Numazawa, Satoshi; Smith, Roger
2011-10-01
Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.
Energy Technology Data Exchange (ETDEWEB)
Castin, N., E-mail: ncastin@sckcen.be [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium); Pascuet, M.I., E-mail: pascuet@cnea.gov.ar [Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires (Argentina); Malerba, L. [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium)
2012-10-15
The formation of Cu-rich precipitates under irradiation is a major cause for changes in the mechanical response to load of reactor pressure vessel steels. In previous works, it has been shown that the mechanism under which precipitation occurs is governed by diffusion of vacancy-copper (VCu) complexes, also in the absence of irradiation. Coarse-grained computer models (such as object kinetic Monte Carlo) aimed at simulating irradiation processes in model alloys or steels should therefore explicitly include the mobility of Cu precipitates, as a consequence of vacancy hops at their surface. For this purpose, in this work we calculate diffusion coefficients and lifetimes for a large variety of VCu complexes. We use an innovative atomistic model, where vacancy migration energies are calculated with little approximations, taking into account all effects of static relaxation and long-range chemical interaction as predicted by an interatomic potential. Our results show that, contrary to what intuition might suggest, saturation in vacancies tend to slow down the transport of Cu atoms.
Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae
2017-06-07
Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.
Atomistic Monte Carlo simulation of lipid membranes
DEFF Research Database (Denmark)
Wüstner, Daniel; Sklenar, Heinz
2014-01-01
Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction...... into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches...... of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol....
National Research Council Canada - National Science Library
Yifan Nie; Chaoping Liang; Pil-Ryung Cha; Luigi Colombo; Robert M Wallace; Kyeongjae Cho
2017-01-01
.... Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW...
Stress-dependence of kinetic transitions at atomistic defects
Ball, S. L.; Alexander, K. C.; Schuh, C. A.
2018-01-01
The full second-rank activation volume tensors associated with vacancy migration in FCC copper and HCP titanium as well as transition events in the Σ5 (2 1 0) grain boundary in copper are calculated and analyzed. The full tensorial results quantitatively illustrate how the conventional use of an activation volume scalar in atomistic studies of the kinetic processes of complex defects can miss important stress dependencies, in that neither hydrostatic pressure nor deviatoric stress dependencies can be considered alone as dominating the response. The results speak to the importance of anisotropies in the stress-dependence of atomistic kinetics, including crystal structure anisotropy, elastic anisotropy, and defect structure or migration-path anisotropies.
A valence force field-Monte Carlo algorithm for quantum dot growth modeling
DEFF Research Database (Denmark)
Barettin, Daniele; Kadkhodazadeh, Shima; Pecchia, Alessandro
2017-01-01
We present a novel kinetic Monte Carlo version for the atomistic valence force fields algorithm in order to model a self-assembled quantum dot growth process. We show our atomistic model is both computationally favorable and capture more details compared to traditional kinetic Monte Carlo models...
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.)
RNA folding kinetics using Monte Carlo and Gillespie algorithms.
Clote, Peter; Bayegan, Amir H
2017-08-05
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 .
Strain in the mesoscale kinetic Monte Carlo model for sintering
DEFF Research Database (Denmark)
Bjørk, Rasmus; Frandsen, Henrik Lund; Tikare, V.
2014-01-01
Shrinkage strains measured from microstructural simulations using the mesoscale kinetic Monte Carlo (kMC) model for solid state sintering are discussed. This model represents the microstructure using digitized discrete sites that are either grain or pore sites. The algorithm used to simulate...
Anisotropic solid-liquid interface kinetics in silicon: an atomistically informed phase-field model
Bergmann, S.; Albe, K.; Flegel, E.; Barragan-Yani, D. A.; Wagner, B.
2017-09-01
We present an atomistically informed parametrization of a phase-field model for describing the anisotropic mobility of liquid-solid interfaces in silicon. The model is derived from a consistent set of atomistic data and thus allows to directly link molecular dynamics and phase field simulations. Expressions for the free energy density, the interfacial energy and the temperature and orientation dependent interface mobility are systematically fitted to data from molecular dynamics simulations based on the Stillinger-Weber interatomic potential. The temperature-dependent interface velocity follows a Vogel-Fulcher type behavior and allows to properly account for the dynamics in the undercooled melt.
A kinetic Monte Carlo approach to study fluid transport in pore networks
Apostolopoulou, M.; Day, R.; Hull, R.; Stamatakis, M.; Striolo, A.
2017-10-01
The mechanism of fluid migration in porous networks continues to attract great interest. Darcy's law (phenomenological continuum theory), which is often used to describe macroscopically fluid flow through a porous material, is thought to fail in nano-channels. Transport through heterogeneous and anisotropic systems, characterized by a broad distribution of pores, occurs via a contribution of different transport mechanisms, all of which need to be accounted for. The situation is likely more complicated when immiscible fluid mixtures are present. To generalize the study of fluid transport through a porous network, we developed a stochastic kinetic Monte Carlo (KMC) model. In our lattice model, the pore network is represented as a set of connected finite volumes (voxels), and transport is simulated as a random walk of molecules, which "hop" from voxel to voxel. We simulated fluid transport along an effectively 1D pore and we compared the results to those expected by solving analytically the diffusion equation. The KMC model was then implemented to quantify the transport of methane through hydrated micropores, in which case atomistic molecular dynamic simulation results were reproduced. The model was then used to study flow through pore networks, where it was able to quantify the effect of the pore length and the effect of the network's connectivity. The results are consistent with experiments but also provide additional physical insights. Extension of the model will be useful to better understand fluid transport in shale rocks.
Self-learning kinetic Monte Carlo simulations of Al diffusion in Mg
Energy Technology Data Exchange (ETDEWEB)
Nandipati, Giridhar; Govind, Niranjan; Andersen, Amity; Rohatgi, Aashish
2016-03-16
Atomistic on-lattice self-learning kinetic Monte Carlo (SLKMC) method was used to examine the vacancy-mediated diffusion of an Al atom in pure hcp Mg. Local atomic environment dependent activation barriers for vacancy-atom exchange processes were calculated on-the-fly using climbing image nudged-elastic band method (CI-NEB) and using a Mg-Al binary modified embedded-atom method (MEAM) interatomic potential. Diffusivities of vacancy and Al atom in pure Mg were obtained from SLKMC simulations and are compared with values available in the literature that are obtained from experiments and first-principle calculations. Al Diffusivities obtained from SLKMC simulations are lower, due to larger activation barriers and lower diffusivity prefactors, than those available in the literature but have same order of magnitude. We present all vacancy-Mg and vacancy-Al atom exchange processes and their activation barriers that were identified in SLKMC simulations. We will describe a simple mapping scheme to map a hcp lattice on to a simple cubic lattice that would enable hcp lattices to be simulated in an on-lattice KMC framework. We also present the pattern recognition scheme used in SLKMC simulations.
The effect of crystal size variation on the rate of dissolution - A kinetic Monte Carlo study
Briese, Laura; Arvidson, Rolf S.; Luttge, Andreas
2017-09-01
Crystal size is an important parameter for many geochemical processes, and is often observed to have a significant influence on crystal dissolution rate. Although size versus solubility relationships are often cast in thermodynamic terms (the critical radius), the mechanistic basis for size versus dissolution rate is not understood in any detail. Here we examine the influence of size on dissolution rate and the mechanistic origin of this relationship isolated from other parameters. We use a kinetic Monte Carlo model approach to observe atomistic changes in the dissolution of four simple cubic crystals (edge dimension d = 25, 64, 125, 187 unit cells). These simulations maintain constant solution boundary conditions representing an under-saturated, far-from-equilibrium state. We observe that surface area-normalized dissolution rates increase non-linearly with decreasing initial crystal size. This relationship can be understood mechanistically, in part as a coupling of kink- and step atom-site formation. Under conditions where these two constraints are in rough balance, the overall dissolution rate is maximized and mass removal is most efficient. This relationship reflects the mutual dependence of the formation of kink and step atoms, whose high detachment frequencies exert the dominant control over the dissolution process.
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.
Khrushcheva, O; Malerba, L; Becquart, C S; Domain, C; Hou, M
2003-01-01
Several variants are possible in the suite of programs forming multiscale predictive tools to estimate the yield strength increase caused by irradiation in RPV steels. For instance, at the atomic scale, both the Metropolis and the lattice kinetic Monte Carlo methods (MMC and LKMC respectively) allow predicting copper precipitation under irradiation conditions. Since these methods are based on different physical models, the present contribution discusses their consistency on the basis of a realistic case study. A cascade debris in iron containing 0.2% of copper was modelled by molecular dynamics with the DYMOKA code, which is part of the REVE suite. We use this debris as input for both the MMC and the LKMC simulations. Thermal motion and lattice relaxation can be avoided in the MMC, making the model closer to the LKMC (LMMC method). The predictions and the complementarity of the three methods for modelling the same phenomenon are then discussed.
Monte Carlo simulation on kinetics of batch and semi-batch free radical polymerization
Shao, Jing
2015-10-27
Based on Monte Carlo simulation technology, we proposed a hybrid routine which combines reaction mechanism together with coarse-grained molecular simulation to study the kinetics of free radical polymerization. By comparing with previous experimental and simulation studies, we showed the capability of our Monte Carlo scheme on representing polymerization kinetics in batch and semi-batch processes. Various kinetics information, such as instant monomer conversion, molecular weight, and polydispersity etc. are readily calculated from Monte Carlo simulation. The kinetic constants such as polymerization rate k p is determined in the simulation without of “steady-state” hypothesis. We explored the mechanism for the variation of polymerization kinetics those observed in previous studies, as well as polymerization-induced phase separation. Our Monte Carlo simulation scheme is versatile on studying polymerization kinetics in batch and semi-batch processes.
Parallel Atomistic Simulations
Energy Technology Data Exchange (ETDEWEB)
HEFFELFINGER,GRANT S.
2000-01-18
Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.
Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H; Steffen, Adam T; Pappu, Rohit V
2012-06-14
Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semirigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ angles, and the coupling between ring puckering and backbone degrees of freedom.
Construction of a kinetics model for liquid-solid transitions built from atomistic simulations
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.
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.
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.
Off-lattice kinetic Monte Carlo simulations of strained heteroepitaxial growth
Biehl, Michael; Much, Florian; Vey, Christian; Voigt, A
2005-01-01
An off-lattice, continuous space Kinetic Monte Carlo (KMC) algorithm is discussed and applied in the investigation of strained heteroepitaxial crystal growth. As a starting point, we study a simplifying (1+1)-dimensional situation with inter-atomic interactions given by simple pair-potentials. The
Interacting multiagent systems kinetic equations and Monte Carlo methods
Pareschi, Lorenzo
2014-01-01
The description of emerging collective phenomena and self-organization in systems composed of large numbers of individuals has gained increasing interest from various research communities in biology, ecology, robotics and control theory, as well as sociology and economics. Applied mathematics is concerned with the construction, analysis and interpretation of mathematical models that can shed light on significant problems of the natural sciences as well as our daily lives. To this set of problems belongs the description of the collective behaviours of complex systems composed by a large enough number of individuals. Examples of such systems are interacting agents in a financial market, potential voters during political elections, or groups of animals with a tendency to flock or herd. Among other possible approaches, this book provides a step-by-step introduction to the mathematical modelling based on a mesoscopic description and the construction of efficient simulation algorithms by Monte Carlo methods. The ar...
DEFF Research Database (Denmark)
Heinisch, H.L.; Trinkaus, H.; Singh, Bachu Narain
2007-01-01
and confirmed by kinetic Monte Carlo (KMC) simulations. Here we report on KMC simulations investigating a different transition from 1D to 3D diffusion of 1D gliding loops for which their 1D migration is interrupted by occasional 2D migration due to conservative climb by dislocation core diffusion within a plane......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...... transverse to their 1D glide direction. Their transition from 1D to 3D kinetics is significantly different from that due to direction changes. The KMC results are compared to an analytical description of this diffusion mode in the form of a master curve relating the 1D normalized sink strength...
Heinisch, H. L.; Trinkaus, H.; Singh, B. N.
2007-08-01
The reaction kinetics of the various species of mobile defects in irradiated materials are crucially dependent on the dimensionality of their migration. Sink strengths for one-dimensionally (1D) gliding interstitial loops undergoing occasional direction changes have been described analytically and confirmed by kinetic Monte Carlo (KMC) simulations. Here we report on KMC simulations investigating a different transition from 1D to 3D diffusion of 1D gliding loops for which their 1D migration is interrupted by occasional 2D migration due to conservative climb by dislocation core diffusion within a plane transverse to their 1D glide direction. Their transition from 1D to 3D kinetics is significantly different from that due to direction changes. The KMC results are compared to an analytical description of this diffusion mode in the form of a master curve relating the 1D normalized sink strength to the frequency of disturbance of 1D migration.
Mobility field and mobility temperature dependence in PC61BM: A kinetic Monte-Carlo study
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.
Directory of Open Access Journals (Sweden)
Michael Müller
2011-01-01
Full Text Available The ordering kinetics in free and supported L10 nanoparticles was studied by means of lattice-based kinetic Monte-Carlo simulations. Starting from a fully disordered particle of Wulff shape, the simulations show that the nucleation of ordered domains is starting quickly on various (100 facets but is retarded in the particle volume due to the lack of vacancies compared with a thin film geometry. If a substrate is present, we do not find significant differences in the ordering behavior. This holds true, even if we impose a massively increased thermodynamic driving force for interface segregation, because the nucleation of ordered domains on free facets is significantly faster than the bulk diffusion of the segregating species to the interface. In cases where wetting of the substrate or surface facetting occurs, we find that diffusional atomic motion on the surface goes along with an enhanced long-range order.
Energy Technology Data Exchange (ETDEWEB)
Winnischofer, Herbert; Araujo, Marcio Peres de; Dias Junior, Lauro Camargo; Novo, Joao Batista Marques [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil)
2010-07-01
A software based in the Monte Carlo method have been developed aiming the teaching of important cases of mechanisms found in luminescence and in excited states decay kinetics, including: multiple decays, consecutive decays and coupled systems decays. The Monte Carlo Method allows the student to easily simulate and visualize the luminescence mechanisms, focusing on the probabilities of the related steps. The software CINESTEX was written for FreeBASIC compiler; it assumes first-order kinetics and any number of excited states, where the pathways are allowed with probabilities assigned by the user. (author)
Yasuda, Shugo
2015-01-01
A Monte Carlo simulation for the chemotactic bacteria is developed on the basis of the kinetic modeling, i.e., the Boltzmann transport equation, and applied to the one-dimensional traveling population wave in a micro channel.In this method, the Monte Carlo method, which calculates the run-and-tumble motions of bacteria, is coupled with a finite volume method to solve the macroscopic transport of the chemical cues in the field. The simulation method can successfully reproduce the traveling population wave of bacteria which was observed experimentally. The microscopic dynamics of bacteria, e.g., the velocity autocorrelation function and velocity distribution function of bacteria, are also investigated. It is found that the bacteria which form the traveling population wave create quasi-periodic motions as well as a migratory movement along with the traveling population wave. Simulations are also performed with changing the sensitivity and modulation parameters in the response function of bacteria. It is found th...
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.
2015-09-01
196–201. 44. Kratzer P. Monte Carlo and kinetic Monte Carlo methods–a tutorial. In: Grotendorst J, Attig N, Blügel S, Marx D, editors. Multiscale...Monte Carlo (kMC) Simulations of Thin Film Growth by James J Ramsey Approved for public release; distribution is...Research Laboratory KMCThinFilm: A C++ Framework for the Rapid Development of Lattice Kinetic Monte Carlo (kMC) Simulations of Thin Film Growth by
Kinetic Monte Carlo Simulation of Oxygen and Cation Diffusion in Yttria-Stabilized Zirconia
Good, Brian
2011-01-01
Yttria-stabilized zirconia (YSZ) is of interest to the aerospace community, notably for its application as a thermal barrier coating for turbine engine components. In such an application, diffusion of both oxygen ions and cations is of concern. Oxygen diffusion can lead to deterioration of a coated part, and often necessitates an environmental barrier coating. Cation diffusion in YSZ is much slower than oxygen diffusion. However, such diffusion is a mechanism by which creep takes place, potentially affecting the mechanical integrity and phase stability of the coating. In other applications, the high oxygen diffusivity of YSZ is useful, and makes the material of interest for use as a solid-state electrolyte in fuel cells. The kinetic Monte Carlo (kMC) method offers a number of advantages compared with the more widely known molecular dynamics simulation method. In particular, kMC is much more efficient for the study of processes, such as diffusion, that involve infrequent events. We describe the results of kinetic Monte Carlo computer simulations of oxygen and cation diffusion in YSZ. Using diffusive energy barriers from ab initio calculations and from the literature, we present results on the temperature dependence of oxygen and cation diffusivity, and on the dependence of the diffusivities on yttria concentration and oxygen sublattice vacancy concentration. We also present results of the effect on diffusivity of oxygen vacancies in the vicinity of the barrier cations that determine the oxygen diffusion energy barriers.
A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks
Slepoy, Alexander; Thompson, Aidan P.; Plimpton, Steven J.
2008-05-01
The time evolution of species concentrations in biochemical reaction networks is often modeled using the stochastic simulation algorithm (SSA) [Gillespie, J. Phys. Chem. 81, 2340 (1977)]. The computational cost of the original SSA scaled linearly with the number of reactions in the network. Gibson and Bruck developed a logarithmic scaling version of the SSA which uses a priority queue or binary tree for more efficient reaction selection [Gibson and Bruck, J. Phys. Chem. A 104, 1876 (2000)]. More generally, this problem is one of dynamic discrete random variate generation which finds many uses in kinetic Monte Carlo and discrete event simulation. We present here a constant-time algorithm, whose cost is independent of the number of reactions, enabled by a slightly more complex underlying data structure. While applicable to kinetic Monte Carlo simulations in general, we describe the algorithm in the context of biochemical simulations and demonstrate its competitive performance on small- and medium-size networks, as well as its superior constant-time performance on very large networks, which are becoming necessary to represent the increasing complexity of biochemical data for pathways that mediate cell function.
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.
Energy Technology Data Exchange (ETDEWEB)
Violi, A; Kubota, A; Truong, T N; Pitz, W; Westbrook, C K; Sarofim, A F
2001-12-17
A new code, named Hybrid Molecular Dynamics--Kinetic Monte Carlo (Hybrid MD/KMC), has been developed and employed to analyze possible growth pathways that lead to high molecular mass compounds. The Hybrid MD-KMC code combines the strengths of two common simulation methods: Kinetic Monte Carlo, and Molecular Dynamics. This code puts the two simulation procedures on an equal footing and involves alternating between MD and KMC steps during the simulation. The strength of this approach is that it provides information on the physical as well as chemical structure of soot precursors providing at the long term potential for information on particle characteristics such as density, porosity, and other physical properties. The Kinetic Monte Carlo and Molecular Dynamics simulation are used in conjunction with high-level quantum chemical calculations.
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.
Billion-atom synchronous parallel kinetic Monte Carlo simulations of critical 3D Ising systems
Martínez, E.; Monasterio, P. R.; Marian, J.
2011-02-01
An extension of the synchronous parallel kinetic Monte Carlo (spkMC) algorithm developed by Martinez et al. [J. Comp. Phys. 227 (2008) 3804] to discrete lattices is presented. The method solves the master equation synchronously by recourse to null events that keep all processors' time clocks current in a global sense. Boundary conflicts are resolved by adopting a chessboard decomposition into non-interacting sublattices. We find that the bias introduced by the spatial correlations attendant to the sublattice decomposition is within the standard deviation of serial calculations, which confirms the statistical validity of our algorithm. We have analyzed the parallel efficiency of spkMC and find that it scales consistently with problem size and sublattice partition. We apply the method to the calculation of scale-dependent critical exponents in billion-atom 3D Ising systems, with very good agreement with state-of-the-art multispin simulations.
Energy Technology Data Exchange (ETDEWEB)
Martin-Bragado, Ignacio, E-mail: ignacio.martin@imdea.org [IMDEA Materials Institute, C/ Eric Kandel 2, 28906 Getafe, Madrid (Spain); Abujas, J.; Galindo, P.L.; Pizarro, J. [Departamento de Ingeniería Informática, Universidad de Cádiz, Puerto Real, Cádiz (Spain)
2015-06-01
An adaptation of the synchronous parallel Kinetic Monte Carlo (spKMC) algorithm developed by Martinez et al. (2008) to the existing KMC code MMonCa (Martin-Bragado et al. 2013) is presented in this work. Two cases, general enough to provide an idea of the current state-of-the-art in parallel KMC, are presented: Object KMC simulations of the evolution of damage in irradiated iron, and Lattice KMC simulations of epitaxial regrowth of amorphized silicon. The results allow us to state that (a) the parallel overhead is critical, and severely degrades the performance of the simulator when it is comparable to the CPU time consumed per event, (b) the balance between domains is important, but not critical, (c) the algorithm and its implementation are correct and (d) further improvements are needed for spKMC to become a general, all-working solution for KMC simulations.
Monte Carlo simulation of heavy ion induced kinetic electron emission from an Al surface
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...
Menzel, Stephan; Kaupmann, Philip; Waser, Rainer
2015-07-01
We report on a 2D kinetic Monte Carlo model that describes the resistive switching in electrochemical metallization cells. To simulate the switching process, we consider several different processes on the atomic scale: electron-transfer reactions at the boundaries, ion migration, adsorption/desorption from/to interfaces, surface diffusion and nucleation. These processes result in a growth/dissolution of a metallic filament within an insulating matrix. In addition, the model includes electron tunneling between the growing filament and the counter electrode, which allows for simulating multilevel switching. It is shown that the simulation model can reproduce the reported switching kinetics, switching variability and multilevel capabilities of ECM devices. As a major result, the influence of mechanical stress working on the host matrix due to the filamentary growth is investigated. It is demonstrated that the size and shape of the filament depend on the Young's modulus of the insulating matrix. For high values a wire-like structure evolves, whereas the shape is dendritic if the Young's modulus is negligible.We report on a 2D kinetic Monte Carlo model that describes the resistive switching in electrochemical metallization cells. To simulate the switching process, we consider several different processes on the atomic scale: electron-transfer reactions at the boundaries, ion migration, adsorption/desorption from/to interfaces, surface diffusion and nucleation. These processes result in a growth/dissolution of a metallic filament within an insulating matrix. In addition, the model includes electron tunneling between the growing filament and the counter electrode, which allows for simulating multilevel switching. It is shown that the simulation model can reproduce the reported switching kinetics, switching variability and multilevel capabilities of ECM devices. As a major result, the influence of mechanical stress working on the host matrix due to the filamentary growth is
Kinetic Monte Carlo simulation of single-electron multiple-trapping transport in disordered media
Javadi, Mohammad; Abdi, Yaser
2017-12-01
The conventional single-particle Monte Carlo simulation of charge transport in disordered media is based on the truncated density of localized states (DOLS) which benefits from very short time execution. Although this model successfully clarifies the properties of electron transport in moderately disordered media, it overestimates the electron diffusion coefficient for strongly disordered media. The origin of this deviation is discussed in terms of zero-temperature approximation in the truncated DOLS and the ignorance of spatial occupation of localized states. Here, based on the multiple-trapping regime we introduce a modified single-particle kinetic Monte Carlo model that can be used to investigate the electron transport in any disordered media independent from the value of disorder parameter. In the proposed model, instead of using a truncated DOLS we imply the raw DOLS. In addition, we have introduced an occupation index for localized states to consider the effect of spatial occupation of trap sites. The proposed model is justified in a simple cubic lattice of trap sites for broad interval of disorder parameters, Fermi levels, and temperatures.
Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations
Arampatzis, Georgios; Katsoulakis, Markos A.
2014-03-01
In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-"coupled"- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz-Kalos-Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB
A First-Passage Kinetic Monte Carlo method for reaction-drift-diffusion processes
Mauro, Ava J.; Sigurdsson, Jon Karl; Shrake, Justin; Atzberger, Paul J.; Isaacson, Samuel A.
