to provide necessary information for detailed modeling and characterization of the process....

Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

International Nuclear Information System (INIS)

Seppä, Jeremias; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Lassila, Antti; Reischl, Bernhard; Raiteri, Paolo; Rohl, Andrew L; Nordlund, Kai

2017-01-01

Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation. (paper)

Hybrid Multilevel Monte Carlo Simulation of Stochastic Reaction Networks

KAUST Repository

Moraes, Alvaro

2015-01-07

Stochastic reaction networks (SRNs) is a class of continuous-time Markov chains intended to describe, from the kinetic point of view, the time-evolution of chemical systems in which molecules of different chemical species undergo a finite set of reaction channels. This talk is based on articles [4, 5, 6], where we are interested in the following problem: given a SRN, X, defined though its set of reaction channels, and its initial state, x0, estimate E (g(X(T))); that is, the expected value of a scalar observable, g, of the process, X, at a fixed time, T. This problem lead us to define a series of Monte Carlo estimators, M, such that, with high probability can produce values close to the quantity of interest, E (g(X(T))). More specifically, given a user-selected tolerance, TOL, and a small confidence level, η, find an estimator, M, based on approximate sampled paths of X, such that, P (|E (g(X(T))) − M| ≤ TOL) ≥ 1 − η; even more, we want to achieve this objective with near optimal computational work. We first introduce a hybrid path-simulation scheme based on the well-known stochastic simulation algorithm (SSA)[3] and the tau-leap method [2]. Then, we introduce a Multilevel Monte Carlo strategy that allows us to achieve a computational complexity of order O(T OL−2), this is the same computational complexity as in an exact method but with a smaller constant. We provide numerical examples to show our results.

Ab-initio modelling of thermodynamics and kinetics of point defects in indium oxide

International Nuclear Information System (INIS)

Agoston, Peter; Klein, Andreas; Albe, Karsten; Erhart, Paul

2008-01-01

The electrical and optical properties of indium oxide films strongly vary with the processing parameters. Especially the oxygen partial pressure and temperature determine properties like electrical conductivity, composition and transparency. Since this material owes its remarkable properties like the intrinsic n-type conductivity to its defect chemistry, it is important to understand both, the equilibrium defect thermodynamics and kinetics of the intrinsic point defects. In this contribution we present a defect model based on DFT total energy calculations using the GGA+U method. Further, the nudged elastic band method is employed in order to obtain a set of migration barriers for each defect species. Due to the complicated crystal structure of indium oxide a Kinetic Monte-Carlo algorithm was implemented, which allows to determine diffusion coefficients. The bulk tracer diffusion constant is predicted as a function of oxygen partial pressure, Fermi level and temperature for the pure material

Extension of the quantum-kinetic model to lunar and Mars return physics

Energy Technology Data Exchange (ETDEWEB)

Liechty, D. S. [Aerothermodynamics Branch, NASA Langley Research Center, Hampton, Virginia 23681 (United States); Lewis, M. J. [Department of Aerospace Engineering, University of Maryland, College Park, Maryland 20742 (United States)

2014-02-15

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high-mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. A recently introduced molecular-level chemistry model, the quantum-kinetic, or Q-K, model that predicts reaction rates for gases in thermal equilibrium and non-equilibrium using only kinetic theory and fundamental molecular properties, is extended in the current work to include electronic energy level transitions and reactions involving charged particles. Like the Q-K procedures for neutral species chemical reactions, these new models are phenomenological procedures that aim to reproduce the reaction/transition rates but do not necessarily capture the exact physics. These engineering models are necessarily efficient due to the requirement to compute billions of simulated collisions in direct simulation Monte Carlo (DSMC) simulations. The new models are shown to generally agree within the spread of reported transition and reaction rates from the literature for near equilibrium conditions.

Lipid-protein interaction induced domains: Kinetics and conformational changes in multicomponent vesicles

Science.gov (United States)

Sreeja, K. K.; Sunil Kumar, P. B.

2018-04-01

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated in the past. We show, using Monte Carlo simulations, that the affinity of proteins for specific lipids can hasten their aggregation kinetics. The lipid membrane is modeled as a dynamically triangulated surface with the proteins defined as in-plane fields at the vertices. We show that, even at low protein concentrations, strong lipid-protein interactions can result in large protein clusters indicating a route to lipid mediated signal amplification. At high protein concentrations, the domains form buds similar to that seen in lipid-lipid interaction induced phase separation. Protein interaction induced domain budding is suppressed when proteins act as anisotropic inclusions and exhibit nematic orientational order. The kinetics of protein clustering and resulting conformational changes are shown to be significantly different for the isotropic and anisotropic curvature inducing proteins.

Monte Carlo simulation of experiments

International Nuclear Information System (INIS)

Opat, G.I.

1977-07-01

An outline of the technique of computer simulation of particle physics experiments by the Monte Carlo method is presented. Useful special purpose subprograms are listed and described. At each stage the discussion is made concrete by direct reference to the programs SIMUL8 and its variant MONTE-PION, written to assist in the analysis of the radiative decay experiments μ + → e + ν sub(e) antiνγ and π + → e + ν sub(e)γ, respectively. These experiments were based on the use of two large sodium iodide crystals, TINA and MINA, as e and γ detectors. Instructions for the use of SIMUL8 and MONTE-PION are given. (author)