2014-02-01
Stochastic reaction-diffusion models are now a popular tool for studying physical systems in which both the explicit diffusion of molecules and noise in the chemical reaction process play important roles. The Smoluchowski diffusion-limited reaction model (SDLR) is one of several that have been used to study biological systems. Exact realizations of the underlying stochastic processes described by the SDLR model can be generated by the recently proposed First-Passage Kinetic Monte Carlo (FPKMC) method. This exactness relies on sampling analytical solutions to one and two-body diffusion equations in simplified protective domains. In this work we extend the FPKMC to allow for drift arising from fixed, background potentials. As the corresponding Fokker-Planck equations that describe the motion of each molecule can no longer be solved analytically, we develop a hybrid method that discretizes the protective domains. The discretization is chosen so that the drift-diffusion of each molecule within its protective domain is approximated by a continuous-time random walk on a lattice. New lattices are defined dynamically as the protective domains are updated, hence we will refer to our method as Dynamic Lattice FPKMC or DL-FPKMC. We focus primarily on the one-dimensional case in this manuscript, and demonstrate the numerical convergence and accuracy of our method in this case for both smooth and discontinuous potentials. We also present applications of our method, which illustrate the impact of drift on reaction kinetics.
Kinetic energy classification and smoothing for compact B-spline basis sets in quantum Monte Carlo
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%.
Montoya, M; Rojas, J
2007-01-01
The mass and kinetic energy distribution of nuclear fragments from thermal neutron induced fission of 235U have been studied using a Monte-Carlo simulation. Besides reproducing the pronounced broadening on the standard deviation of the final fragment kinetic energy distribution $\\sigma_{e}(m)$ around the mass number m = 109, our simulation also produces a second broadening around m = 125, that is in agreement with the experimental data obtained by Belhafaf et al. These results are consequence of the characteristics of the neutron emission, the variation in the primary fragment mean kinetic energy and the yield as a function of the mass.
Literature review report on atomistic modeling tools for FeCrAl alloys
Energy Technology Data Exchange (ETDEWEB)
Zhang, Yongfeng [Idaho National Lab. (INL), Idaho Falls, ID (United States); Schwen, Daniel [Idaho National Lab. (INL), Idaho Falls, ID (United States); Martinez, Enrique [Idaho National Lab. (INL), Idaho Falls, ID (United States)
2015-12-01
This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing for better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.
Monte Carlo kinetics simulations of ice-mantle formation on interstellar grains
Garrod, Robin
2015-08-01
The majority of interstellar dust-grain chemical kinetics models use rate equations, or alternative population-based simulation methods, to trace the time-dependent formation of grain-surface molecules and ice mantles. Such methods are efficient, but are incapable of considering explicitly the morphologies of the dust grains, the structure of the ices formed thereon, or the influence of local surface composition on the chemistry.A new Monte Carlo chemical kinetics model, MIMICK, is presented here, whose prototype results were published recently (Garrod 2013, ApJ, 778, 158). The model calculates the strengths and positions of the potential mimima on the surface, on the fly, according to the individual pair-wise (van der Waals) bonds between surface species, allowing the structure of the ice to build up naturally as surface diffusion and chemistry occur. The prototype model considered contributions to a surface particle's potential only from contiguous (or "bonded") neighbors; the full model considers contributions from surface constituents from short to long range. Simulations are conducted on a fully 3-D user-generated dust-grain with amorphous surface characteristics. The chemical network has also been extended from the simple water system previously published, and now includes 33 chemical species and 55 reactions. This allows the major interstellar ice components to be simulated, such as water, methane, ammonia and methanol, as well as a small selection of more complex molecules, including methyl formate (HCOOCH3).The new model results indicate that the porosity of interstellar ices are dependent on multiple variables, including gas density, the dust temperature, and the relative accretion rates of key gas-phase species. The results presented also have implications for the formation of complex organic molecules on dust-grain surfaces at very low temperatures.
Energy Technology Data Exchange (ETDEWEB)
Byun, H. S.; Pirbadian, S.; Nakano, Aiichiro; Shi, Liang; El-Naggar, Mohamed Y.
2014-09-05
Microorganisms overcome the considerable hurdle of respiring extracellular solid substrates by deploying large multiheme cytochrome complexes that form 20 nanometer conduits to traffic electrons through the periplasm and across the cellular outer membrane. Here we report the first kinetic Monte Carlo simulations and single-molecule scanning tunneling microscopy (STM) measurements of the Shewanella oneidensis MR-1 outer membrane decaheme cytochrome MtrF, which can perform the final electron transfer step from cells to minerals and microbial fuel cell anodes. We find that the calculated electron transport rate through MtrF is consistent with previously reported in vitro measurements of the Shewanella Mtr complex, as well as in vivo respiration rates on electrode surfaces assuming a reasonable (experimentally verified) coverage of cytochromes on the cell surface. The simulations also reveal a rich phase diagram in the overall electron occupation density of the hemes as a function of electron injection and ejection rates. Single molecule tunneling spectroscopy confirms MtrF's ability to mediate electron transport between an STM tip and an underlying Au(111) surface, but at rates higher than expected from previously calculated heme-heme electron transfer rates for solvated molecules.
Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems
Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan
2012-03-01
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.
Yang, Qian; Sing-Long, Carlos; Chen, Enze; Reed, Evan
2017-06-01
Complex chemical processes, such as the decomposition of energetic materials and the chemistry of planetary interiors, are typically studied using large-scale molecular dynamics simulations that run for weeks on high performance parallel machines. These computations may involve thousands of atoms forming hundreds of molecular species and undergoing thousands of reactions. It is natural to wonder whether this wealth of data can be utilized to build more efficient, interpretable, and predictive models. In this talk, we will use techniques from statistical learning to develop a framework for constructing Kinetic Monte Carlo (KMC) models from molecular dynamics data. We will show that our KMC models can not only extrapolate the behavior of the chemical system by as much as an order of magnitude in time, but can also be used to study the dynamics of entirely different chemical trajectories with a high degree of fidelity. Then, we will discuss three different methods for reducing our learned KMC models, including a new and efficient data-driven algorithm using L1-regularization. We demonstrate our framework throughout on a system of high-temperature high-pressure liquid methane, thought to be a major component of gas giant planetary interiors.
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.
Kinetic Monte Carlo Simulations of Diffusion in Environmental Barrier Coating Materials
Good, Brian
2017-01-01
Ceramic Matrix Components (CMC) components for use in turbine engines offer a number of advantages compared with current practice. However, such components are subject to degradation through a variety of mechanisms. In particular, in the hot environment inside a turbine in operation a considerable amount of water vapor is present, and this can lead to corrosion and recession. Environmental Barrier Coating (EBC) systems that limit the amount of oxygen and water reaching the component are required to reduce this degradation and extend component life. A number of silicate-based materials are under consideration for use in such coating systems, including Yttterbium and Yttrium di- and monosilicates. In this work, we present results of kinetic Monte Carlo computer simulations of oxygen diffusion in Yttrium disilicate, and compare with previous work on Yttterbium disilicate. Coatings may also exhibit cracking, and the cracks can provide a direct path for oxygen to reach the component. There is typically a bond coat between the coating and component surface, but the bond coat material is generally chosen for properties other than low oxygen diffusivity. Nevertheless, the degree to which the bond coat can inhibit oxygen diffusion is of interest, as it may form the final defense against oxygen impingement on the component. We have therefore performed similar simulations of oxygen diffusion through HfSiO4, a proposed bond coat material.
Casalegno, Mosè; Raos, Guido; Po, Riccardo
2010-03-07
The kinetic Monte Carlo (KMC) method provides a versatile tool to investigate the mechanisms underlying photocurrent generation in nanostructured organic solar cells. Currently available algorithms can already support the development of more cost-efficient photovoltaic devices, but so far no attempt has been made to test the validity of some fundamental model assumptions and their impact on the simulation result. A meaningful example is given by the treatment of the electrostatic interactions. In most KMC models, electrostatic interactions are approximated by means of cutoff based potentials, irrespective of the long-range nature of the Coulomb interaction. In this paper, the reliability of such approximation is tested against the exact Ewald sum. The results under short-circuit and flat-band conditions show that use of cutoff-based potentials tends to underestimate real device performance, in terms of internal quantum efficiency and current density. Together with this important finding, we formalize other methodological aspects which have been scarcely discussed in the literature.
Metal-Insulator Transition in nanoparticle solids: a kinetic Monte Carlo study
Zimanyi, Gergely; Qu, Luman; Voros, Marton
Nanoparticle (NP) solids recently emerged as a promising platform for high performance electronic/optoelectronic devices, including third generation solar cells, light emitting diodes and field effect transistors. A challenge of NP films is that their charge transport is in the unfavorable hopping/insulating regime. Recent experiments showed that it is possible to tune the NP solids through a Metal-Insulator Transition (MIT) via ligand engineering and ALD matrix infilling. However, the microscopic understanding of this transition is not yet clear. To address this challenge, we developed a Kinetic Monte Carlo transport modeling framework that builds on determining NP parameters from ab initio-based calculations of the energy level structures, charging energies and overlaps, and then uses these to compute the hopping mobility across a disordered NP array by the Marcus and Miller-Abrahams mechanisms. We reproduced and explained the observed non-monotonous dependence of the mobility on the NP diameter. Centrally, we extended our platform to be able to capture the MIT. We determined the MIT phase boundary on the (NP-NP overlap - Electron density) plane. We demonstrated that all mobilities fall on a universal scaling curve, allowing us to determine the critical behavior across the MIT. Supported by: UC Davis Office of Research RISE ANSWER Grant.
Gatsonis, Nikolaos A.; Chamberlin, Ryan E.; Averkin, Sergey N.
2013-01-01
The mathematical and computational aspects of the direct simulation Monte Carlo on unstructured tetrahedral grids (U3DSMC) with a Kinetic-Moment (KM) boundary conditions method are presented. The algorithms for particle injection, particle loading, particle motion, and particle tracking are presented. The KM method applicable to a subsonic or supersonic inflow/outflow boundary, couples kinetic (particle) U3DSMC properties with fluid (moment) properties. The KM method obtains the number density, temperature and mean velocity needed to define the equilibrium, drifting Maxwellian distribution at a boundary. The moment component of KM is based on the local one dimensional inviscid (LODI) boundary conditions method consistent with the 5-moment compressible Euler equations. The kinetic component of KM is based on U3DSMC for interior properties and the equilibrium drifting Maxwellian at the boundary. The KM method is supplemented with a time-averaging procedure, allows for choices in sampling-cell procedures, minimizes fluctuations and accelerates the convergence in subsonic flows. Collision sampling in U3DSMC implements the no-time-counter method and includes elastic and inelastic collisions. The U3DSMC with KM boundary conditions is validated and verified extensively with simulations of subsonic nitrogen flows in a cylindrical tube with imposed inlet pressure and density and imposed outlet pressure. The simulations cover the regime from slip to free-molecular with inlet Knudsen numbers between 0.183 and 18.27 and resulting inlet Mach numbers between 0.037 and 0.027. The pressure and velocity profiles from U3DSMC-KM simulations are compared with analytical solutions obtained from first-order and second-order slip boundary conditions. Mass flow rates from U3DSMC-KM are compared with validated analytical solutions for the entire Knudsen number regime considered. Error and sensitivity analysis is performed and numerical fractional errors are in agreement with theoretical
Three-dimensional kinetic Monte Carlo simulations of cubic transition metal nitride thin film growth
Nita, F.; Mastail, C.; Abadias, G.
2016-02-01
A three-dimensional kinetic Monte Carlo (KMC) model has been developed and used to simulate the microstructure and growth morphology of cubic transition metal nitride (TMN) thin films deposited by reactive magnetron sputtering. Results are presented for the case of stoichiometric TiN, chosen as a representative TMN prototype. The model is based on a NaCl-type rigid lattice and includes deposition and diffusion events for both N and Ti species. It is capable of reproducing voids and overhangs, as well as surface faceting. Simulations were carried out assuming a uniform flux of incoming particles approaching the surface at normal incidence. The ballistic deposition model is parametrized with an interaction parameter r0 that mimics the capture distance at which incoming particles may stick on the surface, equivalently to a surface trapping mechanism. Two diffusion models are implemented, based on the different ways to compute the site-dependent activation energy for hopping atoms. The influence of temperature (300-500 K), deposition flux (0.1-100 monolayers/s), and interaction parameter r0 (1.5-6.0 Å) on the obtained growth morphology are presented. Microstructures ranging from highly porous, [001]-oriented straight columns with smooth top surface to rough columns emerging with different crystallographic facets are reproduced, depending on kinetic restrictions, deposited energy (seemingly captured by r0), and shadowing effect. The development of facets is a direct consequence of the diffusion model which includes an intrinsic (minimum energy-based) diffusion anisotropy, although no crystallographic diffusion anisotropy was explicitly taken into account at this stage. The time-dependent morphological evolution is analyzed quantitatively to extract the growth exponent β and roughness exponent α , as indicators of kinetic roughening behavior. For dense TiN films, values of α ≈0.7 and β =0.24 are obtained in good agreement with existing experimental data. At this
Reaction pathways in atomistic models of thin film growth
Lloyd, Adam L.; Zhou, Ying; Yu, Miao; Scott, Chris; Smith, Roger; Kenny, Steven D.
2017-10-01
The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides.
Comprehensive modeling of solid phase epitaxial growth using Lattice Kinetic Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Martin-Bragado, Ignacio, E-mail: ignacio.martin@imdea.org [IMDEA Materials Institute, C/ Eric Kandel 2, Parque Científico y Tecnológico de Getafe 28906 Madrid, Getafe (Spain)
2013-05-15
Damage evolution of irradiated silicon is, and has been, a topic of interest for the last decades for its applications to the semiconductor industry. In particular, sometimes, the damage is heavy enough to collapse the lattice and to locally amorphize the silicon, while in other cases amorphization is introduced explicitly to improve other implanted profiles. Subsequent annealing of the implanted samples heals the amorphized regions through Solid Phase Epitaxial Regrowth (SPER). SPER is a complicated process. It is anisotropic, it generates defects in the recrystallized silicon, it has a different amorphous/crystalline (A/C) roughness for each orientation, leaving pits in Si(1 1 0), and in Si(1 1 1) it produces two modes of recrystallization with different rates. The recently developed code MMonCa has been used to introduce a physically-based comprehensive model using Lattice Kinetic Monte Carlo that explains all the above singularities of silicon SPER. The model operates by having, as building blocks, the silicon lattice microconfigurations and their four twins. It detects the local configurations, assigns microscopical growth rates, and reconstructs the positions of the lattice locally with one of those building blocks. The overall results reproduce the (a) anisotropy as a result of the different growth rates, (b) localization of SPER induced defects, (c) roughness trends of the A/C interface, (d) pits on Si(1 1 0) regrown surfaces, and (e) bimodal Si(1 1 1) growth. It also provides physical insights of the nature and shape of deposited defects and how they assist in the occurrence of all the above effects.
Kinetic Monte Carlo Simulations of the Grain-surface Back-diffusion Effect
Willis, Eric R.; Garrod, Robin T.
2017-05-01
Rate-equation models are a widely used and inexpensive tool for the simulation of interstellar chemistry under a range of physical conditions. However, their application to grain-surface chemical systems necessitates a number of simplifying assumptions, due to the requirement to treat only the total population of each species, using averaged rates, rather than treating each surface particle as an independent entity. While the outputs from rate-equation models are strictly limited to such population information, the inputs—in the form of the averaged rates that control the time-evolution of chemical populations—can be guided by the results from more exact simulation methods. Here, we examine the effects of back-diffusion, wherein particles diffusing on a surface revisit binding sites on the lattice, slowing the total reaction rate. While this effect has been studied for two-particle systems, its influence at greater surface coverage of reactants has not been explored. Results from two Monte Carlo kinetics models (one a 2D periodic lattice, the other the surface of a three-dimensionally realized grain) were used to develop a means to incorporate the grain-surface back-diffusion effect into rate-equation methods. The effects of grain size, grain morphology, and surface coverage on the magnitude of the back-diffusion effect were studied for the simple H+H reaction system. The results were fit with expressions that can be easily incorporated into astrochemical rate-equation models to accurately reproduce the effects of back-diffusion on grain-surface reaction rates. Back-diffusion reduces reaction rates by a maximum factor of around 5 for the canonical grain of ˜106 surface sites, but this falls to unity at close to full surface coverage.
Kinetic Monte Carlo simulations of GaN homoepitaxy on c- and m-plane surfaces
Xu, Dongwei; Zapol, Peter; Stephenson, G. Brian; Thompson, Carol
2017-04-01
The surface orientation can have profound effects on the atomic-scale processes of crystal growth and is essential to such technologies as GaN-based light-emitting diodes and high-power electronics. We investigate the dependence of homoepitaxial growth mechanisms on the surface orientation of a hexagonal crystal using kinetic Monte Carlo simulations. To model GaN metal-organic vapor phase epitaxy, in which N species are supplied in excess, only Ga atoms on a hexagonal close-packed (HCP) lattice are considered. The results are thus potentially applicable to any HCP material. Growth behaviors on c-plane (0001) and m-plane (01 1 ¯ 0 ) surfaces are compared. We present a reciprocal space analysis of the surface morphology, which allows extraction of growth mode boundaries and direct comparison with surface X-ray diffraction experiments. For each orientation, we map the boundaries between 3-dimensional, layer-by-layer, and step flow growth modes as a function of temperature and growth rate. Two models for surface diffusion are used, which produce different effective Ehrlich-Schwoebel step-edge barriers and different adatom diffusion anisotropies on m-plane surfaces. Simulation results in agreement with observed GaN island morphologies and growth mode boundaries are obtained. These indicate that anisotropy of step edge energy, rather than adatom diffusion, is responsible for the elongated islands observed on m-plane surfaces. Island nucleation spacing obeys a power-law dependence on growth rate, with exponents of -0.24 and -0.29 for the m- and c-plane, respectively.
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
Simulation and development of nanoscale deposition techniques using kinetic Monte Carlo
Clark, Corey
Modeling of deposition processes has become of extreme importance due to the small scale of devices and features as well as the reduction of time to market required by industry. Current modeling procedures have focused on individual aspects of growth as well as made assumptions that cause simplification of the problem to the point the models usefulness is limited. The Kinetic Monte Carlo (KMC) model developed in this work combines rate transitions that have been commonly found in KMC simulation along with energy density equations that help explain the transitions and formations of island in alloy deposition. Specifically the model developed in this study, analyzes both the surface energy and strain energy of the film, which are incorporated to show the dependence of strain relaxation to surface energy during island formation. The developed model also incorporates the anisotropy of crystalline structures to accommodate for the changes in growth rate and morphology based upon crystal orientation. This leads to a more versatile model that will accommodate multiple material sets as well allow for quick simulation results for the development of new devices. Work was also done in increasing the randomness of site selection while minimizing errors due to standard uniform number generators. The developed KMC model incorporates a pseudo random number generator for the purpose of site selection, which reduce the amount of cluster processing that can occur with random number generators. A focus was also placed on the ability to describe flux distributions that are not commonly found in semiconductor device manufacturing. This was done to allow for the expansion of this model into nonplanar environments that might be found in industries such as MEMS/NEMS. This extension also allows for evaluation of non-planar deposition process such as via deposition. The expansion done in this model allow for a wider variety of applications with in the semiconductor field. Accounting for
KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations
Leetmaa, Mikael; Skorodumova, Natalia V.
2014-09-01
KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily extended and customized by the user to allow for the development of complex custom KMC models for specific systems without having to modify the core functionality of the program. Analysis modules and on-the-fly elementary step diffusion rate calculations can be implemented as plugins following a well-defined API. The plugin modules are loosely coupled to the core KMCLib program via the Python scripting language. KMCLib is written as a Python module with a backend C++ library. After initial compilation of the backend library KMCLib is used as a Python module; input to the program is given as a Python script executed using a standard Python interpreter. We give a detailed description of the features and implementation of the code and demonstrate its scaling behavior and parallel performance with a simple one-dimensional A-B-C lattice KMC model and a more complex three-dimensional lattice KMC model of oxygen-vacancy diffusion in a fluorite structured metal oxide. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Catalogue identifier: AESZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 49 064 No. of bytes in distributed program, including test data, etc.: 1 575 172 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer that can run a C++ compiler and a Python interpreter. Operating system: Tested on Ubuntu 12
Mermigkis, Panagiotis G.; Tsalikis, Dimitrios G.; Mavrantzas, Vlasis G.
2015-10-01
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, Deff, of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, Deff is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for Deff as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on Deff (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them
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
Huang, Chen-Hsi; Marian, Jaime
2016-10-01
We derive an Ising Hamiltonian for kinetic simulations involving interstitial and vacancy defects in binary alloys. Our model, which we term ‘ABVI’, incorporates solute transport by both interstitial defects and vacancies into a mathematically-consistent framework, and thus represents a generalization to the widely-used ABV model for alloy evolution simulations. The Hamiltonian captures the three possible interstitial configurations in a binary alloy: A-A, A-B, and B-B, which makes it particularly useful for irradiation damage simulations. All the constants of the Hamiltonian are expressed in terms of bond energies that can be computed using first-principles calculations. We implement our ABVI model in kinetic Monte Carlo simulations and perform a verification exercise by comparing our results to published irradiation damage simulations in simple binary systems with Frenkel pair defect production and several microstructural scenarios, with matching agreement found.
Modeling kinetics of a large-scale fed-batch CHO cell culture by Markov chain Monte Carlo method.
Xing, Zizhuo; Bishop, Nikki; Leister, Kirk; Li, Zheng Jian
2010-01-01
Markov chain Monte Carlo (MCMC) method was applied to model kinetics of a fed-batch Chinese hamster ovary cell culture process in 5,000-L bioreactors. The kinetic model consists of six differential equations, which describe dynamics of viable cell density and concentrations of glucose, glutamine, ammonia, lactate, and the antibody fusion protein B1 (B1). The kinetic model has 18 parameters, six of which were calculated from the cell culture data, whereas the other 12 were estimated from a training data set that comprised of seven cell culture runs using a MCMC method. The model was confirmed in two validation data sets that represented a perturbation of the cell culture condition. The agreement between the predicted and measured values of both validation data sets may indicate high reliability of the model estimates. The kinetic model uniquely incorporated the ammonia removal and the exponential function of B1 protein concentration. The model indicated that ammonia and lactate play critical roles in cell growth and that low concentrations of glucose (0.17 mM) and glutamine (0.09 mM) in the cell culture medium may help reduce ammonia and lactate production. The model demonstrated that 83% of the glucose consumed was used for cell maintenance during the late phase of the cell cultures, whereas the maintenance coefficient for glutamine was negligible. Finally, the kinetic model suggests that it is critical for B1 production to sustain a high number of viable cells. The MCMC methodology may be a useful tool for modeling kinetics of a fed-batch mammalian cell culture process.
van Veenendaal, E.; van Hoof, P.J.C.M.; van Suchtelen, J.; van Enckevort, W.J.P.; Bennema, P.
1998-01-01
Kinetic roughening is not a phase transition and, as such, it lacks an exact definition. Many criteria are used to mark the onset of kinetic roughening. Criteria stemming from the classical two-dimensional nucleation theory are widely used. On the other hand, experimentalists observe a transition
Monte Carlo simulations and fractional kinetics considerations for the Higuchi equation.
Dokoumetzidis, Aristides; Kosmidis, Kosmas; Macheras, Panos
2011-10-10
We highlight some physical and mathematical aspects relevant to the derivation and use of the Higuchi equation. More specifically, the application of the Higuchi equation to different geometries is discussed and Monte Carlo simulations to verify the validity of Higuchi law in one and two dimensions, as well as the derivation of the Higuchi equation under alternative boundary conditions making use of fractional calculus, are presented. Copyright © 2010 Elsevier B.V. All rights reserved.
Kinetics of electron-positron pair plasmas using an adaptive Monte Carlo method
Energy Technology Data Exchange (ETDEWEB)
Pilla, R.P.; Shaham, J. [Department of Physics, Columbia University, 538 West 120th Street, New York, New York 10027 (United States)
1997-09-01
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} {ital 1997} {ital The American Astronomical Society}
Hafeez Allan Agboola
2014-01-01
Pyrolysis of hydrocarbons and catalytic reforming of naphtha are important processes in petroleum refineries and petrochemical industries as they lead to production of light olefins, high octane gasoline, aromatics and so on. Thus, it is important to investigate their chemical kinetics in order to establish rate expressions or models for their reactions. In this research work, Monte-Carlo Simulation was applied to estimate kinetic parameters of two complex reactions: pyrolysis of n-Eicosane a...
Singh, Awaneesh; Singh, Amrita; Chakraborti, Anirban
2017-09-01
We present Monte Carlo (MC) simulation studies of phase separation in binary (AB) mixtures with bond-disorder that is introduced in two different ways: (i) at randomly selected lattice sites and (ii) at regularly selected sites. The Ising model with spin exchange (Kawasaki) dynamics represents the segregation kinetics in conserved binary mixtures. We find that the dynamical scaling changes significantly by varying the number of disordered sites in the case where bond-disorder is introduced at the randomly selected sites. On the other hand, when we introduce the bond-disorder in a regular fashion, the system follows the dynamical scaling for the modest number of disordered sites. For a higher number of disordered sites, the evolution morphology illustrates a lamellar pattern formation. Our MC results are consistent with the Lifshitz-Slyozov power-law growth in all the cases.
Huang, Yanping; Dong, Xiuqin; Yu, Yingzhe; Zhang, Minhua
2017-11-01
On the basis of the activation barriers and reaction energies from DFT calculations, kinetic Monte Carlo (kMC) simulations of vinyl acetate (VA) synthesis from ethylene acetoxylation on Pd(100) and Pd/Au(100) were carried out. Through kMC simulation, it was found that VA synthesis from ethylene acetoxylation proceeds via Moiseev mechanism on both Pd(100) and Pd/Au(100). The addition of Au into Pd can suppress ethylene dehydrogenation while it can promote acetic acid dehydrogenation, which can eventually facilitate VA synthesis as a whole. The addition of Au into Pd can further improve the conversion and selectivity of VA synthesis from ethylene acetoxylation. When the reaction network is analyzed, besides the energetics of each elementary reaction, the surface coverage of each species and the occupancy of the surface sites on the catalyst should also be taken into consideration.
Dybeck, Eric C; Plaisance, Craig P; Neurock, Matthew
2017-04-11
A novel algorithm is presented that achieves temporal acceleration during kinetic Monte Carlo (KMC) simulations of surface catalytic processes. This algorithm allows for the direct simulation of reaction networks containing kinetic processes occurring on vastly disparate time scales which computationally overburden standard KMC methods. Previously developed methods for temporal acceleration in KMC were designed for specific systems and often require a priori information from the user such as identifying the fast and slow processes. In the approach presented herein, quasi-equilibrated processes are identified automatically based on previous executions of the forward and reverse reactions. Temporal acceleration is achieved by automatically scaling the intrinsic rate constants of the quasi-equilibrated processes, bringing their rates closer to the time scales of the slow kinetically relevant nonequilibrated processes. All reactions are still simulated directly, although with modified rate constants. Abrupt changes in the underlying dynamics of the reaction network are identified during the simulation, and the reaction rate constants are rescaled accordingly. The algorithm was utilized here to model the Fischer-Tropsch synthesis reaction over ruthenium nanoparticles. This reaction network has multiple time-scale-disparate processes which would be intractable to simulate without the aid of temporal acceleration. The accelerated simulations are found to give reaction rates and selectivities indistinguishable from those calculated by an equivalent mean-field kinetic model. The computational savings of the algorithm can span many orders of magnitude in realistic systems, and the computational cost is not limited by the magnitude of the time scale disparity in the system processes. Furthermore, the algorithm has been designed in a generic fashion and can easily be applied to other surface catalytic processes of interest.
Ustinov, E A
2017-01-21
The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure-chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs-Duhem equation as a constraint. A detailed thermodynamic analysis of the hard-sphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems.
Energy Technology Data Exchange (ETDEWEB)
Bianchini, G.; Burgio, N.; Carta, M. [ENEA C.R. CASACCIA, via Anguillarese, 301, 00123 S. Maria di Galeria Roma (Italy); Peluso, V. [ENEA C.R. BOLOGNA, Via Martiri di Monte Sole, 4, 40129 Bologna (Italy); Fabrizio, V.; Ricci, L. [Univ. of Rome La Sapienza, C/o ENEA C.R. CASACCIA, via Anguillarese, 301, 00123 S. Maria di Galeria Roma (Italy)
2012-07-01
The GUINEVERE experiment (Generation of Uninterrupted Intense Neutrons at the lead Venus Reactor) is an experimental program in support of the ADS technology presently carried out at SCK-CEN in Mol (Belgium). In the experiment a modified lay-out of the original thermal VENUS critical facility is coupled to an accelerator, built by the French body CNRS in Grenoble, working in both continuous and pulsed mode and delivering 14 MeV neutrons by bombardment of deuterons on a tritium-target. The modified lay-out of the facility consists of a fast subcritical core made of 30% U-235 enriched metallic Uranium in a lead matrix. Several off-line and on-line reactivity measurement techniques will be investigated during the experimental campaign. This report is focused on the simulation by deterministic (ERANOS French code) and Monte Carlo (MCNPX US code) calculations of three reactivity measurement techniques, Slope ({alpha}-fitting), Area-ratio and Source-jerk, applied to a GUINEVERE subcritical configuration (namely SC1). The inferred reactivity, in dollar units, by the Area-ratio method shows an overall agreement between the two deterministic and Monte Carlo computational approaches, whereas the MCNPX Source-jerk results are affected by large uncertainties and allow only partial conclusions about the comparison. Finally, no particular spatial dependence of the results is observed in the case of the GUINEVERE SC1 subcritical configuration. (authors)
Nuclear reactor transient analysis via a quasi-static kinetics Monte Carlo method
Energy Technology Data Exchange (ETDEWEB)
Jo, YuGwon; Cho, Bumhee; Cho, Nam Zin, E-mail: nzcho@kaist.ac.kr [Korea Advanced Institute of Science and Technology 291 Daehak-ro, Yuseong-gu, Daejeon, Korea 305-701 (Korea, Republic of)
2015-12-31
The predictor-corrector quasi-static (PCQS) method is applied to the Monte Carlo (MC) calculation for reactor transient analysis. To solve the transient fixed-source problem of the PCQS method, fission source iteration is used and a linear approximation of fission source distributions during a macro-time step is introduced to provide delayed neutron source. The conventional particle-tracking procedure is modified to solve the transient fixed-source problem via MC calculation. The PCQS method with MC calculation is compared with the direct time-dependent method of characteristics (MOC) on a TWIGL two-group problem for verification of the computer code. Then, the results on a continuous-energy problem are presented.
Diffusion of small Cu islands on the Ni(111) surface: A self-learning kinetic Monte Carlo study
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.
Domain-growth kinetics and aspects of pinning: A Monte Carlo simulation study
DEFF Research Database (Denmark)
Castán, T.; Lindgård, Per-Anker
1991-01-01
transformations, surface reconstructions, and magnetic transitions. No external impurities are introduced, but the model has a number of intrinsic, annealable pinning mechanisms, which strongly influences the growth kinetics. It allows a study of pinning effects of three kinds: (a) pinning of domain walls...... by defects-this is found in effect to stop the growth, forming a metastable state at low temperatures T; (b) temporary pinning by stacking faults or zero-curvature domain walls; and (c) topological pinnings, which are also found to be temporary. These just slow down the growth. The pinning mechanisms...... and the depinning probability at higher temperatures are studied. The excess energy of the domain walls is found to follow an algebraic decay DELTA-E(t) = E(M) + At(-n), with E(M) = 0 for cases (b) and (c) and decaying toward a metastable state with energy E(M) not-equal-to 0 for case (a). The exponent is found...
Rate dependence of grain boundary sliding via time-scaling atomistic simulations
Hammami, Farah; Kulkarni, Yashashree
2017-02-01
Approaching experimentally relevant strain rates has been a long-standing challenge for molecular dynamics method which captures phenomena typically on the scale of nanoseconds or at strain rates of 107 s-1 and higher. Here, we use grain boundary sliding in nanostructures as a paradigmatic problem to investigate rate dependence using atomistic simulations. We employ a combination of time-scaling computational approaches, including the autonomous basin climbing method, the nudged elastic band method, and kinetic Monte Carlo, to access strain rates ranging from 0.5 s-1 to 107 s-1. Combined with a standard linear solid model for viscoelastic behavior, our simulations reveal that grain boundary sliding exhibits noticeable rate dependence only below strain rates on the order of 10 s-1 but is rate independent and consistent with molecular dynamics at higher strain rates.
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
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.
Shah, Syed Islamuddin; Nandipati, Giridhar; Kara, Abdelkader; Rahman, Talat S.
2013-07-01
We have examined the self-diffusion of small 2D Ni islands (consisting of up to 10 atoms) on the Ni(111) surface using a self-learning kinetic Monte Carlo (SLKMC-II) method with an improved pattern-recognition scheme that allows inclusion of both fcc and hcp sites in the simulations. Activation energy barriers for the identified diffusion processes were calculated on the fly using a semiempirical interaction potential based on the embedded-atom method. Although a variety of concerted, multiatom, and single-atom processes were automatically revealed in our simulations, we found that, in the temperature range of 300 K-700 K, these small islands diffuse primarily via concerted motion. Single-atom processes play an important role in ensuring that diffusion is random for islands containing 5 or more atoms, while multiatom processes (shearing and reptation) come into play for noncompact islands. The effective activation energy barriers obtained from the Arrhenius plot of the diffusion coefficients showed an increase with the size of the island, although there were interesting deviations from linear dependence. Several other processes also contributing to diffusion of islands were identified.
Lattice kinetic Monte Carlo simulation study of the early stages of epitaxial GaN(0001) growth
Chugh, Manjusha; Ranganathan, Madhav
2017-11-01
The early stages of GaN(0001) epitaxial growth are modeled using a lattice-based kinetic Monte Carlo simulation. The simulation explicitly includes both the constituent atoms and is performed on the wurtzite crystal structure of GaN. The deposition flux is chosen to mimic conditions in a molecular beam epitaxy chamber. The surface diffusion barriers used for the growth simulation are obtained from ab initio density functional theory based calculations. The evolution of submonolayer islands from small random clusters to ordered triangular islands is captured in these simulations. Further the submonolayer island density statistics is calculated to illustrate standard scaling behavior. The island density as a function of coverage is used to show the different regimes of submonolayer growth and the transition to multi-layer growth. The island density dependence on deposition flux, Ga:N flux ratio, and temperature are also shown to be reasonable and consistent with experiments. We further highlight the importance of N-rotation, which is a diffusion mechanism for nitrogen adatoms under moderate gallium excess.
Energy Technology Data Exchange (ETDEWEB)
Chiapetto, M. [SCK-CEN, Nuclear Materials Science Institute, Mol (Belgium); Unite Materiaux et Transformations (UMET), UMR 8207, Universite de Lille 1, ENSCL, Villeneuve d' Ascq (France); Becquart, C.S. [Unite Materiaux et Transformations (UMET), UMR 8207, Universite de Lille 1, ENSCL, Villeneuve d' Ascq (France); Laboratoire commun EDF-CNRS, Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Domain, C. [EDF R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Moret sur Loing (France); Laboratoire commun EDF-CNRS, Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Malerba, L. [SCK-CEN, Nuclear Materials Science Institute, Mol (Belgium)
2015-01-01
Post-irradiation annealing experiments are often used to obtain clearer information on the nature of defects produced by irradiation. However, their interpretation is not always straightforward without the support of physical models. We apply here a physically-based set of parameters for object kinetic Monte Carlo (OKMC) simulations of the nanostructural evolution of FeMnNi alloys under irradiation to the simulation of their post-irradiation isochronal annealing, from 290 to 600 C. The model adopts a ''grey alloy'' scheme, i.e. the solute atoms are not introduced explicitly, only their effect on the properties of point-defect clusters is. Namely, it is assumed that both vacancy and SIA clusters are significantly slowed down by the solutes. The slowing down increases with size until the clusters become immobile. Specifically, the slowing down of SIA clusters by Mn and Ni can be justified in terms of the interaction between these atoms and crowdions in Fe. The results of the model compare quantitatively well with post-irradiation isochronal annealing experimental data, providing clear insight into the mechanisms that determine the disappearance or re-arrangement of defects as functions of annealing time and temperature. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Good, Brian S.
2011-01-01
Yttria-stabilized zirconia s high oxygen diffusivity and corresponding high ionic conductivity, and its structural stability over a broad range of temperatures, have made the material of interest for use in a number of applications, for example, as solid electrolytes in fuel cells. At low concentrations, the stabilizing yttria also serves to increase the oxygen diffusivity through the presence of corresponding oxygen vacancies, needed to maintain charge neutrality. At higher yttria concentration, however, diffusivity is impeded by the larger number of relatively high energy migration barriers associated with yttrium cations. In addition, there is evidence that oxygen vacancies preferentially occupy nearest-neighbor sites around either dopant or Zr cations, further affecting vacancy diffusion. We present the results of ab initio calculations that indicate that it is energetically favorable for oxygen vacancies to occupy nearest-neighbor sites adjacent to Y ions, and that the presence of vacancies near either species of cation lowers the migration barriers. Kinetic Monte Carlo results from simulations incorporating this effect are presented and compared with results from simulations in which the effect is not present.
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.
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.
Andersen, Mie; Plaisance, Craig P.; Reuter, Karsten
2017-10-01
First-principles screening studies aimed at predicting the catalytic activity of transition metal (TM) catalysts have traditionally been based on mean-field (MF) microkinetic models, which neglect the effect of spatial correlations in the adsorbate layer. Here we critically assess the accuracy of such models for the specific case of CO methanation over stepped metals by comparing to spatially resolved kinetic Monte Carlo (kMC) simulations. We find that the typical low diffusion barriers offered by metal surfaces can be significantly increased at step sites, which results in persisting correlations in the adsorbate layer. As a consequence, MF models may overestimate the catalytic activity of TM catalysts by several orders of magnitude. The potential higher accuracy of kMC models comes at a higher computational cost, which can be especially challenging for surface reactions on metals due to a large disparity in the time scales of different processes. In order to overcome this issue, we implement and test a recently developed algorithm for achieving temporal acceleration of kMC simulations. While the algorithm overall performs quite well, we identify some challenging cases which may lead to a breakdown of acceleration algorithms and discuss possible directions for future algorithm development.
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.
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.
Atomistic modeling at experimental strain rates and timescales
Yan, Xin; Cao, Penghui; Tao, Weiwei; Sharma, Pradeep; Park, Harold S.
2016-12-01
Modeling physical phenomena with atomistic fidelity and at laboratory timescales is one of the holy grails of computational materials science. Conventional molecular dynamics (MD) simulations enable the elucidation of an astonishing array of phenomena inherent in the mechanical and chemical behavior of materials. However, conventional MD, with our current computational modalities, is incapable of resolving timescales longer than microseconds (at best). In this short review article, we briefly review a recently proposed approach—the so-called autonomous basin climbing (ABC) method—that in certain instances can provide valuable information on slow timescale processes. We provide a general summary of the principles underlying the ABC approach, with emphasis on recent methodological developments enabling the study of mechanically-driven processes at slow (experimental) strain rates and timescales. Specifically, we show that by combining a strong physical understanding of the underlying phenomena, kinetic Monte Carlo, transition state theory and minimum energy pathway methods, the ABC method has been found to be useful in a variety of mechanically-driven problems ranging from the prediction of creep-behavior in metals, constitutive laws for grain boundary sliding, void nucleation rates, diffusion in amorphous materials to protein unfolding. Aside from reviewing the basic ideas underlying this approach, we emphasize some of the key challenges encountered in our own personal research work and suggest future research avenues for exploration.
Cheng, Tao; Xiao, Hai; Goddard, William A
2017-02-21
A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of -0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than -0.6 V (RHE) ethylene, the major product, is produced via the Eley-Rideal (ER) mechanism using H2O + e- The rate-determining step (RDS) is C-C coupling of two CO, with ΔG‡ = 0.69 eV. For an applied potential less than -0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than -0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4 These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface.
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.
Huang, Chen-Hsi; Gharaee, Leili; Zhao, Yue; Erhart, Paul; Marian, Jaime
2017-09-01
High-temperature, high-dose, neutron irradiation of W results in the formation of Re-rich clusters at concentrations one order of magnitude lower than the thermodynamic solubility limit. These clusters may eventually transform into brittle W-Re intermetallic phases, which can lead to high levels of hardening and thermal conductivity losses. Standard theories of radiation-enhanced diffusion and precipitation cannot explain the formation of these precipitates and so understanding the mechanism by which nonequilibrium clusters form under irradiation is crucial to predict material degradation and devise mitigation strategies. Here we carry out a thermodynamic study of W-Re alloys and conduct kinetic Monte Carlo simulations of Re cluster formation in irradiated W-2Re alloys. We use a generalized Hamiltonian for crystals containing point defects parametrized entirely with electronic structure calculations. Our model incorporates recently gained mechanistic information of mixed-interstitial solute transport, which is seen to control cluster nucleation and growth by forming quasispherical nuclei after an average incubation time of 13.5(±8.5 ) s at 1800 K. These nuclei are seen to grow by attracting more mixed interstitials bringing solute atoms, which in turn attracts vacancies leading to recombination and solute agglomeration. Owing to the arrival of both Re and W atoms from the mixed dumbbells, the clusters are not fully dense in Re, which amounts to no more than 50% of the atomic concentration of the cluster near the center. Our simulations are in qualitative agreement with recent atom probe examinations of ion-irradiated W-2Re systems at 773 K.
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.
Atomistic simulations of bicelle mixtures.
Jiang, Yong; Wang, Hao; Kindt, James T
2010-06-16
Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets. (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Yang, Judith C. [Univ. of Pittsburgh, Pittsburgh, PA (United States)
2015-01-09
The purpose of this grant is to develop the multi-scale theoretical methods to describe the nanoscale oxidation of metal thin films, as the PI (Yang) extensive previous experience in the experimental elucidation of the initial stages of Cu oxidation by primarily in situ transmission electron microscopy methods. Through the use and development of computational tools at varying length (and time) scales, from atomistic quantum mechanical calculation, force field mesoscale simulations, to large scale Kinetic Monte Carlo (KMC) modeling, the fundamental underpinings of the initial stages of Cu oxidation have been elucidated. The development of computational modeling tools allows for accelerated materials discovery. The theoretical tools developed from this program impact a wide range of technologies that depend on surface reactions, including corrosion, catalysis, and nanomaterials fabrication.
From atomistic interfaces to dendritic patterns
Galenko, P. K.; Alexandrov, D. V.
2018-01-01
Transport processes around phase interfaces, together with thermodynamic properties and kinetic phenomena, control the formation of dendritic patterns. Using the thermodynamic and kinetic data of phase interfaces obtained on the atomic scale, one can analyse the formation of a single dendrite and the growth of a dendritic ensemble. This is the result of recent progress in theoretical methods and computational algorithms calculated using powerful computer clusters. Great benefits can be attained from the development of micro-, meso- and macro-levels of analysis when investigating the dynamics of interfaces, interpreting experimental data and designing the macrostructure of samples. The review and research articles in this theme issue cover the spectrum of scales (from nano- to macro-length scales) in order to exhibit recently developing trends in the theoretical analysis and computational modelling of dendrite pattern formation. Atomistic modelling, the flow effect on interface dynamics, the transition from diffusion-limited to thermally controlled growth existing at a considerable driving force, two-phase (mushy) layer formation, the growth of eutectic dendrites, the formation of a secondary dendritic network due to coalescence, computational methods, including boundary integral and phase-field methods, and experimental tests for theoretical models-all these themes are highlighted in the present issue. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.
Atomistic Properties of Solids
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.
Energy Technology Data Exchange (ETDEWEB)
Aliaga, Maria J.; Caturla, Maria J. [Facultad de Ciencias, Department Fisica Aplicada, Fase II, Universidad de Alicante, 03690, Alicante (Spain); Dopico, Ignacio; Martin-Bragado, Ignacio [IMDEA Materials Institute, C/Eric Kandel 2, 28906, Getafe, Madrid (Spain)
2016-11-15
The influence of surfaces on the evolution of damage of irradiated Fe is studied using object kinetic Monte Carlo with input from molecular dynamics simulations and ab initio calculations. Two effects are analysed: the influence of traps and the initial distribution of damage in the cascade. These simulations show that for a trap concentration of around 100 appm, there are no significant differences between defect concentrations in bulk and thin films. However, the initial distribution of defects plays an important role not only on total defect concentration but also on defect type, for the model used in this study. Damage produced by a 100 keV Fe ion impinging a Fe thin film. Blue (dark) spheres are self-interstitials, red (light) spheres are vacancies. (copyright 2016 The Authors/Employers. Phys. Status Solidi A published by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Aldana, S.; García-Fernández, P.; Rodríguez-Fernández, Alberto; Romero-Zaliz, R.; González, M. B.; Jiménez-Molinos, F.; Campabadal, F.; Gómez-Campos, F.; Roldán, J. B.
2017-08-01
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/HfO2/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.
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%CrC 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.
Hazelbaker, Eric D; Budhathoki, Samir; Wang, Han; Shah, Jindal; Maginn, Edward J; Vasenkov, Sergey
2014-05-15
NMR exchange spectroscopy (EXSY) and NMR diffusion spectroscopy (PFG NMR) were applied in combination with kinetic Monte Carlo (MC) simulations to investigate self-diffusion in a mixture of carbon dioxide and an amine-functionalized ionic liquid under conditions of an exchange of carbon dioxide molecules between the reacted and unreacted states in the mixture. EXSY studies enabled residence times of carbon dioxide molecules to be obtained in the two states, whereas PFG NMR revealed time-dependent effective diffusivities for diffusion times comparable with and larger than the residence times. Analytical treatment of the PFG NMR attenuation curves as well as fitting of the PFG NMR effective diffusivities by KMC simulations enabled determination of diffusivities of carbon dioxide in the reacted and unreacted states. In contrast to carbon dioxide, the ion diffusivities were found to be diffusion time independent.
Energy Technology Data Exchange (ETDEWEB)
Mauche, C W; Liedahl, D A; Akiyama, S; Plewa, T
2008-02-08
We describe the results of an effort, funded by the Lawrence Livermore National Laboratory Directed Research and Development Program, to model, using FLASH time-dependent adaptive-mesh hydrodynamic simulations, XSTAR photoionization calculations, HULLAC atomic data, and Monte Carlo radiation transport, the radiatively-driven photoionized wind and accretion flow of high-mass X-ray binaries (HMXBs). In this final report, we describe the purpose, approach, and technical accomplishments of this effort, including maps of the density, temperature, velocity, ionization parameter, and emissivity distributions of the X-ray emission lines of the well-studied HMXB Vela X-1.
Berkemeier, Thomas; Ammann, Markus; Krieger, Ulrich K.; Peter, Thomas; Spichtinger, Peter; Pöschl, Ulrich; Shiraiwa, Manabu; Huisman, Andrew J.
2017-06-01
We present a Monte Carlo genetic algorithm (MCGA) for efficient, automated, and unbiased global optimization of model input parameters by simultaneous fitting to multiple experimental data sets. The algorithm was developed to address the inverse modelling problems associated with fitting large sets of model input parameters encountered in state-of-the-art kinetic models for heterogeneous and multiphase atmospheric chemistry. The MCGA approach utilizes a sequence of optimization methods to find and characterize the solution of an optimization problem. It addresses an issue inherent to complex models whose extensive input parameter sets may not be uniquely determined from limited input data. Such ambiguity in the derived parameter values can be reliably detected using this new set of tools, allowing users to design experiments that should be particularly useful for constraining model parameters. We show that the MCGA has been used successfully to constrain parameters such as chemical reaction rate coefficients, diffusion coefficients, and Henry's law solubility coefficients in kinetic models of gas uptake and chemical transformation of aerosol particles as well as multiphase chemistry at the atmosphere-biosphere interface. While this study focuses on the processes outlined above, the MCGA approach should be portable to any numerical process model with similar computational expense and extent of the fitting parameter space.
Huang, C-H; Marian, J
2016-01-01
We derive an Ising Hamiltonian for kinetic simulations involving interstitial and vacancy defects in binary alloys. Our model, which we term `ABVI', incorporates solute transport by both interstitial defects and vacancies into a mathematically-consistent framework , and thus represents a generalization to the widely-used ABV model for alloy evolution simulations. The Hamiltonian captures the three possible interstitial configurations in a binary alloy: A-A, A-B, and B-B, which makes it partic...
He, Xiang; Chen, Zhao-Xu
2016-05-01
We studied the thermal-stability of supported Au nanoparticles on the substrates of different binding strength to gold by Monte Carlo simulations. It has been revealed that the stable Au morphology is determined by the temperature and the binding strength. When heated on the strongly-binding substrates, the Au nanoparticles would wet the substrate completely and form monolayer. The stable Au layered structure of few layers can be formed by the incomplete wetting of clusters on the intermediate-binding substrates. The simulation results are in good agreement with pertinent experimental and theoretical results. Based on the simulation results and experimental observations, we find the strong linkage between the top edge sites and the activity TOF of low-temperature CO oxidation. We conclude that the top edges sites of Au layered structures are possible reactive sites. This study may provide new perspective for controlling morphology and understanding catalytic activity of supported metallic clusters.
Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics
Energy Technology Data Exchange (ETDEWEB)
Wijesinghe, S; Hornung, R; Garcia, A; Hadjiconstantinou, N
2004-04-15
We present an adaptive mesh and algorithmic refinement (AMAR) scheme for modeling multi-scale hydrodynamics. The AMAR approach extends standard conservative adaptive mesh refinement (AMR) algorithms by providing a robust flux-based method for coupling an atomistic fluid representation to a continuum model. The atomistic model is applied locally in regions where the continuum description is invalid or inaccurate, such as near strong flow gradients and at fluid interfaces, or when the continuum grid is refined to the molecular scale. The need for such ''hybrid'' methods arises from the fact that hydrodynamics modeled by continuum representations are often under-resolved or inaccurate while solutions generated using molecular resolution globally are not feasible. In the implementation described herein, Direct Simulation Monte Carlo (DSMC) provides an atomistic description of the flow and the compressible two-fluid Euler equations serve as our continuum-scale model. The AMR methodology provides local grid refinement while the algorithm refinement feature allows the transition to DSMC where needed. The continuum and atomistic representations are coupled by matching fluxes at the continuum-atomistic interfaces and by proper averaging and interpolation of data between scales. Our AMAR application code is implemented in C++ and is built upon the SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) framework developed at Lawrence Livermore National Laboratory. SAMRAI provides the parallel adaptive gridding algorithm and enables the coupling between the continuum and atomistic methods.
Li, Xuegeng
The primary accomplishment of the research presented in this thesis is the development of a technology to produce light emitting silicon nanoparticles in macroscopic quantities by gas phase laser-driven pyrolysis of silane and post etching treatment. Theoretical exploration of the homogenous gas phase particle nucleation during pyrolysis of silane is another parallel focus of this thesis. Production of nano-scale materials by CO2 laser-driven gas phase reactions has been studied by several groups during the past two decades. The particle sizes can be controlled to below 10 nm. Although the silicon nanoparticles that are produced by this method are not photoluminescent, we have discovered that etching these particles with HF/HNO3 mixture can controllably reduce their size and passivate their surface such that they become photoluminescent. The photoluminescence can be controlled by the etching conditions. In order to obtain silicon nanoparticles with stable photoluminescence properties and stable colloidal dispersions for further applications, it is important to passivate the silicon nanoparticle surfaces and coat them with functional groups. Well-dispersed particle dispersions with stable PL were obtained after surface functionalization. This provides an important step toward the further potential applications of silicon nanoparticles. One key advantage of the gas phase laser pyrolysis process is the flexibility to make nanoparticles of different materials. Nickel and iron nanoparticles were produced successfully with controlled size distribution. Preliminary results show that this method is capable of producing metallic nanoparticles with interesting magnetic properties. Kinetic Monte Carlo simulation of particle nucleation during thermal decomposition of silane can also be used to obtain useful information about the synthesis of silicon nanoparticles. In this approach, a simulation follows the evolution of a single silicon-hydrogen cluster as it reacts with its
Directory of Open Access Journals (Sweden)
D. E. Panayotounakos
2002-01-01
Full Text Available We present the construction of the general solutions concerning the one-dimensional (1D fully dynamic nonlinear partial differential equations (PDEs, for the erosion kinetics. After an uncoupling procedure of the above mentioned equations a second–order nonlinear PDE of the Monge type governing the porosity is derived, the general solution of which is constructed in the sense that a full complement of arbitrary functions (as many as the order is introduced. Afterwards, we specify the above solution according to convenient initial conditions.
Atomistic Simulations of Bicelle Mixtures
Jiang, Yong; Wang, Hao; Kindt, James T.
2010-01-01
Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironmen...
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.
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.
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 H2 + I2 ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H2 and I2 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 [H2]eq and equilibrium constants Keq 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 [H2] 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.
Atomistic stimulation of defective oxides
Minervini, L
2000-01-01
defect processes. The predominant intrinsic disorder reaction and the mechanism by which excess oxygen is accommodated are established. Furthermore, the most favourable migration mechanism and pathway for oxygen ions is predicted. Chapters 7 and 8 investigate pyrochlore oxides. These materials are candidates for solid oxide fuel cell components and as actinide host phases. Such applications require a detailed understanding of the defect processes. The defect energies, displayed as contour maps, are able to account for structure stability and, given an appropriate partial charge potential model, to accurately determine the oxygen positional parameter. In particular, the dependence of the positional parameter on intrinsic disorder is predicted. It is demonstrated, by radiation damage experiments, that these results are able to predict the radiation performance of pyrochlore oxides. Atomistic simulation calculations based on energy minimization techniques and classical pair potentials are used to study several i...
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
Strikwold, Marije; Spenkelink, Bert; Woutersen, Ruud A.; Rietjens, Ivonne M.C.M.; Punt, Ans
2017-01-01
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
Calculation of Elastic Bond Constants in Atomistic Strain Analysis
Chen, Haiyuan; Wang, Juanjuan; Ashalley, Eric; Li, Handong; Niu, Xiaobin
2015-10-01
Strain analysis has significance both for tailoring material properties and designing nanoscale devices. In particular, strain plays a vital role in engineering the growth thermodynamics and kinetics and is applicable for designing optoelectronic devices. In this paper, we present a methodology for establishing the relationship between elastic bond constants and measurable parameters, i.e., Poisson's ratio ν and systematic elastic constant K. At the atomistic level, this approach is within the framework of linear elastic theory and encompasses the neighbor interactions when an atom is introduced to stress. Departing from the force equilibrium equations, the relationships between ν, K, and spring constants are successfully established. Both the two-dimensional (2D) square lattice and common three-dimensional (3D) structures are taken into account in the procedure for facilitating, bridging the gap between structural complexity and numerical experiments. A new direction for understanding the physical phenomena in strain engineering is established.
Atomistic computer simulations a practical guide
Brazdova, Veronika
2013-01-01
Many books explain the theory of atomistic computer simulations; this book teaches you how to run them This introductory ""how to"" title enables readers to understand, plan, run, and analyze their own independent atomistic simulations, and decide which method to use and which questions to ask in their research project. It is written in a clear and precise language, focusing on a thorough understanding of the concepts behind the equations and how these are used in the simulations. As a result, readers will learn how to design the computational model and which parameters o
Atomistic Galois insertions for flow sensitive integrity
DEFF Research Database (Denmark)
Nielson, Flemming; Nielson, Hanne Riis
2017-01-01
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...
Speck, Thomas; Chandler, David
2012-05-14
Recent progress has demonstrated that trajectory space for both kinetically constrained lattice models and atomistic models can be partitioned into a liquid-like and an inactive basin with a non-equilibrium phase transition separating these behaviors. Recent work has also established that excitations in atomistic models have statistics and dynamics like those in a specific class of kinetically constrained models. But it has not been known whether the non-equilibrium phase transitions occurring in the two classes of models have similar origins. Here, we show that the origin is indeed similar. In particular, we show that the number of excitations identified in an atomistic model serves as the order parameter for the inactive-active phase transition for that model. In this way, we show that the mechanism by which excitations are correlated in an atomistic model - by dynamical facilitation - is the mechanism from which the active-inactive phase transition emerges. We study properties of the inactive phase and show that it is amorphous lacking long-range order. We also discuss the choice of dynamical order parameters.
Atomistic spin dynamics and surface magnons
Etz, Corina; Bergqvist, Lars; Bergman, Anders; Taroni, Andrea; Eriksson, Olle
2015-06-01
Atomistic spin dynamics simulations have evolved to become a powerful and versatile tool for simulating dynamic properties of magnetic materials. It has a wide range of applications, for instance switching of magnetic states in bulk and nano-magnets, dynamics of topological magnets, such as skyrmions and vortices and domain wall motion. In this review, after a brief summary of the existing investigation tools for the study of magnons, we focus on calculations of spin-wave excitations in low-dimensional magnets and the effect of relativistic and temperature effects in such structures. In general, we find a good agreement between our results and the experimental values. For material specific studies, the atomistic spin dynamics is combined with electronic structure calculations within the density functional theory from which the required parameters are calculated, such as magnetic exchange interactions, magnetocrystalline anisotropy, and Dzyaloshinskii-Moriya vectors.
Addressing uncertainty in atomistic machine learning
DEFF Research Database (Denmark)
Peterson, Andrew A.; Christensen, Rune; Khorshidi, Alireza
2017-01-01
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......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...
Cassandra: An open source Monte Carlo package for molecular simulation.
Shah, Jindal K; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy; Keene, Brian P; Khan, Sandip; Paluch, Andrew S; Rai, Neeraj; Romanielo, Lucienne L; Rosch, Thomas W; Yoo, Brian; Maginn, Edward J
2017-07-15
Cassandra is an open source atomistic Monte Carlo software package that is effective in simulating the thermodynamic properties of fluids and solids. The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures
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
Neilson, James R; McQueen, Tyrel M
2015-10-01
With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atoms in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. This method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.
Energy Technology Data Exchange (ETDEWEB)
Stoller, Roger E [ORNL; Golubov, Stanislav I [ORNL; Becquart, C. S. [Universite de Lille; Domain, C. [EDF R& D, Clamart, France
2007-08-01
The multiscale modeling scheme encompasses models from the atomistic to the continuum scale. Phenomena at the mesoscale are typically simulated using reaction rate theory, Monte Carlo, or phase field models. These mesoscale models are appropriate for application to problems that involve intermediate length scales, and timescales from those characteristic of diffusion to long-term microstructural evolution (~s to years). Although the rate theory and Monte Carlo models can be used simulate the same phenomena, some of the details are handled quite differently in the two approaches. Models employing the rate theory have been extensively used to describe radiation-induced phenomena such as void swelling and irradiation creep. The primary approximations in such models are time- and spatial averaging of the radiation damage source term, and spatial averaging of the microstructure into an effective medium. Kinetic Monte Carlo models can account for these spatial and temporal correlations; their primary limitation is the computational burden which is related to the size of the simulation cell. A direct comparison of RT and object kinetic MC simulations has been made in the domain of point defect cluster dynamics modeling, which is relevant to the evolution (both nucleation and growth) of radiation-induced defect structures. The primary limitations of the OKMC model are related to computational issues. Even with modern computers, the maximum simulation cell size and the maximum dose (typically much less than 1 dpa) that can be simulated are limited. In contrast, even very detailed RT models can simulate microstructural evolution for doses up 100 dpa or greater in clock times that are relatively short. Within the context of the effective medium, essentially any defect density can be simulated. Overall, the agreement between the two methods is best for irradiation conditions which produce a high density of defects (lower temperature and higher displacement rate), and for
Atomistic simulations of dislocation processes in copper
DEFF Research Database (Denmark)
Vegge, T.; Jacobsen, K.W.
2002-01-01
We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example, the sta...... of vacancy controlled climb show the jogs to climb easily in their extended form. The stability of small vacancy dipoles is discussed and it is seen that the introduction of jogs may lead to the formation of Z-type faulted vacancy dipoles....
Addressing uncertainty in atomistic machine learning.
Peterson, Andrew A; Christensen, Rune; Khorshidi, Alireza
2017-05-10
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 of the uncertainty when the width is comparable to that in the training data. Intriguingly, we also show that the uncertainty can be localized to specific atoms in the simulation, which may offer hints for the generation of training data to strategically improve the machine-learned representation.
Atomistic Modeling of Gas Adsorption in Nanocarbons
Directory of Open Access Journals (Sweden)
G. Zollo
2012-01-01
Full Text Available Carbon nanostructures are currently under investigation as possible ideal media for gas storage and mesoporous materials for gas sensors. The recent scientific literature concerning gas adsorption in nanocarbons, however, is affected by a significant variation in the experimental data, mainly due to the different characteristics of the investigated samples arising from the variety of the synthesis techniques used and their reproducibility. Atomistic simulations have turned out to be sometimes crucial to study the properties of these systems in order to support the experiments, to indicate the physical limits inherent in the investigated structures, and to suggest possible new routes for application purposes. In consideration of the extent of the theme, we have chosen to treat in this paper the results obtained within some of the most popular atomistic theoretical frameworks without any purpose of completeness. A significant part of this paper is dedicated to the hydrogen adsorption on C-based nanostructures for its obvious importance and the exceptional efforts devoted to it by the scientific community.
Energy Technology Data Exchange (ETDEWEB)
Gendt, D
2001-07-01
The aim of this study is to develop a NbC precipitation modelling in ferrite. This theoretical study is motivated by the fact it considers a ternary system and focus on the concurrence of two different diffusion mechanisms. An experimental study with TEP, SANS and Vickers micro-hardening measurements allows a description of the NbC precipitation kinetics. The mean radius of the precipitates is characterized by TEM observations. To focus on the nucleation stage, we use the Tomographic Atom Probe that analyses, at an atomistic scale, the position of the solute atoms in the matrix. A first model based on the classical nucleation theory and the diffusion-limited growth describes the precipitation of spherical precipitates. To solve the set of equations, we use a numerical algorithm that furnishes an evaluation of the precipitated fraction, the mean radius and the whole size distribution of the particles. The parameters that are the interface energy, the solubility product and the diffusion coefficients are fitted with the data available in the literature and our experimental results. It allows a satisfactory agreement as regards to the simplicity of the model. Monte Carlo simulations are used to describe the evolution of a ternary alloy Fe-Nb-C on a cubic centred rigid lattice with vacancy and interstitial mechanisms. This is realized with an atomistic description of the atoms jumps and their related frequencies. The model parameters are fitted with phase diagrams and diffusion coefficients. For the sake of simplicity, we consider that the precipitation of NbC is totally coherent and we neglect any elastic strain effect. We can observe different kinetic paths: for low supersaturations, we find an expected precipitation of NbC but for higher supersaturations, the very fast diffusivity of carbon atoms conducts to the nucleation of iron carbide particles. We establish that the occurrence of this second phenomenon depends on the vacancy arrival kinetics and can be related
An atomistic vision of the Mass Action Law: Prediction of carbon/oxygen defects in silicon
Energy Technology Data Exchange (ETDEWEB)
Brenet, G.; Timerkaeva, D.; Caliste, D.; Pochet, P. [CEA, INAC-SP2M, Atomistic Simulation Laboratory, F-38000 Grenoble (France); Univ. Grenoble Alpes, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Sgourou, E. N.; Londos, C. A. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece)
2015-09-28
We introduce an atomistic description of the kinetic Mass Action Law to predict concentrations of defects and complexes. We demonstrate in this paper that this approach accurately predicts carbon/oxygen related defect concentrations in silicon upon annealing. The model requires binding and migration energies of the impurities and complexes, here obtained from density functional theory (DFT) calculations. Vacancy-oxygen complex kinetics are studied as a model system during both isochronal and isothermal annealing. Results are in good agreement with experimental data, confirming the success of the methodology. More importantly, it gives access to the sequence of chain reactions by which oxygen and carbon related complexes are created in silicon. Beside the case of silicon, the understanding of such intricate reactions is a key to develop point defect engineering strategies to control defects and thus semiconductors properties.
Scalable Atomistic Simulation Algorithms for Materials Research
Directory of Open Access Journals (Sweden)
Aiichiro Nakano
2002-01-01
Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.
Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy
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.
Choi, Won-Mi; Jo, Yong Hee; Sohn, Seok Su; Lee, Sunghak; Lee, Byeong-Joo
2018-01-01
Although high-entropy alloys (HEAs) are attracting interest, the physical metallurgical mechanisms related to their properties have mostly not been clarified, and this limits wider industrial applications, in addition to the high alloy costs. We clarify the physical metallurgical reasons for the materials phenomena (sluggish diffusion and micro-twining at cryogenic temperatures) and investigate the effect of individual elements on solid solution hardening for the equiatomic CoCrFeMnNi HEA based on atomistic simulations (Monte Carlo, molecular dynamics and molecular statics). A significant number of stable vacant lattice sites with high migration energy barriers exists and is thought to cause the sluggish diffusion. We predict that the hexagonal close-packed (hcp) structure is more stable than the face-centered cubic (fcc) structure at 0 K, which we propose as the fundamental reason for the micro-twinning at cryogenic temperatures. The alloying effect on the critical resolved shear stress (CRSS) is well predicted by the atomistic simulation, used for a design of non-equiatomic fcc HEAs with improved strength, and is experimentally verified. This study demonstrates the applicability of the proposed atomistic approach combined with a thermodynamic calculation technique to a computational design of advanced HEAs.
Atomistic simulation of damage accumulation and amorphization in Ge
Energy Technology Data Exchange (ETDEWEB)
Gomez-Selles, Jose L., E-mail: joseluis.gomezselles@imdea.org; Martin-Bragado, Ignacio [IMDEA Materials Institute, Eric Kandel 2, 28906 Getafe, Madrid (Spain); Claverie, Alain [CEMES/CNRS, 29 rue J. Marvig, 31055 Toulouse Cedex (France); Sklenard, Benoit [CEA, LETI, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Benistant, Francis [GLOBALFOUNDRIES Singapore Pte Ltd., 60 Woodlands Industrial Park D Street 2, Singapore 738406 (Singapore)
2015-02-07
Damage accumulation and amorphization mechanisms by means of ion implantation in Ge are studied using Kinetic Monte Carlo and Binary Collision Approximation techniques. Such mechanisms are investigated through different stages of damage accumulation taking place in the implantation process: from point defect generation and cluster formation up to full amorphization of Ge layers. We propose a damage concentration amorphization threshold for Ge of ∼1.3 × 10{sup 22} cm{sup −3} which is independent on the implantation conditions. Recombination energy barriers depending on amorphous pocket sizes are provided. This leads to an explanation of the reported distinct behavior of the damage generated by different ions. We have also observed that the dissolution of clusters plays an important role for relatively high temperatures and fluences. The model is able to explain and predict different damage generation regimes, amount of generated damage, and extension of amorphous layers in Ge for different ions and implantation conditions.
Atomistic mechanisms of ReRAM cell operation and reliability
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.
NiTi superelasticity via atomistic simulations
Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin
2015-12-01
The NiTi shape memory alloys (SMAs) are promising candidates for the next-generation multifunctional materials. These materials are superelastic i.e. they can fully recover their original shape even after fairly large inelastic deformations once the mechanical forces are removed. The superelasticity reportedly stems from atomic scale crystal transformations. However, very few computer simulations have emerged, elucidating the transformation mechanisms at the discrete lattice level, which underlie the extraordinary strain recoverability. Here, we conduct breakthrough molecular dynamics modelling on the superelastic behaviour of the NiTi single crystals, and unravel the atomistic genesis thereof. The deformation recovery is clearly traced to the reversible transformation between austenite and martensite crystals through simulations. We examine the mechanistic origin of the tension-compression asymmetries and the effects of pressure/temperature/strain rate variation isolatedly. Hence, this work essentially brings a new dimension to probing the NiTi performance based on the mesoscale physics under more complicated thermo-mechanical loading scenarios.
Atomistic Simulation of Non-Equilibrium Phenomena in Hypersonic Flows
Norman, Paul Erik
The goal of this work is to model the heterogeneous recombination of atomic oxygen on silica surfaces, which is of interest for accurately predicting the heating on vehicles traveling at hypersonic speeds. This is accomplished by creating a finite rate catalytic model, which describes recombination with a set of elementary gas-surface reactions. Fundamental to a description of surface catalytic reactions are the in situ chemical structures on the surface where recombination can occur. Using molecular dynamics simulations with the Reax GSISiO potential, we find that the chemical sites active in direct gas-phase reactions on silica surfaces consist of a small number of specific structures (or defects). The existence of these defects on real silica surfaces is supported by experimental results and the structure and energetics of these defects have been verified with quantum chemical calculations. The reactions in the finite rate catalytic model are based on the interaction of molecular and atomic oxygen with these defects. Trajectory calculations are used to find the parameters in the forward rate equations, while a combination of detailed balance and transition state theory are used to find the parameters in the reverse rate equations. The rate model predicts that the oxygen recombination coefficient is relatively constant at T (300-1000 K), in agreement with experimental results. At T > 1000 K the rate model predicts a drop off in the oxygen recombination coefficient, in disagreement with experimental results, which predict that the oxygen recombination coefficient increases with temperature. A discussion of the possible reasons for this disagreement, including non-adiabatic collision dynamics, variable surface site concentrations, and additional recombination mechanisms is presented. This thesis also describes atomistic simulations with Classical Trajectory Calculation Direction Simulation Monte Carlo (CTC-DSMC), a particle based method for modeling non
Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics
Energy Technology Data Exchange (ETDEWEB)
Amani, Ehsan, E-mail: eamani@aut.ac.ir; Movahed, Saeid, E-mail: smovahed@aut.ac.ir
2016-06-07
In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. - Highlights: • A hybrid continuum-atomistic model is proposed for electrokinetics in nanochannels. • The model is validated by molecular dynamics. • This is a promising approach to model more complicated geometries and physics.
A robust, coupled approach for atomistic-continuum simulation.
Energy Technology Data Exchange (ETDEWEB)
Aubry, Sylvie; Webb, Edmund Blackburn, III (Sandia National Laboratories, Albuquerque, NM); Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John (Sandia National Laboratories, Albuquerque, NM); Kimmer, Christopher J.
2004-09-01
This report is a collection of documents written by the group members of the Engineering Sciences Research Foundation (ESRF), Laboratory Directed Research and Development (LDRD) project titled 'A Robust, Coupled Approach to Atomistic-Continuum Simulation'. Presented in this document is the development of a formulation for performing quasistatic, coupled, atomistic-continuum simulation that includes cross terms in the equilibrium equations that arise due to kinematic coupling and corrections used for the calculation of system potential energy to account for continuum elements that overlap regions containing atomic bonds, evaluations of thermo-mechanical continuum quantities calculated within atomistic simulations including measures of stress, temperature and heat flux, calculation used to determine the appropriate spatial and time averaging necessary to enable these atomistically-defined expressions to have the same physical meaning as their continuum counterparts, and a formulation to quantify a continuum 'temperature field', the first step towards constructing a coupled atomistic-continuum approach capable of finite temperature and dynamic analyses.
Atomistic Modelling of Si Nanoparticles Synthesis
Directory of Open Access Journals (Sweden)
Giovanni Barcaro
2017-02-01
Full Text Available Silicon remains the most important material for electronic technology. Presently, some efforts are focused on the use of Si nanoparticles—not only for saving material, but also for improving the efficiency of optical and electronic devices, for instance, in the case of solar cells coated with a film of Si nanoparticles. The synthesis by a bottom-up approach based on condensation from low temperature plasma is a promising technique for the massive production of such nanoparticles, but the knowledge of the basic processes occurring at the atomistic level is still very limited. In this perspective, numerical simulations can provide fundamental information of the nucleation and growth mechanisms ruling the bottom-up formation of Si nanoclusters. We propose to model the low temperature plasma by classical molecular dynamics by using the reactive force field (ReaxFF proposed by van Duin, which can properly describe bond forming and breaking. In our approach, first-principles quantum calculations are used on a set of small Si clusters in order to collect all the necessary energetic and structural information to optimize the parameters of the reactive force-field for the present application. We describe in detail the procedure used for the determination of the force field and the following molecular dynamics simulations of model systems of Si gas at temperatures in the range 2000–3000 K. The results of the dynamics provide valuable information on nucleation rate, nanoparticle size distribution, and growth rate that are the basic quantities for developing a following mesoscale model.
Atomistic Method Applied to Computational Modeling of Surface Alloys
Bozzolo, Guillermo H.; Abel, Phillip B.
2000-01-01
The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on
Emergence of step flow from an atomistic scheme of epitaxial growth in 1+1 dimensions.
Lu, Jianfeng; Liu, Jian-Guo; Margetis, Dionisios
2015-03-01
The Burton-Cabrera-Frank (BCF) model for the flow of line defects (steps) on crystal surfaces has offered useful insights into nanostructure evolution. This model has rested on phenomenological grounds. Our goal is to show via scaling arguments the emergence of the BCF theory for noninteracting steps from a stochastic atomistic scheme of a kinetic restricted solid-on-solid model in one spatial dimension. Our main assumptions are: adsorbed atoms (adatoms) form a dilute system, and elastic effects of the crystal lattice are absent. The step edge is treated as a front that propagates via probabilistic rules for atom attachment and detachment at the step. We formally derive a quasistatic step flow description by averaging out the stochastic scheme when terrace diffusion, adatom desorption, and deposition from above are present.
Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids
Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily
2014-01-01
Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space–time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space–time, a novel hybrid atomistic–fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided. PMID:24982246
Definition and detection of contact in atomistic simulations
Solhjoo, Soheil; Vakis, Antonis I.
2015-01-01
In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,
Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics.
Amani, Ehsan; Movahed, Saeid
2016-06-07
In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. Copyright © 2016 Elsevier B.V. All rights reserved.
Atomistic simulations of jog migration on extended screw dislocations
DEFF Research Database (Denmark)
Vegge, T.; Leffers, T.; Pedersen, O.B.
2001-01-01
We have performed large-scale atomistic simulations of the migration of elementary jogs on dissociated screw dislocations in Cu. The local crystalline configurations, transition paths. effective masses. and migration barriers for the jogs are determined using an interatomic potential based...
Atomistic approach for modeling metal-semiconductor interfaces
DEFF Research Database (Denmark)
Stradi, Daniele; Martinez, Umberto; Blom, Anders
2016-01-01
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 re...
Energy Technology Data Exchange (ETDEWEB)
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.
2016-10-14
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
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
Atomistic microstructures in short-range ordered alloys
Hata, S
2002-01-01
Short-range order (SRO) in Ni-Mo alloys and their relatives has been controversial for decades, since it causes clearly diffraction intensity maxima at positions which do not coincide with the superlattice reflections in the long-range order (LRO) state. This paper gives an overview of recent studies on the structure of SRO and the transition from SRO to LRO in Ni-Mo alloys, including our results obtained in atomic level by combination of kinetic Monte Carlo simulation and semi-quantitative high-resolution transmission electron microscopy. It is rationalized in our results that the SRO state is set up by local ordering of A sub 4 B, A sub 3 B and A sub 2 B types in sub-unit cell scale. The dispersed mixture of the sub-unit cell clusters gives diffraction intensity maxima at the particular positions. An LRO state is formed by selected growth of the A sub 4 B, A sub 3 B and A sub 2 B type clusters into LRO domains depending on alloy-composition.
Long-time atomistic simulations with the Parallel Replica Dynamics method
Perez, Danny
Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.
Mohan, Nisha
Modeling the evolution of microstructure during sintering is a persistent challenge in ceramics science, although needed as the microstructure impacts properties of an engineered material. Bridging the gap between microscopic and continuum models, kinetic Monte Carlo (kMC) methods provide a stochastic approach towards sintering and microstructure evolution. These kMC models work at the mesoscale, with length and time-scales between those of atomistic and continuum approaches. We develop a sintering/compacting model for the two-phase sintering of boron nitride ceramics and allotropes alike. Our formulation includes mechanisms for phase transformation between h-BN and c-BN and takes into account thermodynamics of pressure and temperature on interaction energies and mechanism rates. In addition to replicating the micro-structure evolution observed in experiments, it also captures the phase diagram of Boron Nitride materials. Results have been analyzed in terms of phase diagrams and crystal growth. It also serves with insights to guide the choice of additives and conditions for the sintering process.While detailed time and spatial resolutions are lost in any MC, the progression of stochastic events still captures plausible local energy minima and long-time temporal developments. DARPA.
Atomistic potential for graphene and other sp(2) carbon systems.
Fthenakis, Zacharias G; Kalosakas, George; Chatzidakis, Georgios D; Galiotis, Costas; Papagelis, Konstantinos; Lathiotakis, Nektarios N
2017-11-14
We introduce a torsional force field for sp(2) carbon to augment an in-plane atomistic potential of a previous work [G. Kalosakas et al., J. Appl. Phys., 2013, 113, 134307] so that it is applicable to out-of-plane deformations of graphene and related carbon materials. The introduced force field is fit to reproduce density-functional-theory calculation data of appropriately chosen structures. The aim is to create a force field that is as simple as possible so it can be efficient for large scale atomistic simulations of various sp(2) carbon structures without significant loss of accuracy. We show that the complete proposed potential reproduces characteristic properties of fullerenes and carbon nanotubes. In addition, it reproduces very accurately the out-of-plane acoustic and optical modes of graphene's phonon dispersion as well as all phonons with frequencies up to 1000 cm(-1).
The atomistic representation of first strain-gradient elastic tensors
Admal, Nikhil Chandra; Marian, Jaime; Po, Giacomo
2017-02-01
We derive the atomistic representations of the elastic tensors appearing in the linearized theory of first strain-gradient elasticity for an arbitrary multi-lattice. In addition to the classical second-Piola) stress and elastic moduli tensors, these include the rank-three double-stress tensor, the rank-five tensor of mixed elastic moduli, and the rank-six tensor of strain-gradient elastic moduli. The atomistic representations are closed-form analytical expressions in terms of the first and second derivatives of the interatomic potential with respect to interatomic distances, and dyadic products of relative atomic positions. Moreover, all expressions are local, in the sense that they depend only on the atomic neighborhood of a lattice site. Our results emanate from the condition of energetic equivalence between continuum and atomistic representations of a crystal, when the kinematics of the latter is governed by the Cauchy-Born rule. Using the derived expressions, we prove that the odd-order tensors vanish if the lattice basis admits central-symmetry. The analytical expressions are implemented as a KIM compliant algorithm to compute the strain gradient elastic tensors for various materials. Numerical results are presented to compare representative interatomic potentials used in the literature for cubic crystals, including simple lattices (fcc Al and Cu and bcc Fe and W) and multi-lattices (diamond-cubic Si). We observe that central potentials exhibit generalized Cauchy relations for the rank-six tensor of strain-gradient elastic moduli. In addition, this tensor is found to be indefinite for many potentials. We discuss the relationship between indefiniteness and material stability. Finally, the atomistic representations are specialized to central potentials in simple lattices. These expressions are used with analytical potentials to study the sensitivity of the elastic tensors to the choice of the cutoff radius.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Beretta, G P; Al-Abbasi, Omar; von Spakovsky, M R
2017-04-01
The steepest entropy ascent (SEA) dynamical principle provides a general framework for modeling the dynamics of nonequilibrium (NE) phenomena at any level of description, including the atomistic one. It has recently been shown to provide a precise implementation and meaning to the maximum entropy production principle and to encompass many well-established theories of nonequilibrium thermodynamics into a single unifying geometrical framework. Its original formulation in the framework of quantum thermodynamics (QT) assumes the simplest and most natural Fisher-Rao metric to geometrize from a dynamical standpoint the manifold of density operators, which represent the thermodynamic NE states of the system. This simplest SEAQT formulation is used here to develop a general mathematical framework for modeling the NE time evolution of the quantum state of a chemically reactive mixture at an atomistic level. The method is illustrated for a simple two-reaction kinetic scheme of the overall reaction F+H_{2}⇔HF+F in an isolated tank of fixed volume. However, the general formalism is developed for a reactive system subject to multiple reaction mechanisms. To explicitly implement the SEAQT nonlinear law of evolution for the density operator, both the energy and the particle number eigenvalue problems are set up and solved analytically under the dilute gas approximation. The system-level energy and particle number eigenvalues and eigenstates are used in the SEAQT equation of motion to determine the time evolution of the density operator, thus effectively describing the overall kinetics of the reacting system as it relaxes toward stable chemical equilibrium. The predicted time evolution in the near-equilibrium limit is compared to the reaction rates given by a standard detailed kinetic model so as to extract the single time constant needed by the present SEA model.
Energy Technology Data Exchange (ETDEWEB)
Duco-Sivagnanam, J
1967-07-01
The Cupidon 2 CODE aims to calculate the mono-kinetic neutrons flux in an assembly of cubes cavities jointed by rectangular holes. This report is a partial description of the code Cupidon 2 which explains the calculation procedure: data entry, code limits...). (A.L.B.)
Control of density fluctuations in atomistic-continuum simulations of dense liquids
DEFF Research Database (Denmark)
Kotsalis, E.M.; Walther, Jens Honore; Koumoutsakos, P.
2007-01-01
We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a co......We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system...
Stadlbauer, Petr; Mazzanti, Liuba; Cragnolini, Tristan; Wales, David J; Derreumaux, Philippe; Pasquali, Samuela; Šponer, Jiří
2016-12-13
G-quadruplexes are the most important noncanonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite the availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradictory models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach thermodynamic equilibrium. Based on atomistic simulations of diverse classes of intermediates in G-quadruplex folding, we have suggested that the folding is an extremely multipathway process combining a kinetic partitioning mechanism with conformational diffusion. However, complete G-quadruplex folding is far beyond the time scale of atomistic simulations. Here we use high-resolution coarse-grained simulations to investigate potential unfolding intermediates, whose structural dynamics are then further explored with all-atom simulations. This multiscale approach indicates how various pathways are interconnected in a complex network. Spontaneous conversions between different folds are observed. We demonstrate the inability of simple order parameters, such as radius of gyration or the number of native H-bonds, to describe the folding landscape of the G-quadruplexes. Our study also provides information relevant to further development of the coarse-grained force field.
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.
Atomistic simulations of Mg-Cu metallic glasses: Mechanical properties
DEFF Research Database (Denmark)
Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel
2004-01-01
The atomistic mechanisms of plastic deformation in amorphous metals are far from being understood. We have derived potential parameters for molecular dynamics simulations of Mg-Cu amorphous alloys using the Effective Medium Theory. We have simulated the formation of alloys by cooling from the melt......, and have used these glassy configurations to carry out simulations of plastic deformation. These involved different compositions, temperatures (including zero), and types of deformation (uniaxial strain/pure shear), and yielded stress-strain curves and values of flow stress. Separate simulations were...
2016-12-19
Dislocations ; Atomistic simulations; Concentrated multicomponent solid solution alloy; BCC crystal 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...This has implications for higher-scale modeling ( dislocation dynamics or crystal plasticity) of HEA alloys, relative to elemental BCC metals, which...AFRL-RX-WP-JA-2017-0302 ATOMISTIC SIMULATIONS OF DISLOCATIONS IN A MODEL BCC MULTICOMPONENT CONCENTRATED SOLID SOLUTION ALLOY
Monte Carlo Generation of the 2BN Bremsstrahlung Distribution
Peralta, L; Trindade, A
2003-01-01
The 2BN bremsstrahlung cross-section is a well-adapted distribution to describe the radiative processes at low electron kinetic energy (Ek<500 keV). In this work a method to implement this distribution in a Monte Carlo generator is developed.
Pan, Xiaoliang; Schwartz, Steven
2015-03-01
It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.
Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene
Energy Technology Data Exchange (ETDEWEB)
Guin, Laurent [LMS, École Polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau (France); Department of Mechanical Engineering, Columbia University, New York, New York 10027 (United States); Raphanel, Jean L. [LMS, École Polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau (France); Kysar, Jeffrey W. [Department of Mechanical Engineering, Columbia University, New York, New York 10027 (United States)
2016-06-28
Pristine single crystal graphene is the strongest known two-dimensional material, and its nonlinear anisotropic mechanical properties are well understood from the atomic length scale up to a continuum description. However, experiments indicate that grain boundaries in the polycrystalline form reduce the mechanical behavior of polycrystalline graphene. Herein, we perform atomistic-scale molecular dynamics simulations of the deformation and fracture of graphene grain boundaries and express the results as continuum cohesive zone models (CZMs) that embed notions of the grain boundary ultimate strength and fracture toughness. To facilitate energy balance, we employ a new methodology that simulates a quasi-static controlled crack propagation which renders the kinetic energy contribution to the total energy negligible. We verify good agreement between Griffith's critical energy release rate and the work of separation of the CZM, and we note that the energy of crack edges and fracture toughness differs by about 35%, which is attributed to the phenomenon of bond trapping. This justifies the implementation of the CZM within the context of the finite element method (FEM). To enhance computational efficiency in the FEM implementation, we discuss the use of scaled traction-separation laws (TSLs) for larger element sizes. As a final result, we have established that the failure characteristics of pristine graphene and high tilt angle bicrystals differ by less than 10%. This result suggests that one could use a unique or a few typical TSLs as a good approximation for the CZMs associated with the mechanical simulations of the polycrystalline graphene.
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.
Energy Technology Data Exchange (ETDEWEB)
Radhakrishnan, B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Eisenbach, M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Burress, Timothy A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
2017-01-24
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. In conclusion, 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.
Ouyang, Runhai; Liu, Jin-Xun; Li, Wei-Xue
2013-02-06
Understanding Ostwald ripening and disintegration of supported metal particles under operating conditions has been of central importance in the study of sintering and dispersion of heterogeneous catalysts for long-term industrial implementation. To achieve a quantitative description of these complicated processes, an atomistic and generic theory taking into account the reaction environment, particle size and morphology, and metal-support interaction is developed. It includes (1) energetics of supported metal particles, (2) formation of monomers (both the metal adatoms and metal-reactant complexes) on supports, and (3) corresponding sintering rate equations and total activation energies, in the presence of reactants at arbitrary temperature and pressure. The thermodynamic criteria for the reactant assisted Ostwald ripening and induced disintegration are formulated, and the influence of reactants on sintering kinetics and redispersion are mapped out. Most energetics and kinetics barriers in the theory can be obtained conveniently by first-principles theory calculations. This allows for the rapid exploration of sintering and disintegration of supported metal particles in huge phase space of structures and compositions under various reaction environments. General strategies of suppressing the sintering of the supported metal particles and facilitating the redispersions of the low surface area catalysts are proposed. The theory is applied to TiO(2)(110) supported Rh particles in the presence of carbon monoxide, and reproduces well the broad temperature, pressure, and particle size range over which the sintering and redispersion occurred in such experiments. The result also highlights the importance of the metal-carbonyl complexes as monomers for Ostwald ripening and disintegration of supported metal catalysts in the presence of CO.
Qin, Sanbo; Cai, Lu; Zhou, Huan-Xiang
2012-12-01
In cellular environments, two protein molecules on their way to form a specific complex encounter many bystander macromolecules. The latter molecules, or crowders, affect both the energetics of the interaction between the test molecules and the dynamics of their relative motion. In earlier work (Zhou and Szabo 1991 J. Chem. Phys. 95 5948-52), it has been shown that, in modeling the association kinetics of the test molecules, the presence of crowders can be accounted for by their energetic and dynamic effects. The recent development of the transient-complex theory for protein association in dilute solutions makes it possible to easily incorporate the energetic and dynamic effects of crowders. The transient complex refers to a late on-pathway intermediate, in which the two protein molecules have near-native relative separation and orientation, but have yet to form the many short-range specific interactions of the native complex. The transient-complex theory predicts the association rate constant as ka = ka0exp( - ΔG*el/kBT), where ka0 is the ‘basal’ rate constant for reaching the transient complex by unbiased diffusion, and the Boltzmann factors captures the influence of long-range electrostatic interactions between the protein molecules. Crowders slow down the diffusion, therefore reducing the basal rate constant (to kac0), and induce an effective interaction energy ΔGc. We show that the latter interaction energy for atomistic proteins in the presence of spherical crowders is ‘long’-ranged, allowing the association rate constant under crowding to be computed as kac = kac0exp[ - (ΔG*el + ΔG*c)/kBT]. Applications demonstrate that this computational method allows for realistic modeling of protein association kinetics under crowding.
3d visualization of atomistic simulations on every desktop
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.
Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation
Energy Technology Data Exchange (ETDEWEB)
Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J
2005-12-31
Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process.
Variational Monte Carlo Technique
Indian Academy of Sciences (India)
ias
Major ad- vances of the MC techniques were made during World. War II by scientists such as John Von Neumann, En- rico Fermi, S M Ulam and Nicholas Metropolis working on the development of nuclear weapons in Los Alamos. National Laboratory, USA [10, 11]. 3. Monte Carlo Integration Using Importance. Sampling.
Indian Academy of Sciences (India)
GENERAL I ARTICLE. Markov Chain Monte Carlo. 1. ... Note that I have numbered only those squares that are. 'stable', 'i. e., do not have .... probability approaches 1 in the limit as t tends to infinity was obvious even without all this mathematics, since it is a common experience that all games of Ludo eventually end since.
DEFF Research Database (Denmark)
van Leeuwen, Theo; Djonov, Emilia
2014-01-01
After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images....
Handleiding Mont Ventoux on Wheels
Dr. A.E. Schep-Akkerman; Drs. J.T. van der Vinne
2017-01-01
De handleiding Mont Ventoux on Wheels is ontwikkeld door Stichting WIEL en Werkplaats Sociaal Domein. In 2017-2018 wordt (evaluatie)onderzoek gedaan naar praktijkervaringen met de aanpak van Mont Ventoux on Wheels. De kern van Mont Ventoux on Wheels is dat een gemengde groep van deelnemers,
Atomistic Structure, Strength, and Kinetic Properties of Intergranular Films in Ceramics
Energy Technology Data Exchange (ETDEWEB)
Garofalini, Stephen H
2015-01-08
Intergranular films (IGFs) present in polycrystalline oxide and nitride ceramics provide an excellent example of nanoconfined glasses that occupy only a small volume percentage of the bulk ceramic, but can significantly influence various mechanical, thermal, chemical, and optical properties. By employing molecular dynamics computer simulations, we have been able to predict structures and the locations of atoms at the crystal/IGF interface that were subsequently verified with the newest electron microscopies. Modification of the chemistry of the crystal surface in the simulations provided the necessary mechanism for adsorption of specific rare earth ions from the IGF in the liquid state to the crystal surface. Such results had eluded other computational approaches such as ab-initio calculations because of the need to include not only the modified chemistry of the crystal surfaces but also an accurate description of the adjoining glassy IGF. This segregation of certain ions from the IGF to the crystal caused changes in the local chemistry of the IGF that affected fracture behavior in the simulations. Additional work with the rare earth ions La and Lu in the silicon oxynitride IGFs showed the mechanisms for their different affects on crystal growth, even though both types of ions are seen adhering to a bounding crystal surface that would normally imply equivalent affects on grain growth.
Atomistic design of semiconductor nanostructures with optimal thermoelectric properties
Galli, Giulia
2008-03-01
The search for novel materials with optimal thermoelectric properties (for either thermoelectric power generation or heat dissipation) is an active field of research. We present atomistic and ab-initio simulations of selected nanomaterials, aimed at predicting thermal conductivities and electronic transport properties, and ultimately at designing materials with optimal thermoelectric figure of merit. In particular we focus on carbon nanotubes [1], silicon wires [2] and nanoporous silicon [3] and we discuss both strategies and algorithms to optimize thermoelectric properties at the nanoscale. [1] D. Donadio and G.Galli, Phys. Rev. Lett. 2007 (in press). [2] T.Vo, A.Williamson, V.Lordi and G.Galli (submitted) and J.Reed, A.Williamson, E.Schwegler and G.Galli (submitted). [3] J.-H. Lee, J.C.Grossman, J.Reed and G.Galli, Appl. Phys. Lett. 2007 (in press).
Atomistic Simulation of Polymer Crystallization at Realistic Length Scales
Energy Technology Data Exchange (ETDEWEB)
Gee, R H; Fried, L E
2005-01-28
Understanding the dynamics of polymer crystallization during the induction period prior to crystal growth is a key goal in polymer physics. Here we present the first study of primary crystallization of polymer melts via molecular dynamics simulations at physically realistic (about 46 nm) length scales. Our results show that the crystallization mechanism involves a spinodal decomposition microphase separation caused by an increase in the average length of rigid trans segments along the polymer backbone during the induction period. Further, the characteristic length of the growing dense domains during the induction period is longer than predicted by classical nucleation theory. These results indicate a new 'coexistence period' in the crystallization, where nucleation and growth mechanisms coexist with a phase separation mechanism. Our results provide an atomistic verification of the fringed micelle model.
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...
Atomistic simulation of graphene-based polymer nanocomposites
Energy Technology Data Exchange (ETDEWEB)
Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis [Crete Center for Quantum Complexity and Nanotechnology (CQCN), Department of Physics, University of Crete, Heraklion, Crete (Greece)
2016-05-18
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.
Atomistic modeling of ion implantation technologies in silicon
Energy Technology Data Exchange (ETDEWEB)
Marqués, Luis A., E-mail: lmarques@ele.uva.es; Santos, Iván; Pelaz, Lourdes; López, Pedro; Aboy, María
2015-06-01
Requirements for the manufacturing of electronic devices at the nanometric scale are becoming more and more demanding on each new technology node, driving the need for the fabrication of ultra-shallow junctions and finFET structures. Main implantation strategies, cluster and cold implants, are aimed to reduce the amount of end-of-range defects through substrate amorphization. During finFET doping the device body gets amorphized, and its regrowth is more problematic than in the case of conventional planar devices. Consequently, there is a renewed interest on the modeling of amorphization and recrystallization in the front-end processing of Si. We present multi-scale simulation schemes to model amorphization and recrystallization in Si from an atomistic perspective. Models are able to correctly predict damage formation, accumulation and regrowth, both in the ballistic and thermal-spike regimes, in very good agreement with conventional molecular dynamics techniques but at a much lower computational cost.
Diffusion in energy materials: Governing dynamics from atomistic modelling
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.
Atomistic Determination of Cross-Slip Pathway and Energetics
DEFF Research Database (Denmark)
Rasmussen, Torben; Jacobsen, Karsten Wedel; Leffers, Torben
1997-01-01
plane. The transition state and activation energy for cross slip as well as the energies of the involved dislocation constrictions are determined. One constriction has a negative energy compared to parallel partials. The energy vs splitting width for recombination of parallel partials into a perfect......The mechanism for cross slip of a screw dislocation in Cu is determined by atomistic simulations that only presume the initial and final states of the process. The dissociated dislocation constricts in the primary plane and redissociates into the cross-slip plane while still partly in the primary...... dislocation is determined. The breakdown of linear elasticity theory for small splitting widths is studied. [S0031-9007(97)04444-X]....
Monte Carlo and nonlinearities
Dauchet, Jérémi; Blanco, Stéphane; Caliot, Cyril; Charon, Julien; Coustet, Christophe; Hafi, Mouna El; Eymet, Vincent; Farges, Olivier; Forest, Vincent; Fournier, Richard; Galtier, Mathieu; Gautrais, Jacques; Khuong, Anaïs; Pelissier, Lionel; Piaud, Benjamin; Roger, Maxime; Terrée, Guillaume; Weitz, Sebastian
2016-01-01
The Monte Carlo method is widely used to numerically predict systems behaviour. However, its powerful incremental design assumes a strong premise which has severely limited application so far: the estimation process must combine linearly over dimensions. Here we show that this premise can be alleviated by projecting nonlinearities on a polynomial basis and increasing the configuration-space dimension. Considering phytoplankton growth in light-limited environments, radiative transfer in planetary atmospheres, electromagnetic scattering by particles and concentrated-solar-power-plant productions, we prove the real world usability of this advance on four test-cases that were so far regarded as impracticable by Monte Carlo approaches. We also illustrate an outstanding feature of our method when applied to sharp problems with interacting particles: handling rare events is now straightforward. Overall, our extension preserves the features that made the method popular: addressing nonlinearities does not compromise o...
Improved diffusion Monte Carlo
Hairer, Martin; Weare, Jonathan
2012-01-01
We propose a modification, based on the RESTART (repetitive simulation trials after reaching thresholds) and DPR (dynamics probability redistribution) rare event simulation algorithms, of the standard diffusion Monte Carlo (DMC) algorithm. The new algorithm has a lower variance per workload, regardless of the regime considered. In particular, it makes it feasible to use DMC in situations where the "na\\"ive" generalisation of the standard algorithm would be impractical, due to an exponential e...
Energy Technology Data Exchange (ETDEWEB)
Wollaber, Allan Benton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2016-06-16
This is a powerpoint presentation which serves as lecture material for the Parallel Computing summer school. It goes over the fundamentals of the Monte Carlo calculation method. The material is presented according to the following outline: Introduction (background, a simple example: estimating π), Why does this even work? (The Law of Large Numbers, The Central Limit Theorem), How to sample (inverse transform sampling, rejection), and An example from particle transport.
Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.
Spiridon, Laurentiu; Minh, David D L
2017-10-10
Compared to fully flexible molecular dynamics, simulations of constrained systems can use larger time steps and focus kinetic energy on soft degrees of freedom. Achieving ergodic sampling from the Boltzmann distribution, however, has proven challenging. Using recent generalizations of the equipartition principle and Fixman potential, here we implement Hamiltonian Monte Carlo based on constrained molecular dynamics as a Gibbs sampling move. By mixing Hamiltonian Monte Carlo based on fully flexible and torsional dynamics, we are able to reproduce free energy landscapes of simple model systems and enhance sampling of macrocycles.
Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Paavilainen, S.; Rog, T.; Vattulainen, I.
2011-01-01
We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile, no sign......We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile...
Atomistic study of hydrogen embrittlement of grain boundaries in nickel: II. Decohesion
Tehranchi, A.; Curtin, W. A.
2017-10-01
Atomistic simulations of bicrystal samples containing a grain boundary are used to examine the effect of hydrogen atoms on the nucleation of intergranular cracks in Ni. Specifically, the theoretical strength is obtained by rigid separation of the two crystals above and below the GB and the yield strength (point of dislocation emission) is obtained by standard tension testing normal to the GB. These strengths are computed in pure Ni and Ni with H segregated to the grain boundaries under conditions typical of H embrittlement in Ni, and in artificially highly-H-saturated states. In all GBs studied here, the theoretical strength \\hat{σ } is not significantly reduced by the presence of the hydrogen atoms. Similarly, with the exception of the Ni {{Σ }}27(115) boundary, the yield strength {σ }{{y}} is not significantly altered by the presence of segregated H atoms. In all cases, the theoretical strengths are ˜25 GPa and the yield strengths are ˜10 GPa, so that (i) the theoretical strength is always well above the yield strength, with or without H, and (ii) both strengths are far above the bulk plastic flow stress, {σ }{{y}}{{B}} of Ni and Ni alloys. Significant reductions in fracture energy (25%-45%) are only achieved for some of the artificially high-H-segregation cases and then only when all the H around the GB is allow to diffuse locally to the fracture surface, which corresponds to unlikely out-of-equilibrium segregation plus local kinetics. Complementing recent work showing that H does not change the ability of GB cracks to emit dislocations and blunt, the present work indicates that equilibrium segregation of hydrogen atoms to GBs has little effect on lowering the GB strength and energy, and so does not significantly facilitate nucleation of intergranular cracks.
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
Energy Technology Data Exchange (ETDEWEB)
Welland, Michael J.; Lau, Kah Chun; Redfern, Paul C.; Wolf, Dieter; Curtiss, Larry A., E-mail: curtiss@anl.gov [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Liang, Linyun [Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Zhai, Denyun [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)
2015-12-14
An atomistically informed mesoscale model is developed for the deposition of a discharge product in a Li-O{sub 2} battery. This mescocale model includes particle growth and coarsening as well as a simplified nucleation model. The model involves LiO{sub 2} formation through reaction of O{sub 2}{sup −} and Li{sup +} in the electrolyte, which deposits on the cathode surface when the LiO{sub 2} concentration reaches supersaturation in the electrolyte. A reaction-diffusion (rate-equation) model is used to describe the processes occurring in the electrolyte and a phase-field model is used to capture microstructural evolution. This model predicts that coarsening, in which large particles grow and small ones disappear, has a substantial effect on the size distribution of the LiO{sub 2} particles during the discharge process. The size evolution during discharge is the result of the interplay between this coarsening process and particle growth. The growth through continued deposition of LiO{sub 2} has the effect of causing large particles to grow ever faster while delaying the dissolution of small particles. The predicted size evolution is consistent with experimental results for a previously reported cathode material based on activated carbon during discharge and when it is at rest, although kinetic factors need to be included. The approach described in this paper synergistically combines models on different length scales with experimental observations and should have applications in studying other related discharge processes, such as Li{sub 2}O{sub 2} deposition, in Li-O{sub 2} batteries and nucleation and growth in Li-S batteries.
Signature of microscale kinetics in mesoscale description of epitaxial growth
Schneider, Joshua P.; Margetis, Dionisios
2017-08-01
We describe the effect of kinetic interactions of adsorbed atoms in a mesoscale model of epitaxial growth without elasticity. Our goal is to understand how atomic correlations due to kinetics leave their signature in mechanisms governing the motion of crystal line defects (steps) at the nanoscale. We focus on the key atomistic processes related to external material deposition, desorption, and asymmetric energy barriers on a stepped surface. By starting with a kinetic, restricted solid-on-solid model in 1+1 dimensions, we derive laws that govern the motion of a single step when deposition is nearly balanced out by desorption. These mesoscale laws reveal how kinetic processes, e.g., bond breaking at the step edge, influence step motion via the correlated motion of atoms.
LMC: Logarithmantic Monte Carlo
Mantz, Adam B.
2017-06-01
LMC is a Markov Chain Monte Carlo engine in Python that implements adaptive Metropolis-Hastings and slice sampling, as well as the affine-invariant method of Goodman & Weare, in a flexible framework. It can be used for simple problems, but the main use case is problems where expensive likelihood evaluations are provided by less flexible third-party software, which benefit from parallelization across many nodes at the sampling level. The parallel/adaptive methods use communication through MPI, or alternatively by writing/reading files, and mostly follow the approaches pioneered by CosmoMC (ascl:1106.025).
Jazz Club
2012-01-01
The 5th edition of the "Monts Jura Jazz Festival" that will take place on September 21st and 22nd 2012 at the Esplanade du Lac in Divonne-les-Bains. This festival is organized by the "CERN Jazz Club" with the support of the "CERN Staff Association". This festival is a major musical event in the French/Swiss area and proposes a world class program with jazz artists such as D.Lockwood and D.Reinhardt. More information on http://www.jurajazz.com.
2012-01-01
The 5th edition of the "Monts Jura Jazz Festival" will take place at the Esplanade du Lac in Divonne-les-Bains, France on September 21 and 22. This festival organized by the CERN Jazz Club and supported by the CERN Staff Association is becoming a major musical event in the Geneva region. International Jazz artists like Didier Lockwood and David Reinhardt are part of this year outstanding program. Full program and e-tickets are available on the festival website. Don't miss this great festival!
Atomistic calculations of dislocation core energy in aluminium
Zhou, X. W.; Sills, R. B.; Ward, D. K.; Karnesky, R. A.
2017-02-01
A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy: Ec=A sin2β +B cos2β , and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. With our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.
An atomistic study of the deformation behavior of tungsten nanowires
Xu, Shuozhi; Su, Yanqing; Chen, Dengke; Li, Longlei
2017-12-01
Large-scale atomistic simulations are performed to study tensile and compressive loading of single-crystalline nanowires in body-centered cubic tungsten (W). Effects of loading mode, wire cross-sectional shape, wire size, strain rate, and crystallographic orientations of the lateral surfaces are explored. Uniaxial deformation of a W bulk single crystal is also investigated for reference. Our results reveal a strong tension-compression asymmetry in both the stress-strain response and the deformation behavior due to different yielding/failure modes: while the nanowires fail by brittle fracture under tensile loading, they yield by nucleation of dislocations from the wire surface under compressive loading. It is found that (1) nanowires have a higher strength than the bulk single crystal; (2) with a cross-sectional size larger than 10 nm, there exists a weak dependence of strength on wire size; (3) when the wire size is equal to or smaller than 10 nm, nanowires buckle under compressive loading; (4) the cross-sectional shape, strain rate, and crystallographic orientations of the lateral surfaces affect the strength and the site of defect initiation but not the overall deformation behavior.
Compression deformation of WC: atomistic description of hard ceramic material
Feng, Qing; Song, Xiaoyan; Liu, Xuemei; Liang, Shuhua; Wang, Haibin; Nie, Zuoren
2017-11-01
The deformation characteristics of WC, as a typical hard ceramic material, were studied on the nanoscale using atomistic simulations for both the single-crystal and polycrystalline forms under uniaxial compression. In particular, the effects of crystallographic orientation, grain boundary coordination and grain size on the origin of deformation were investigated. The deformation behavior of the single-crystal and polycrystalline WC both depend strongly on the orientation towards the loading direction. The grain boundaries play a significant role in the deformation coordination and the potential high fracture toughness of the nanocrystalline WC. In contrast to conventional knowledge of ceramics, maximum strength was obtained at a critical grain size corresponding to the turning point from a Hall–Petch to an inverse Hall–Petch relationship. For this the mechanism of the combined effect of dislocation motion within grains and the coordination of stress concentration at the grain boundaries were proposed. The present work has moved forward our understanding of plastic deformability and the possibility of achieving a high strength of nanocrystalline ceramic materials.
Constant-pressure nested sampling with atomistic dynamics
Baldock, Robert J. N.; Bernstein, Noam; Salerno, K. Michael; Pártay, Lívia B.; Csányi, Gábor
2017-10-01
The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are inefficient for condensed systems with general interactions where single-particle moves cannot be evaluated faster than the energy of the whole system. Here we enhance the method by using all-particle moves: either Galilean Monte Carlo or the total enthalpy Hamiltonian Monte Carlo algorithm, introduced in this paper. We show that these algorithms enable the determination of phase transition temperatures with equivalent accuracy to the previous method at 1 /N of the cost for an N -particle system with general interactions, or at equal cost when single-particle moves can be done in 1 /N of the cost of a full N -particle energy evaluation. We demonstrate this speed-up for the freezing and condensation transitions of the Lennard-Jones system and show the utility of the algorithms by calculating the order-disorder phase transition of a binary Lennard-Jones model alloy, the eutectic of copper-gold, the density anomaly of water, and the condensation and solidification of bead-spring polymers. The nested sampling method with all three algorithms is implemented in the pymatnest software.
Energy Technology Data Exchange (ETDEWEB)
Marcus, Ryan C. [Los Alamos National Laboratory
2012-07-25
MCMini is a proof of concept that demonstrates the possibility for Monte Carlo neutron transport using OpenCL with a focus on performance. This implementation, written in C, shows that tracing particles and calculating reactions on a 3D mesh can be done in a highly scalable fashion. These results demonstrate a potential path forward for MCNP or other Monte Carlo codes.
Monte Carlo methods for electromagnetics
Sadiku, Matthew NO
2009-01-01
Until now, novices had to painstakingly dig through the literature to discover how to use Monte Carlo techniques for solving electromagnetic problems. Written by one of the foremost researchers in the field, Monte Carlo Methods for Electromagnetics provides a solid understanding of these methods and their applications in electromagnetic computation. Including much of his own work, the author brings together essential information from several different publications.Using a simple, clear writing style, the author begins with a historical background and review of electromagnetic theory. After addressing probability and statistics, he introduces the finite difference method as well as the fixed and floating random walk Monte Carlo methods. The text then applies the Exodus method to Laplace's and Poisson's equations and presents Monte Carlo techniques for handing Neumann problems. It also deals with whole field computation using the Markov chain, applies Monte Carlo methods to time-varying diffusion problems, and ...
Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.
Energy Technology Data Exchange (ETDEWEB)
Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.
2010-09-01
This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and
Atomistic Mechanisms for Viscoelastic Damping in Inorganic Solids
Ranganathan, Raghavan
Viscoelasticity, a ubiquitous material property, can be tuned to engineer a wide range of fascinating applications such as mechanical dampers, artificial tissues, functional foams and optoelectronics, among others. Traditionally, soft matter such as polymers and polymer composites have been used extensively for viscoelastic damping applications, owing to the inherent viscous nature of interactions between polymer chains. Although this leads to good damping characteristics, the stiffness in these materials is low, which in turn leads to limitations. In this context, hard inorganic materials and composites are promising candidates for enhanced damping, owing to their large stiffness and, in some cases large loss modulus. Viscoelasticity in these materials has been relatively unexplored and atomistic mechanisms responsible for damping are not apparent. Therefore, the overarching goal of this work is to understand mechanisms for viscoelastic damping in various classes of inorganic composites and alloys at an atomistic level from molecular dynamics simulations. We show that oscillatory shear deformation serves as a powerful probe to explain mechanisms for exceptional damping in hitherto unexplored systems. The first class of inorganic materials consists of crystalline phases of a stiff inclusion in a soft matrix. The two crystals within the composite, namely the soft and a stiff phase, individually show a highly elastic behavior and a very small loss modulus. On the other hand, a composite with the two phases is seen to exhibit damping that is about 20 times larger than predicted theoretical bounds. The primary reason for the damping is due to large anharmonicity in phonon-phonon coupling, resulting from the composite microstructure. A concomitant effect is the distribution of shear strain, which is observed to be highly inhomogeneous and mostly concentrated in the soft phase. Interestingly, the shear frequency at which the damping is greatest is observed to scale with
DEFF Research Database (Denmark)
2009-01-01
A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises.......A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises....
Metropolis Methods for Quantum Monte Carlo Simulations
Ceperley, D.M.
2003-01-01
Since its first description fifty years ago, the Metropolis Monte Carlo method has been used in a variety of different ways for the simulation of continuum quantum many-body systems. This paper will consider some of the generalizations of the Metropolis algorithm employed in quantum Monte Carlo: Variational Monte Carlo, dynamical methods for projector monte carlo ({\\it i.e.} diffusion Monte Carlo with rejection), multilevel sampling in path integral Monte Carlo, the sampling of permutations, ...
An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations
Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.
2013-12-01
In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations
Lectures on Monte Carlo methods
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
Pfalzgraff, William C; Kelly, Aaron; Markland, Thomas E
2015-12-03
The development of methods that can efficiently and accurately treat nonadiabatic dynamics in quantum systems coupled to arbitrary atomistic environments remains a significant challenge in problems ranging from exciton transport in photovoltaic materials to electron and proton transfer in catalysis. Here we show that our recently introduced MF-GQME approach, which combines Ehrenfest mean field theory with the generalized quantum master equation framework, is able to yield quantitative accuracy over a wide range of charge-transfer regimes in fully atomistic environments. This is accompanied by computational speed-ups of up to 3 orders of magnitude over a direct application of Ehrenfest theory. This development offers the opportunity to efficiently investigate the atomistic details of nonadiabatic quantum relaxation processes in regimes where obtaining accurate results has previously been elusive.
Wormhole Hamiltonian Monte Carlo.
Lan, Shiwei; Streets, Jeffrey; Shahbaba, Babak
2014-07-31
In machine learning and statistics, probabilistic inference involving multimodal distributions is quite difficult. This is especially true in high dimensional problems, where most existing algorithms cannot easily move from one mode to another. To address this issue, we propose a novel Bayesian inference approach based on Markov Chain Monte Carlo. Our method can effectively sample from multimodal distributions, especially when the dimension is high and the modes are isolated. To this end, it exploits and modifies the Riemannian geometric properties of the target distribution to create wormholes connecting modes in order to facilitate moving between them. Further, our proposed method uses the regeneration technique in order to adapt the algorithm by identifying new modes and updating the network of wormholes without affecting the stationary distribution. To find new modes, as opposed to redis-covering those previously identified, we employ a novel mode searching algorithm that explores a residual energy function obtained by subtracting an approximate Gaussian mixture density (based on previously discovered modes) from the target density function.
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 Ca2+ 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.
Advanced Multilevel Monte Carlo Methods
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.
Directory of Open Access Journals (Sweden)
Mojtaba Ahmadi
2016-11-01
Full Text Available The aqueous degradation of Reactive Yellow 84 (RY84 by potassium peroxydisulfate (K2S2O8 has been studied in laboratory scale experiments. The effect of the initial concentrations of potassium peroxydisulfate and RY84, pH and temperature on RY84 degradation were also examined. Experimental data were analyzed using first and second-order kinetics. The degradation kinetics of RY84 of the potassium peroxydisulfate process followed the second-order reaction kinetics. These rate constants have an extreme values similar to of 9.493 mM−1min−1 at a peroxydisulfate dose of 4 mmol/L. Thermodynamic parameters such as activation (Ea and Gibbs free energy (ΔG° were also evaluated. The negative value of ΔGo and Ea shows the spontaneous reaction natural conditions and exothermic nature.
Scalable and portable visualization of large atomistic datasets
Sharma, Ashish; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2004-10-01
A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data
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.
Atomistic study on the FCC/BCC interface structure with {112}KS orientation
Energy Technology Data Exchange (ETDEWEB)
Kang, Keonwook [Los Alamos National Laboratory; Beyerlein, Irene [Los Alamos National Laboratory
2011-09-23
In this study, atomistic simulation is used to explore the atomic interface structure, the intrinsic defect network, and mechanism of twin formation from the {112}KS Cu-Nb interface. The interface structure of different material systems AI-Fe and AI-Nb are also compared with Cu-Nb interface.
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" interrogates the phenomenon of migration in general and in the Southern African Development Community in particular. The point of departure of the paper is the African Union and the Southern African Development Community's legal framework on ...
A Mathematical Analysis of Atomistic-to-Continuum (AtC) Multiscale Coupling Methods
Energy Technology Data Exchange (ETDEWEB)
Gunzburger, Max
2013-11-13
We have worked on several projects aimed at improving the efficiency and understanding of multiscale methods, especially those applicable to problems involving atomistic-to-continuum coupling. Activities include blending methods for AtC coupling and efficient quasi-continuum methods for problems with long-range interactions.
Electron and phonon transport in silicon nanowires: Atomistic approach to thermoelectric properties
DEFF Research Database (Denmark)
Markussen, Troels; Jauho, Antti-Pekka; Brandbyge, Mads
2009-01-01
We compute both electron and phonon transmissions in thin disordered silicon nanowires (SiNWs). Our atomistic approach is based on tight-binding and empirical potential descriptions of the electronic and phononic systems, respectively. Surface disorder is modeled by introducing surface silicon va...
Xiawa Wu; Robert J. Moon; Ashlie Martini
2013-01-01
The elastic modulus of cellulose IÃ 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...
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...
Robust mode space approach for atomistic modeling of realistically large nanowire transistors
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.
Fundamental aspects of plasma chemical physics kinetics
Capitelli, Mario; Colonna, Gianpiero; Esposito, Fabrizio; Gorse, Claudine; Hassouni, Khaled; Laricchiuta, Annarita; Longo, Savino
2016-01-01
Describing non-equilibrium "cold" plasmas through a chemical physics approach, this book uses the state-to-state plasma kinetics, which considers each internal state as a new species with its own cross sections. Extended atomic and molecular master equations are coupled with Boltzmann and Monte Carlo methods to solve the electron energy distribution function. Selected examples in different applied fields, such as microelectronics, fusion, and aerospace, are presented and discussed including the self-consistent kinetics in RF parallel plate reactors, the optimization of negative ion sources and the expansion of high enthalpy flows through nozzles of different geometries. The book will cover the main aspects of the state-to-state kinetic approach for the description of nonequilibrium cold plasmas, illustrating the more recent achievements in the development of kinetic models including the self-consistent coupling of master equations and Boltzmann equation for electron dynamics. To give a complete portrayal, the...
Multilevel sequential Monte Carlo samplers
Beskos, Alexandros
2016-08-29
In this article we consider the approximation of expectations w.r.t. probability distributions associated to the solution of partial differential equations (PDEs); this scenario appears routinely in Bayesian inverse problems. In practice, one often has to solve the associated PDE numerically, using, for instance finite element methods which depend on the step-size level . hL. In addition, the expectation cannot be computed analytically and one often resorts to Monte Carlo methods. In the context of this problem, it is known that the introduction of the multilevel Monte Carlo (MLMC) method can reduce the amount of computational effort to estimate expectations, for a given level of error. This is achieved via a telescoping identity associated to a Monte Carlo approximation of a sequence of probability distributions with discretization levels . âˆž>h0>h1â‹¯>hL. In many practical problems of interest, one cannot achieve an i.i.d. sampling of the associated sequence and a sequential Monte Carlo (SMC) version of the MLMC method is introduced to deal with this problem. It is shown that under appropriate assumptions, the attractive property of a reduction of the amount of computational effort to estimate expectations, for a given level of error, can be maintained within the SMC context. That is, relative to exact sampling and Monte Carlo for the distribution at the finest level . hL. The approach is numerically illustrated on a Bayesian inverse problem. Â© 2016 Elsevier B.V.
Molecular cooperativity and compatibility via full atomistic simulation
Kwan Yang, Kenny
Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules
Confinement effect in diffusion-controlled stepwise polymerization by Monte Carlo simulation
Malvaldi, M; Bruzzone, S; Picchioni, F
2006-01-01
Diffusion-controlled stepwise polymerization of a linear polymer confined in nanoscopic slits is simulated through a Monte Carlo approach. A noticeable influence of the confinement on the kinetics is found. The confinement modifies both the spatial pair distribution function and the diffusive
Jäntschi, Lorentz
2003-01-01
Mathematics and computer programming have a major contribution to chemistry. Two directions can be identified: one that searches and tries (rich) to explain the structural binding and shape of the chemical compounds [1] with major applications in QSPR/QSAR studies [2], and applied sciences such as engineering of materials or agriculture [3]; the second direction is to models the kinetic processes that are involved in chemical reactions [4]. Many such models are available here. The present pap...
Directory of Open Access Journals (Sweden)
Lorentz JÄNTSCHI
2003-03-01
Full Text Available Mathematics and computer programming have a major contribution to chemistry. Two directions can be identified: one that searches and tries (rich to explain the structural binding and shape of the chemical compounds [1] with major applications in QSPR/QSAR studies [2], and applied sciences such as engineering of materials or agriculture [3]; the second direction is to models the kinetic processes that are involved in chemical reactions [4]. Many such models are available here. The present paper describes three variants of well the known kinetic models and presents the mathematical equations associated with them. The differential equations are numerically solved and fitted with MathCad program. [1] Diudea M., Gutman I., Jäntschi L., Molecular Topology, Nova Science, Huntington, New York, 332 p., 2001, 2002. [2] Diudea M. V., Ed., QSPR / QSAR Studies by Molecular Descriptors, Nova Science, Huntington, New York, 438 p., 2001. [3] Jäntschi L., Microbiology and Toxicology. Phytochemistry Studies (in Romanian, Amici, Cluj-Napoca, 184 p., 2003. [4] Jäntschi L., Unguresan M., Physical Chemistry. Molecular Kinetic and Dynamic (in Romanian, Mediamira, Cluj-Napoca, 159 p., 2001.
Kreuzer, Hans Jürgen
1986-01-01
This monograph deals with the kinetics of adsorption and desorption of molecules physisorbed on solid surfaces. Although frequent and detailed reference is made to experiment, it is mainly concerned with the theory of the subject. In this, we have attempted to present a unified picture based on the master equation approach. Physisorption kinetics is by no means a closed and mature subject; rather, in writing this monograph we intended to survey a field very much in flux, to assess its achievements so far, and to give a reasonable basis from which further developments can take off. For this reason we have included many papers in the bibliography that are not referred to in the text but are of relevance to physisorption. To keep this monograph to a reasonable size, and also to allow for some unity in the presentation of the material, we had to omit a number of topics related to physisorption kinetics. We have not covered to any extent the equilibrium properties of physisorbed layers such as structures, phase tr...
Proton Upset Monte Carlo Simulation
O'Neill, Patrick M.; Kouba, Coy K.; Foster, Charles C.
2009-01-01
The Proton Upset Monte Carlo Simulation (PROPSET) program calculates the frequency of on-orbit upsets in computer chips (for given orbits such as Low Earth Orbit, Lunar Orbit, and the like) from proton bombardment based on the results of heavy ion testing alone. The software simulates the bombardment of modern microelectronic components (computer chips) with high-energy (.200 MeV) protons. The nuclear interaction of the proton with the silicon of the chip is modeled and nuclear fragments from this interaction are tracked using Monte Carlo techniques to produce statistically accurate predictions.
Magnetic atomistic modelling and simulation of nanocrystalline thin films
Agudelo-Giraldo, J. D.; Ortiz-Álvarez, H. H.; Restrepo, J.; Restrepo-Parra, E.
2017-05-01
In this study, a methodology, for polycrystalline magnetic thin films construction composed by nano-grains, was developed. The size and shape of grains and samples under scale considerations of magnetic materials were developed, taking into account periodic boundary conditions. A comparative analysis of results obtained with experimental grains' distribution is presented. Lognormal distribution was proposed as a function of number of atoms per grain that agrees with experimental reports. A test of the magnetization as a function of the temperature was obtained by the parallelized Monte Carlo method dividing the sample in cells. The Hamiltonian considered variations of the exchange constant with atomic distance from RKKY approximation and a cubic magneto-crystalline anisotropy as a function of the temperature also was implemented. Results showed changes over critical behavior and different values for magnetization of saturation at low temperatures. Critical temperature is affected by the increments of disorder into the sample when grain size is reduced. A reduction of magnetization is correlated with mono-domain regimen in the sample for most of grains. These states are favored during the cooling process by the disorder in grain boundaries.
Markov Chain Monte Carlo Methods
Indian Academy of Sciences (India)
Monte Carlo is a city in Monaco, famous for its casinos offering games of chance. Games of chance ex- hibit random behaviour, much like the random variables generated for the statistical simulation exercises. Early ideas of probability and simulation were developed in the context of gambling here and hence these simula-.
Markov Chain Monte Carlo Methods
Indian Academy of Sciences (India)
Markov Chain Monte Carlo Methods. 2. The Markov Chain Case. K B Athreya, Mohan Delampady and T Krishnan. K B Athreya is a Professor at. Cornell University. His research interests include mathematical analysis, probability theory and its application and statistics. He enjoys writing for Resonance. His spare time is ...
Exact Monte Carlo for molecules
Energy Technology Data Exchange (ETDEWEB)
Lester, W.A. Jr.; Reynolds, P.J.
1985-03-01
A brief summary of the fixed-node quantum Monte Carlo method is presented. Results obtained for binding energies, the classical barrier height for H + H2, and the singlet-triplet splitting in methylene are presented and discussed. 17 refs.
Monte Carlo calculations of nuclei
Energy Technology Data Exchange (ETDEWEB)
Pieper, S.C. [Argonne National Lab., IL (United States). Physics Div.
1997-10-01
Nuclear many-body calculations have the complication of strong spin- and isospin-dependent potentials. In these lectures the author discusses the variational and Green`s function Monte Carlo techniques that have been developed to address this complication, and presents a few results.
Markov Chain Monte Carlo Methods
Indian Academy of Sciences (India)
Introduction. In parts 1 and 2 of this series it was shown how Markov chain Monte Carlo (MCMC) methods can be employed to obtain satisfactory approximations for integrals that are not easy to evaluate analytically. Such integrals arise routinely in statistical problems. Some of the statistical concepts that are relevant for the ...
2016-01-01
Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460
Accelerated Monte Carlo Methods for Coulomb Collisions
Rosin, Mark; Ricketson, Lee; Dimits, Andris; Caflisch, Russel; Cohen, Bruce
2014-03-01
We present a new highly efficient multi-level Monte Carlo (MLMC) simulation algorithm for Coulomb collisions in a plasma. The scheme, initially developed and used successfully for applications in financial mathematics, is applied here to kinetic plasmas for the first time. The method is based on a Langevin treatment of the Landau-Fokker-Planck equation and has a rich history derived from the works of Einstein and Chandrasekhar. The MLMC scheme successfully reduces the computational cost of achieving an RMS error ɛ in the numerical solution to collisional plasma problems from (ɛ-3) - for the standard state-of-the-art Langevin and binary collision algorithms - to a theoretically optimal (ɛ-2) scaling, when used in conjunction with an underlying Milstein discretization to the Langevin equation. In the test case presented here, the method accelerates simulations by factors of up to 100. We summarize the scheme, present some tricks for improving its efficiency yet further, and discuss the method's range of applicability. Work performed for US DOE by LLNL under contract DE-AC52- 07NA27344 and by UCLA under grant DE-FG02-05ER25710.
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...
(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.
Cui, Cheng Bin; Beom, Hyeon Gyu
2018-01-01
The intergranular fracture toughness of Cu bicrystals with symmetric tilt grain boundaries was investigated using atomistic simulations. Mode I fracture of Cu bicrystals with an intergranular crack was considered. The boundary conditions were specified by the near-tip displacement fields obtained based on linear elastic fracture mechanics (LEFM). Based on the energy interpretation of the energy release rate, a two-specimen method was adopted to determine the fracture toughness. The simulation results of the fracture toughness matched well with those determined using LEFM. In contrast to the toughness obtained using the Griffith energy criterion, the atomistic simulation results for the same bicrystal were not constants, but dependent on the crack-tip circumstances. This behavior was mainly associated with the different local stress conditions and fracture patterns observed for the different models.
Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level
Buerkle, Marius; Asai, Yoshihiro
2017-02-01
The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations.
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.
Modified NEGF method for atomistic modeling of field emission from carbon nanotube
Monshipouri, Mahta; Behrooz, Milad; Abdi, Yaser
2017-09-01
A model to simulate the atomistic properties of the field emission (FE) from a zigzag-single walled carbon nanotube (Z-SWCNT) is presented. By a modification of the self-energy in non-equilibrium Green's function (NEGF) method, we simulated the field emission current, considering the quantum transport of electrons within the CNT. The paper involves investigation on the effect of the n index of the (n , 0) Z-SWCNT and the number of carbon dimers in the length direction as well as the anode-cathode separation on the FE current. Effect of additional gate voltage and substitutional impurities on the FE current is also studied. A comparison between the experimental data and simulation results are also included in the paper. The model can be used to consider different quantum effects of the atomistic emitter structure on the FE current.
Ignition in an Atomistic Model of Hydrogen Oxidation.
Alaghemandi, Mohammad; Newcomb, Lucas B; Green, Jason R
2017-03-02
Hydrogen is a potential substitute for fossil fuels that would reduce the combustive emission of carbon dioxide. However, the low ignition energy needed to initiate oxidation imposes constraints on the efficiency and safety of hydrogen-based technologies. Microscopic details of the combustion processes, ephemeral transient species, and complex reaction networks are necessary to control and optimize the use of hydrogen as a commercial fuel. Here, we report estimates of the ignition time of hydrogen-oxygen mixtures over a wide range of equivalence ratios from extensive reactive molecular dynamics simulations. These data show that the shortest ignition time corresponds to a fuel-lean mixture with an equivalence ratio of 0.5, where the number of hydrogen and oxygen molecules in the initial mixture are identical, in good agreement with a recent chemical kinetic model. We find two signatures in the simulation data precede ignition at pressures above 200 MPa. First, there is a peak in hydrogen peroxide that signals ignition is imminent in about 100 ps. Second, we find a strong anticorrelation between the ignition time and the rate of energy dissipation, suggesting the role of thermal feedback in stimulating ignition.
Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures
Directory of Open Access Journals (Sweden)
Aruna Prakash
2017-01-01
Full Text Available Single-crystal Ni-base superalloys, consisting of a two-phase γ/ γ ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/ γ ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ ′ particles with planar γ/ γ ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions.
Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.
Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J
2014-12-31
RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.
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.
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.
Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal
Energy Technology Data Exchange (ETDEWEB)
Huang, Liangliang; Gubbins, Keith E., E-mail: keg@ncsu.edu [Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695 (United States); Seredych, Mykola; Bandosz, Teresa J. [Department of Chemistry, The City College of New York and the Graduate School of the City University of New York, New York 10031 (United States); Duin, Adri C. T. van [Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, Pennsylvania 16801 (United States); Lu, Xiaohua [State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing 210009 (China)
2013-11-21
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{sub 2}S and H{sub 2}O/H{sub 2}S mixtures on GO materials and compare the results with experiment. We find that H{sub 2}S molecules dissociate on the carbonyl functional groups, and H{sub 2}O, CO{sub 2}, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H{sub 2}O/H{sub 2}S mixtures, H{sub 2}O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H{sub 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.
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 modeling of the dislocation dynamics and evaluation of static yield stress
Directory of Open Access Journals (Sweden)
Karavaev A.V.
2015-01-01
Full Text Available Static strength characteristics of structural materials are of great importance for the analysis of the materials behaviour under mechanical loadings. Mechanical characteristics of structural materials such as elastic limit, strength limit, ultimate tensile strength, plasticity are, unlike elastic moduli, very sensitive to the presence of impurities and defects of crystal structure. Direct atomistic modeling of the static mechanical strength characteristics of real materials is an extremely difficult task since the typical time scales available for the direct modeling in the frames of classical molecular dynamics do not exceed a hundred of nanoseconds. This means that the direct atomistic modeling of the material deformation can be done for the regimes with rather high strain rates at which the yield stress and other mechanical strength characteristics are controlled by microscopic mechanisms different from those at low (quasi-static strain rates. In essence, the plastic properties of structural materials are determined by the dynamics of the extended defects of crystal structure (edge and screw dislocations and by interactions between them and with the other defects in the crystal. In the present work we propose a method that is capable to model the dynamics of edge dislocations in the fcc and hcp materials at dynamic deformations and to estimate the material static yield stress in the states of interest in the frames of the atomistic approach. The method is based on the numerical characterization of the stress relaxation processes in specially generated samples containing solitary edge dislocations.
Atomistic calculation of electronic and optical properties of a single InAs quantum dots
Zielinski, M.; Korkusinski, M.; Sheng, W.; Hawrylak, P.
2008-03-01
We present an atomistic tight-binding (TB) theory of electronic structure and optical properties of a single self-assembled InAs quantum dot (SAD). In previous work an effective-bond-orbital model (EBOM) was used to calculate electron and hole states of the SAD. The strain distribution was calculated using the continuum elasticity theory and EBOM was coupled to the strain via the Bir-Pikus Hamiltonian. However, the properties of these multimillion-atom systems are influenced by the presence of crystal facets and the symmetry of underlying zinc-blende lattice. In current work we present a fully atomistic TB model, accounting for the atomistic symmetry, and extended to include d-orbitals for proper treatment of interband/intervalley couplings. Strain is included in the Hamiltonian via Slater-Koster rules and a generalized Harrison law, with the equilibrium positions of atoms calculated using the valence force field method. Coulomb matrix elements are found using the TB functions, and electronic properties of N confined excitons (N=1-6) are determined in the CI approach. Emission spectra of multiexcitons are also obtained. Comparison with the previous approach and the experimental results is presented.
Alibrandi, Giuseppe; Fabbrizzi, Luigi; Licchelli, Maurizio; Puglisi, Antonio
2015-01-12
This paper proposes a new type of molecular device that is able to act as an inverse proton sponge to slowly decrease the pH inside a reaction vessel. This makes the automatic monitoring of the concentration of pH-sensitive systems possible. The device is a composite formed of an alkyl chloride, which kinetically produces acidity, and a buffer that thermodynamically modulates the variation in pH value. Profiles of pH versus time (pH-t plots) have been generated under various experimental conditions by computer simulation, and the device has been tested by carrying out automatic spectrophotometric titrations, without using an autoburette. To underline the wide variety of possible applications, this new system has been used to realize and monitor HCl uptake by a di-copper(II) bistren complex in a single run, in a completely automatic experiment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Protein sliding and hopping kinetics on DNA
DeSantis, Michael C; Wang, Y M
2010-01-01
Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (1) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of ms; (2) sliding dominates the root mean square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (3) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; furthermore, (4) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins.
Monte Carlo Particle Lists: MCPL
DEFF Research Database (Denmark)
Kittelmann, Thomas; Klinkby, Esben Bryndt; Bergbäck Knudsen, Erik
2017-01-01
simulation packages. Program summary: Program Title: MCPL. Program Files doi: http://dx.doi.org/10.17632/cby92vsv5g.1 Licensing provisions: CC0 for core MCPL, see LICENSE file for details. Programming language: C and C++ External routines/libraries: Geant4, MCNP, McStas, McXtrace Nature of problem: Saving......A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community, along with converters and plugins for several popular...... particle states in Monte Carlo simulations, for interchange between simulation packages or for reuse within a single package. Solution method: Binary interchange format with associated code written in portable C along with tools and interfaces for relevant simulation packages....
Shell model Monte Carlo methods
Energy Technology Data Exchange (ETDEWEB)
Koonin, S.E. [California Inst. of Tech., Pasadena, CA (United States). W.K. Kellogg Radiation Lab.; Dean, D.J. [Oak Ridge National Lab., TN (United States)
1996-10-01
We review quantum Monte Carlo methods for dealing with large shell model problems. These methods reduce the imaginary-time many-body evolution operator to a coherent superposition of one-body evolutions in fluctuating one-body fields; resultant path integral is evaluated stochastically. We first discuss the motivation, formalism, and implementation of such Shell Model Monte Carlo methods. There then follows a sampler of results and insights obtained from a number of applications. These include the ground state and thermal properties of pf-shell nuclei, thermal behavior of {gamma}-soft nuclei, and calculation of double beta-decay matrix elements. Finally, prospects for further progress in such calculations are discussed. 87 refs.
Adaptive Multilevel Monte Carlo Simulation
Hoel, H
2011-08-23
This work generalizes a multilevel forward Euler Monte Carlo method introduced in Michael B. Giles. (Michael Giles. Oper. Res. 56(3):607–617, 2008.) for the approximation of expected values depending on the solution to an Itô stochastic differential equation. The work (Michael Giles. Oper. Res. 56(3):607– 617, 2008.) proposed and analyzed a forward Euler multilevelMonte Carlo method based on a hierarchy of uniform time discretizations and control variates to reduce the computational effort required by a standard, single level, Forward Euler Monte Carlo method. This work introduces an adaptive hierarchy of non uniform time discretizations, generated by an adaptive algorithmintroduced in (AnnaDzougoutov et al. Raùl Tempone. Adaptive Monte Carlo algorithms for stopped diffusion. In Multiscale methods in science and engineering, volume 44 of Lect. Notes Comput. Sci. Eng., pages 59–88. Springer, Berlin, 2005; Kyoung-Sook Moon et al. Stoch. Anal. Appl. 23(3):511–558, 2005; Kyoung-Sook Moon et al. An adaptive algorithm for ordinary, stochastic and partial differential equations. In Recent advances in adaptive computation, volume 383 of Contemp. Math., pages 325–343. Amer. Math. Soc., Providence, RI, 2005.). This form of the adaptive algorithm generates stochastic, path dependent, time steps and is based on a posteriori error expansions first developed in (Anders Szepessy et al. Comm. Pure Appl. Math. 54(10):1169– 1214, 2001). Our numerical results for a stopped diffusion problem, exhibit savings in the computational cost to achieve an accuracy of ϑ(TOL),from(TOL−3), from using a single level version of the adaptive algorithm to ϑ(((TOL−1)log(TOL))2).
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.
Mittal, Anuradha; Lyle, Nicholas; Harmon, Tyler S; Pappu, Rohit V
2014-08-12
There is growing interest in the topic of intrinsically disordered proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations based on novel implicit solvation models have yielded useful insights regarding sequence-ensemble relationships for IDPs modeled as autonomous units. However, a majority of naturally occurring IDPs are tethered to ordered domains. Tethering introduces additional energy scales and this creates the challenge of broken ergodicity for standard MMC sampling or molecular dynamics that cannot be readily alleviated by using generalized tempering methods. We have designed, deployed, and tested our adaptation of the Nested Markov Chain Monte Carlo sampling algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis Monte Carlo (HS-MMC) sampling. In this method, transitions out of energetic traps are enabled by the introduction of an auxiliary Markov chain that draws conformations for the disordered region from a Boltzmann distribution that is governed by an alternative potential function that only includes short-range steric repulsions and conformational restraints on the ordered domain. We show using multiple, independent runs that the HS-MMC method yields conformational distributions that have similar and reproducible statistical properties, which is in direct contrast to standard MMC for equivalent amounts of sampling. The method is efficient and can be deployed for simulations of a range of biologically relevant disordered regions that are tethered to ordered domains.
The fermion Monte Carlo revisited
Assaraf, Roland; Caffarel, Michel; Khelif, Anatole
2007-02-01
In this work we present a detailed study of the fermion Monte Carlo algorithm (FMC), a recently proposed stochastic method for calculating fermionic ground-state energies. A proof that the FMC method is an exact method is given. In this work the stability of the method is related to the difference between the lowest (bosonic-type) eigenvalue of the FMC diffusion operator and the exact Fermi energy. It is shown that within a FMC framework the lowest eigenvalue of the new diffusion operator is no longer the bosonic ground-state eigenvalue as in standard exact diffusion Monte Carlo (DMC) schemes but a modified value which is strictly greater. Accordingly, FMC can be viewed as an exact DMC method built from a correlated diffusion process having a reduced Bose-Fermi gap. As a consequence, the FMC method is more stable than any transient method (or nodal release-type approaches). It is shown that the most recent ingredient of the FMC approach (Kalos M H and Pederiva F 2000 Phys. Rev. Lett. 85 3547), namely the introduction of non-symmetric guiding functions, does not necessarily improve the stability of the algorithm. We argue that the stability observed with such guiding functions is in general a finite-size population effect disappearing for a very large population of walkers. The counterpart of this stability is a control population error which is different in nature from the standard diffusion Monte Carlo algorithm and which is at the origin of an uncontrolled approximation in FMC. We illustrate the various ideas presented in this work with calculations performed on a very simple model having only nine states but a full 'sign problem'. Already for this toy model it is clearly seen that FMC calculations are inherently uncontrolled.
Monte Carlo techniques in radiation therapy
Verhaegen, Frank
2013-01-01
Modern cancer treatment relies on Monte Carlo simulations to help radiotherapists and clinical physicists better understand and compute radiation dose from imaging devices as well as exploit four-dimensional imaging data. With Monte Carlo-based treatment planning tools now available from commercial vendors, a complete transition to Monte Carlo-based dose calculation methods in radiotherapy could likely take place in the next decade. Monte Carlo Techniques in Radiation Therapy explores the use of Monte Carlo methods for modeling various features of internal and external radiation sources, including light ion beams. The book-the first of its kind-addresses applications of the Monte Carlo particle transport simulation technique in radiation therapy, mainly focusing on external beam radiotherapy and brachytherapy. It presents the mathematical and technical aspects of the methods in particle transport simulations. The book also discusses the modeling of medical linacs and other irradiation devices; issues specific...
Mean field simulation for Monte Carlo integration
Del Moral, Pierre
2013-01-01
In the last three decades, there has been a dramatic increase in the use of interacting particle methods as a powerful tool in real-world applications of Monte Carlo simulation in computational physics, population biology, computer sciences, and statistical machine learning. Ideally suited to parallel and distributed computation, these advanced particle algorithms include nonlinear interacting jump diffusions; quantum, diffusion, and resampled Monte Carlo methods; Feynman-Kac particle models; genetic and evolutionary algorithms; sequential Monte Carlo methods; adaptive and interacting Marko
Nguyen, H. K.; Mankowski, J.; Dickens, J. C.; Neuber, A. A.; Joshi, R. P.
2017-12-01
Calculations of electron impact ionization of nitrogen gas at atmospheric pressure are presented based on the kinetic Monte Carlo technique. The emphasis is on energy partitioning between primary and secondary electrons, and three different energy sharing schemes have been evaluated. The ionization behavior is based on Wannier's classical treatment. Our Monte Carlo results for the field-dependent drift velocities match the available experimental data. More interestingly, the field-dependent first Townsend coefficient predicted by the Monte Carlo calculations is shown to be in close agreement with reported data for E/N values ranging as high as 4000 Td, only when a random assignment of excess energies between the primary and secondary particles is used.
Uncertainty Propagation with Fast Monte Carlo Techniques
Rochman, D.; van der Marck, S. C.; Koning, A. J.; Sjöstrand, H.; Zwermann, W.
2014-04-01
Two new and faster Monte Carlo methods for the propagation of nuclear data uncertainties in Monte Carlo nuclear simulations are presented (the "Fast TMC" and "Fast GRS" methods). They are addressing the main drawback of the original Total Monte Carlo method (TMC), namely the necessary large time multiplication factor compared to a single calculation. With these new methods, Monte Carlo simulations can now be accompanied with uncertainty propagation (other than statistical), with small additional calculation time. The new methods are presented and compared with the TMC methods for criticality benchmarks.
Directional pair distribution function for diffraction line profile analysis of atomistic models.
Leonardi, Alberto; Leoni, Matteo; Scardi, Paolo
2013-02-01
The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren-Averbach method.
Ameen, Tarek A.; Ilatikhameneh, Hesameddin; Huang, Jun Z.; Povolotskyi, Michael; Rahman, Rajib; Klimeck, Gerhard
2017-06-01
Tunneling hetero-junctions (THJs) usually induce confined states at the regions close to the tunnel junction which significantly affect their transport properties. Accurate numerical modeling of such effects requires combining the non-equilibrium coherent quantum transport through tunnel junction, as well as the quasi-equilibrium statistics arising from the strong scattering in the induced quantum wells. In this work, a novel atomistic model is proposed to include both effects: the strong scattering in the regions around THJ and the coherent tunneling. The new model matches reasonably well with experimental measurements of Nitride THJ and provides an efficient engineering tool for performance prediction and design of THJ based devices.
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.
Predicting growth of graphene nanostructures using high-fidelity atomistic simulations
Energy Technology Data Exchange (ETDEWEB)
McCarty, Keven F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Zhou, Xiaowang [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ward, Donald K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schultz, Peter A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Foster, Michael E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bartelt, Norman Charles [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-09-01
In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expand the number of potential types of graphene electronic devices.
Energy Technology Data Exchange (ETDEWEB)
Weaver, B. [American Geophysical Union, Washington, DC (United States)
1994-12-31
This report presents details of the Chapman Conference given on June 6--9, 1994 in Lincoln, New Hampshire. This conference covered the scale of processes involved in coupled hydrogeologic mass transport and a concept of modeling and testing from the atomistic- to the basin- scale. Other topics include; the testing of fundamental atomic level parameterizations in the laboratory and field studies of fluid flow and mass transport and the next generation of hydrogeologic models. Individual papers from this conference are processed separately for the database.
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.
Monte Carlo simulation of excitation and ionization collisions with complexity reduction
Le, Hai P.; Yan, Bokai; Caflisch, Russel E.; Cambier, Jean-Luc
2017-10-01
Kinetic simulation of plasmas with detailed excitation and ionization collisions presents a significant computational challenge due to the multiscale feature of the collisional rates. In the present work, we propose a complexity reduction method based on atomic level grouping for modeling excitation and ionization collisions. High order of accuracy of the reduction method is realized by allowing an internal distribution within each group. We apply the reduction method to the standard Monte Carlo collision algorithm to model an atomic Hydrogen plasma. Numerical results suggest that the stiffness of the collisional kinetics can be significantly reduced with minimal loss in accuracy.
Energy Technology Data Exchange (ETDEWEB)
Ronald L. Boring; David I. Gertman; Jeffrey C. Joe; Julie L. Marble
2005-09-01
A variety of methods have been developed to generate human error probabilities for use in the US nuclear power industry. When actual operations data are not available, it is necessary for an analyst to estimate these probabilities. Most approaches, including THERP, ASEP, SLIM-MAUD, and SPAR-H, feature an atomistic approach to characterizing and estimating error. The atomistic approach is based on the notion that events and their causes can be decomposed and individually quantified. In contrast, in the holistic approach, such as found in ATHEANA, the analysis centers on the entire event, which is typically quantified as an indivisible whole. The distinction between atomistic and holistic approaches is important in understanding the nature of human reliability analysis quantification and the utility and shortcomings associated with each approach.
Path integral Monte Carlo simulations of silicates
Rickwardt, Chr.; Nielaba, P.; Müser, M. H.; Binder, K.
2000-01-01
We investigate the thermal expansion of crystalline SiO$_2$ in the $\\beta$-- cristobalite and the $\\beta$-quartz structure with path integral Monte Carlo (PIMC) techniques. This simulation method allows to treat low-temperature quantum effects properly. At temperatures below the Debye temperature, thermal properties obtained with PIMC agree better with experimental results than those obtained with classical Monte Carlo methods.
Advanced Computational Methods for Monte Carlo Calculations
Energy Technology Data Exchange (ETDEWEB)
Brown, Forrest B. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2018-01-12
This course is intended for graduate students who already have a basic understanding of Monte Carlo methods. It focuses on advanced topics that may be needed for thesis research, for developing new state-of-the-art methods, or for working with modern production Monte Carlo codes.
Monte Carlo simulation of model Spin systemsr
Indian Academy of Sciences (India)
three~dimensional Ising models and Heisenberg models are dealt with in some detail. Recent applications of the Monte Carlo method to spin glass systems and to estimate renormalisation group critical exponents are reviewod. Keywords. _ Monte-carlo simulation; critical phenomena; Ising models; Heisenberg models ...
Monte Carlo Simulation of Phase Transitions
村井, 信行; N., MURAI; 中京大学教養部
1983-01-01
In the Monte Carlo simulation of phase transition, a simple heat bath method is applied to the classical Heisenberg model in two dimensions. It reproduces the correlation length predicted by the Monte Carlo renor-malization group and also computed in the non-linear σ model
Monte Carlo calculations for HTRs
Energy Technology Data Exchange (ETDEWEB)
Hogenbirk, A. [ECN Nuclear Research, Petten (Netherlands)
1998-09-01
From a neutronics point of view pebble-bed HTRs are completely different from standard LWRs. The most important differences are to be found in the reactor geometry, the properties of the moderator (graphite instead of water) and the self-shielding of the fuel regions. Therefore, computer packages normally used for core analyses should be validated with experimental data before they can be used for HTR analyses. This especially holds for deterministic computer codes, in which approximations are made which may not be valid in pebble-bed HTRs. Monte Carlo codes more based on first principles suffer much less from this problem. In order to study small- and medium-sized LEU-HTR systems in the late 1980s an IAEA Coordinated Research Programme (CRP) was started. This CRP was mainly directed to the effects of water ingress and neutron streaming. The PROTEUS facility at the Paul Scherrer Institute (PSI) in Villigen, Switzerland, played a central role in this CRP. Benchmark quality measurements were provided in clean, easy-to-interpret critical configurations, using pebble-type fuel. ECN in Petten, Netherlands, contributed to the CRP by performing reactor calculations using the WIMS code system with deterministic calculations. However, a need was felt for reference calculations, in which as few approximations as possible were made. These analyses were performed with the Monte Carlo code MCNP-4A. In this contribution the results are given of the main MCNP-calculations. In these analyses a detailed model of the PROTEUS experimental set-up was used, whereas in the calculations use was made of high-quality continuous-energy cross-section data. The attention was focused on the calculation of the value of k{sub eff} and of streaming effects in the pebble-bed core. 15 refs.
Challenges of Monte Carlo Transport
Energy Technology Data Exchange (ETDEWEB)
Long, Alex Roberts [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2016-06-10
These are slides from a presentation for Parallel Summer School at Los Alamos National Laboratory. Solving discretized partial differential equations (PDEs) of interest can require a large number of computations. We can identify concurrency to allow parallel solution of discrete PDEs. Simulated particles histories can be used to solve the Boltzmann transport equation. Particle histories are independent in neutral particle transport, making them amenable to parallel computation. Physical parameters and method type determine the data dependencies of particle histories. Data requirements shape parallel algorithms for Monte Carlo. Then, Parallel Computational Physics and Parallel Monte Carlo are discussed and, finally, the results are given. The mesh passing method greatly simplifies the IMC implementation and allows simple load-balancing. Using MPI windows and passive, one-sided RMA further simplifies the implementation by removing target synchronization. The author is very interested in implementations of PGAS that may allow further optimization for one-sided, read-only memory access (e.g. Open SHMEM). The MPICH_RMA_OVER_DMAPP option and library is required to make one-sided messaging scale on Trinitite - Moonlight scales poorly. Interconnect specific libraries or functions are likely necessary to ensure performance. BRANSON has been used to directly compare the current standard method to a proposed method on idealized problems. The mesh passing algorithm performs well on problems that are designed to show the scalability of the particle passing method. BRANSON can now run load-imbalanced, dynamic problems. Potential avenues of improvement in the mesh passing algorithm will be implemented and explored. A suite of test problems that stress DD methods will elucidate a possible path forward for production codes.
Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces.
Ardham, Vikram Reddy; Leroy, Frédéric
2017-08-21
In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics.
An atomistic model for cross-linked HNBR elastomers used in seals
Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash
2015-03-01
Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.
A universal strategy for the creation of machine learning-based atomistic force fields
Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi
2017-09-01
Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.
Baik, Sung-Il; Ma, Lulu; Kim, Yoon-Jun; Li, Bo; Liu, Mingjie; Isheim, Dieter; Yakobson, Boris I; Ajayan, Pulickel M; Seidman, David N
2015-11-25
The properties and growth processes of graphene are greatly influenced by the elemental distributions of impurity atoms and their functional groups within or on the hexagonal carbon lattice. Oxygen and hydrogen atoms and their functional molecules (OH, CO, and CO2 ) positions' and chemical identities are tomographically mapped in three dimensions in a graphene monolayer film grown on a copper substrate, at the atomic part-per-million (atomic ppm) detection level, employing laser assisted atom-probe tomography. The atomistic plan and cross-sectional views of graphene indicate that oxygen, hydrogen, and their co-functionalities, OH, CO, and CO2 , which are locally clustered under or within the graphene lattice. The experimental 3D atomistic portrait of the chemistry is combined with computational density-functional theory (DFT) calculations to enhance the understanding of the surface state of graphene, the positions of the chemical functional groups, their interactions with the underlying Cu substrate, and their influences on the growth of graphene. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Atomistic theory of excitonic fine structure in InAs/InP nanowire quantum dot molecules
Świderski, M.; Zieliński, M.
2017-03-01
Nanowire quantum dots have peculiar electronic and optical properties. In this work we use atomistic tight binding to study excitonic spectra of artificial molecules formed by a double nanowire quantum dot. We demonstrate a key role of atomistic symmetry and nanowire substrate orientation rather than cylindrical shape symmetry of a nanowire and a molecule. In particular for [001 ] nanowire orientation we observe a nonvanishing bright exciton splitting for a quasimolecule formed by two cylindrical quantum dots of different heights. This effect is due to interdot coupling that effectively reduces the overall symmetry, whereas single uncoupled [001 ] quantum dots have zero fine structure splitting. We found that the same double quantum dot system grown on [111 ] nanowire reveals no excitonic fine structure for all considered quantum dot distances and individual quantum dot heights. Further we demonstrate a pronounced, by several orders of magnitude, increase of the dark exciton optical activity in a quantum dot molecule as compared to a single quantum dot. For [111 ] systems we also show spontaneous localization of single particle states in one of nominally identical quantum dots forming a molecule, which is mediated by strain and origins from the lack of the vertical inversion symmetry in [111 ] nanostructures of overall C3 v symmetry. Finally, we study lowering of symmetry due to alloy randomness that triggers nonzero excitonic fine structure and the dark exciton optical activity in realistic nanowire quantum dot molecules of intermixed composition.
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.
Scaling of slip avalanches in sheared amorphous materials based on large-scale atomistic simulations
Zhang, Dansong; Dahmen, Karin A.; Ostoja-Starzewski, Martin
2017-03-01
Atomistic simulations of binary amorphous systems with over 4 million atoms are performed. Systems of two interatomic potentials of the Lennard-Jones type, LJ12-6 and LJ9-6, are simulated. The athermal quasistatic shearing protocol is adopted, where the shear strain is applied in a stepwise fashion with each step followed by energy minimization. For each avalanche event, the shear stress drop (Δ σ ), the hydrostatic pressure drop (Δ σh ), and the potential energy drop (Δ E ) are computed. It is found that, with the avalanche size increasing, the three become proportional to each other asymptotically. The probability distributions of avalanche sizes are obtained and values of scaling exponents fitted. In particular, the distributions follow a power law, P (Δ U )˜Δ U-τ , where Δ U is a measure of avalanche sizes defined based on shear stress drops. The exponent τ is 1.25 ±0.1 for the LJ12-6 systems, and 1.15 ±0.1 for the LJ9-6 systems. The value of τ for the LJ12-6 systems is consistent with that from an earlier atomistic simulation study by Robbins et al. [Phys. Rev. Lett. 109, 105703 (2012)], 10.1103/PhysRevLett.109.105703, but the fitted values of other scaling exponents differ, which may be because the shearing protocol used here differs from that in their study.
The Q-Cycle Mechanism of the bc1 Complex: A Biologist's Perspective on Atomistic Studies.
Crofts, Antony R; Rose, Stuart W; Burton, Rodney L; Desai, Amit V; Kenis, Paul J A; Dikanov, Sergei A
2017-04-20
The Q-cycle mechanism of the bc1 complex is now well enough understood to allow application of advanced computational approaches to the study of atomistic processes. In addition to the main features of the mechanism, these include control and gating of the bifurcated reaction at the Qo-site, through which generation of damaging reactive oxygen species is minimized. We report a new molecular dynamics model of the Rhodobacter sphaeroides bc1 complex implemented in a native membrane, and constructed so as to eliminate blemishes apparent in earlier Rhodobacter models. Unconstrained MD simulations after equilibration with ubiquinol and ubiquinone respectively at Qo- and Qi-sites show that substrate binding configurations at both sites are different in important details from earlier models. We also demonstrate a new Qo-site intermediate, formed in the sub-ms time range, in which semiquinone remains complexed with the reduced iron sulfur protein. We discuss this, and a spring-loaded mechanism for modulating interactions of the iron sulfur protein with occupants of the Qo-site, in the context of control and gating roles. Such atomistic features of the mechanism can usefully be explored through simulation, but we stress the importance of constraints from physical chemistry and biology, both in setting up a simulation and in interpreting results.
Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations
Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.
2009-01-01
Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.
Equivalence principle and bound kinetic energy.
Hohensee, Michael A; Müller, Holger; Wiringa, R B
2013-10-11
We consider the role of the internal kinetic energy of bound systems of matter in tests of the Einstein equivalence principle. Using the gravitational sector of the standard model extension, we show that stringent limits on equivalence principle violations in antimatter can be indirectly obtained from tests using bound systems of normal matter. We estimate the bound kinetic energy of nucleons in a range of light atomic species using Green's function Monte Carlo calculations, and for heavier species using a Woods-Saxon model. We survey the sensitivities of existing and planned experimental tests of the equivalence principle, and report new constraints at the level of between a few parts in 10(6) and parts in 10(8) on violations of the equivalence principle for matter and antimatter.
DEFF Research Database (Denmark)
Orlowski, A.; St-Pierre, J. F.; Magarkar, A.
2011-01-01
We used atomistic simulations to study the membrane-bound form of catechol-O-methyltransferase (MB-COMT). In particular we investigated the 26-residue transmembrane a-helical segment of MB-COMT together with the 24-residue fragment that links the transmembrane component to the main protein unit...
Vedula, Ravi Pramod Kumar
Scaling of CMOS towards its ultimate limits, where quantum effects and atomistic variability due to fabrication, along with recent emphasis on heterogeneous integration of non-digital devices for increasing the functional diversification presents us with fundamentally new challenges. A comprehensive understanding of design and operation of these nanoscale transistors, and other electronic devices like RF-MEMS, requires an insight into their electronic and mechanical properties that are strongly influenced by underlying atomic structure. Hence, continuum descriptions of materials and use of empirical models at these scales become questionable. This increase in complexity of electronic devices necessitates an understanding at a more fundamental level to accurately predict the performance and reliability of these devices. The objective of this thesis is to outline the application of multiscale predictive modeling methods, ranging from atoms to devices, for addressing these challenges. This capability is demonstrated using two examples: characterization of (i) dielectric charging in RF-MEMS, and (ii) transport properties of Ge-nanofins. For characterizing the dielectric charging phenomenon, a continuum dielectric charging model, augmented by first principles informed trap distributions, is used to predict current transient measurements across a broad range of voltages and temperatures. These simulations demonstrate using ab initio informed model not only reduces the empiricism (number of adjustable parameters) in the model but also leads to a more accurate model over a broad range of operating conditions, and enable the precise determination of additional material parameters. These atomistic calculations also provide detailed information about the nature of charge traps and their trapping mechanisms that are not accessible experimentally; such information could prove invaluable in defect engineering. The second problem addresses the effect of the in-homogeneous strain
Powell, Andrew D.; Dattani, Nikesh S.; Spada, Rene F. K.; Machado, Francisco B. C.; Lischka, Hans; Dawes, Richard
2017-09-01
The association/dissociation reaction path for ozone (O2 + O ↔ O3) is notoriously difficult to describe accurately using ab initio electronic structure theory, due to the importance of both strong and dynamic electron correlations. Experimentally, spectroscopic studies of the highest lying recorded vibrational states combined with the observed negative temperature dependence of the kinetics of oxygen isotope exchange reactions confirm that the reaction is barrierless, consistent with the latest potential energy surfaces. Previously reported potentials based on Davidson-corrected internally contracted multireference configuration interaction (MRCI) suffer from a spurious reef feature in the entrance channel even when extrapolated towards the complete basis set limit. Here, we report an analysis of comparisons between a variety of electronic structure methods including internally contracted and uncontracted MRCI (with and without Davidson corrections), as well as full configuration interaction quantum Monte Carlo, fixed-node diffusion Monte Carlo, and density matrix renormalization group.
Monte carlo simulation for soot dynamics
Zhou, Kun
2012-01-01
A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.
Adaptive Markov Chain Monte Carlo
Jadoon, Khan
2016-08-08
A substantial interpretation of electromagnetic induction (EMI) measurements requires quantifying optimal model parameters and uncertainty of a nonlinear inverse problem. For this purpose, an adaptive Bayesian Markov chain Monte Carlo (MCMC) algorithm is used to assess multi-orientation and multi-offset EMI measurements in an agriculture field with non-saline and saline soil. In the MCMC simulations, posterior distribution was computed using Bayes rule. The electromagnetic forward model based on the full solution of Maxwell\\'s equations was used to simulate the apparent electrical conductivity measured with the configurations of EMI instrument, the CMD mini-Explorer. The model parameters and uncertainty for the three-layered earth model are investigated by using synthetic data. Our results show that in the scenario of non-saline soil, the parameters of layer thickness are not well estimated as compared to layers electrical conductivity because layer thicknesses in the model exhibits a low sensitivity to the EMI measurements, and is hence difficult to resolve. Application of the proposed MCMC based inversion to the field measurements in a drip irrigation system demonstrate that the parameters of the model can be well estimated for the saline soil as compared to the non-saline soil, and provide useful insight about parameter uncertainty for the assessment of the model outputs.
11th International Conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing
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.
Atomistic study of structures and elastic properties of single crystalline ZnO nanotubes.
Moon, Wonha; Hwang, Hojung
2008-06-04
The structural stability and Young's modulus of single crystalline ZnO nanotubes are investigated using atomistic simulations. Unlike the case for conventional layered nanotubes, the energetic stability of single crystalline ZnO nanotubes is related to the wall thickness. The potential energy of ZnO nanotubes with fixed outer and inner diameters decreases with increasing wall thickness, while the nanotubes with the same wall thickness are independent of the outer and inner diameters. The transformation of single crystalline ZnO nanotubes with a double layer from wurtzite phase to graphitic phase suggests the possibility of wall-typed ZnO nanotubes. The size-dependent Young's modulus of ZnO nanotubes is also investigated. The wall thickness plays a significant role in the Young's modulus of single crystalline ZnO nanotubes, whereas the variation of outer and inner diameters slightly affects the Young's modulus of nanotubes with same wall thickness.
Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties
DEFF Research Database (Denmark)
Voroshylova, I. V.; Chaban, V. V.
2014-01-01
Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....
Displacement field of a screw dislocation in a Cu nanowire: An atomistic study
Gailhanou, Marc; Roussel, Jean-Marc
2013-12-01
By performing atomistic calculations with a tight-binding potential, we study the displacement field induced by a screw dislocation lying along a free Cu cylindrical nanowire. For this anisotropic orientation that is often encountered experimentally, we show that the displacement field uz along the nanowire can be seen as the superposition of three different fields: the screw dislocation field in an infinite medium, the warping displacement field caused by the so-called Eshelby twist, and an additional image field induced by the free surfaces. A Fourier series analysis of this latter image displacement and stress fields is given. For a circular cross section of the wire, this image field corresponds mainly to an additional warping displacement uz∝xy. The dissociation mechanism of the dislocation into partials and the surface stress effects being also captured in our simulations, the present study enables one to quantify the various contributions to the formation of the x-ray diffractograms.
Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code
Energy Technology Data Exchange (ETDEWEB)
Schiffgens, J.O.; Graves, N.J.; Oster, C.A.
1980-04-01
This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.
Directory of Open Access Journals (Sweden)
Ramon Reigada
Full Text Available The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic and carbon tetrachloride (non-anesthetic. Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.
Atomistic model of metal nanocrystals with line defects: contribution to diffraction line profile
Directory of Open Access Journals (Sweden)
Alberto eLeonardi
2015-02-01
Full Text Available Molecular Dynamics (MD was used to simulate cylindrical Pd and Ir domains with ideal dislocations parallel to the axis. Results show significant discrepancies with respect to predictions of traditional continuum mechanics. When MD atomistic models are used to generate powder diffraction patterns, strong deviations are observed from the usual paradigm of a small crystal perturbed by the strain field of lattice defects. The Krivoglaz-Wilkens model for dislocation effects of diffraction line profiles seems correct for the screw dislocation case if most parameters are known or strongly constrained. Nevertheless the practical implementation of the model, i.e., a free refinement of all microstructural parameters, leads to instability. Possible effects of the experimental practice based on Line Profile Analysis are discussed.
Tölle, Pia; Köhler, Christof; Marschall, Roland; Sharifi, Monir; Wark, Michael; Frauenheim, Thomas
2012-08-07
The conventional polymer electrolyte membrane (PEM) materials for fuel cell applications strongly rely on temperature and pressure conditions for optimal performance. In order to expand the range of operating conditions of these conventional PEM materials, mesoporous functionalised SiO(2) additives are developed. It has been demonstrated that these additives themselves achieve proton conductivities approaching those of conventional materials. However, the proton conduction mechanisms and especially factors influencing charge carrier mobility under different hydration conditions are not well known and difficult to separate from concentration effects in experiments. This tutorial review highlights contributions of atomistic computer simulations to the basic understanding and eventual design of these materials. Some basic introduction to the theoretical and computational framework is provided to introduce the reader to the field, the techniques are in principle applicable to a wide range of other situations as well. Simulation results are directly compared to experimental data as far as possible.
Theoretical modeling of zircon's crystal morphology according to data of atomistic calculations
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
Simulations of micron-scale fracture using atomistic-based boundary element method
Wu, Xiaojie; Li, Xiantao
2017-12-01
A new formulation of a boundary element method (BEM) is proposed in this paper to simulate cracks at the micron scale. The main departure from the traditional BEMs is that the current model is derived from the underlying atomistic model, which involves the interactions of atoms at the scale of Angstroms. By using the lattice Green’s function, the new BEM formulation eliminates the excessive atomic degrees of freedom away from crack tips, and directly couples the process zones with the physical boundary conditions. We show that with such a drastic reduction, one can simulate brittle fracture process on the scale of microns, for which the entire system consists of a few billion atoms. We discuss several numerical issues to make the implementation more efficient. Examples will be presented for cracks in the bcc iron system.
Mechanism of the Cassie-Wenzel transition via the atomistic and continuum string methods
Energy Technology Data Exchange (ETDEWEB)
Giacomello, Alberto, E-mail: alberto.giacomello@uniroma1.it; Casciola, Carlo Massimo [Dipartimento di Ingegneria Meccanica e Aerospaziale, Università di Roma “La Sapienza,” 00184 Rome (Italy); Meloni, Simone, E-mail: simone.meloni@epfl.ch [Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland); Müller, Marcus [Institut für Theoretische Physik, Georg-August-Universität Göttingen, 37077 Göttingen (Germany)
2015-03-14
The string method is a general and flexible strategy to compute the most probable transition path for an activated process (rare event). We apply here the atomistic string method in the density field to the Cassie-Wenzel transition, a central problem in the field of superhydrophobicity. We discuss in detail the mechanism of wetting of a submerged hydrophobic cavity of nanometer size and its dependence on the geometry of the cavity. Furthermore, we analyze the algorithmic analogies between the continuum “interface” string method and CREaM [Giacomello et al., Phys. Rev. Lett. 109, 226102 (2012)], a method inspired by the string that allows for a faster and simpler computation of the mechanism and of the free-energy profiles of the wetting process.
Atomistic Investigation of Cu-Induced Misfolding in the Onset of Parkinson's Disease
Rose, Francis; Hodak, Miroslav; Bernholc, Jerry
2009-03-01
A nucleation mechanism for the misfolding of α-synuclein, the protein implicated in Parkinson's Disease (PD), is investigated using computer simulations. Through a combination of ab initio and classical simulation techniques, the conformational evolution of copper-ion-initiated misfolding of α-synuclein is determined. Based on these investigations and available experimental evidence, an atomistic model detailing the nucleation-initiated pathogenesis of PD is proposed. Once misfolded, the proteins can assemble into fibrils, the primary structural components of the deleterious PD plaques. Our model identifies a process of structural modifications to an initially unfolded α-synuclein that results in a partially folded intermediate with a well defined nucleation site as a precursor to the fully misfolded protein. The identified pathway can enable studies of reversal mechanisms and inhibitory agents, potentially leading to the development of effective therapies.
Identifying early stage precipitation in large-scale atomistic simulations of superalloys
Schmidt, Eric; Bristowe, Paul D.
2017-04-01
A method for identifying and classifying ordered phases in large chemically and thermally disordered atomistic models is presented. The method uses Steinhardt parameters to represent local atomic configurations and develops probability density functions to classify individual atoms using naïve Bayes. The method is applied to large molecular dynamics simulations of supersaturated Ni-20 at% Al solid solutions in order to identify the formation of embryonic γ‧-Ni3Al. The composition and temperatures are chosen to promote precipitation, which is observed in the form of ordering and is found to occur more likely in regions with above average Al concentration producing ‘clusters’ of increasing size. The results are interpreted in terms of a precipitation mechanism in which the solid solution is unstable with respect to ordering and potentially followed by either spinodal decomposition or nucleation and growth.
NATO Advanced Study Institute on Surface Diffusion : Atomistic and Collective Processes
1997-01-01
The interest in the problem of surface diffusion has been steadily growing over the last fifteen years. This is clearly evident from the increase in the number of papers dealing with the problem, the development of new experimental techniques, and the specialized sessions focusing on diffusion in national and international meetings. Part of the driving force behind this increasing activity is our recently acquired ability to observe and possibly control atomic scale phenomena. It is now possible to look selectively at individual atomistic processes and to determine their relative importance during growth and reactions at surfaces. The number of researchers interested in this problem also has been growing steadily which generates the need for a good reference source to farniliarize newcomers to the problem. While the recent emphasis is on the role of diffusion during growth, there is also continuing progress on the more traditional aspects of the problem describing mass transport in an ensemble of particles. S...
Energy Technology Data Exchange (ETDEWEB)
Giuseppe Palmiotti
2015-05-01
In this work, the implementation of a collision history-based approach to sensitivity/perturbation calculations in the Monte Carlo code SERPENT is discussed. The proposed methods allow the calculation of the eects of nuclear data perturbation on several response functions: the eective multiplication factor, reaction rate ratios and bilinear ratios (e.g., eective kinetics parameters). SERPENT results are compared to ERANOS and TSUNAMI Generalized Perturbation Theory calculations for two fast metallic systems and for a PWR pin-cell benchmark. New methods for the calculation of sensitivities to angular scattering distributions are also presented, which adopts fully continuous (in energy and angle) Monte Carlo estimators.
Simulation and the Monte Carlo method
Rubinstein, Reuven Y
2016-01-01
Simulation and the Monte Carlo Method, Third Edition reflects the latest developments in the field and presents a fully updated and comprehensive account of the major topics that have emerged in Monte Carlo simulation since the publication of the classic First Edition over more than a quarter of a century ago. While maintaining its accessible and intuitive approach, this revised edition features a wealth of up-to-date information that facilitates a deeper understanding of problem solving across a wide array of subject areas, such as engineering, statistics, computer science, mathematics, and the physical and life sciences. The book begins with a modernized introduction that addresses the basic concepts of probability, Markov processes, and convex optimization. Subsequent chapters discuss the dramatic changes that have occurred in the field of the Monte Carlo method, with coverage of many modern topics including: Markov Chain Monte Carlo, variance reduction techniques such as the transform likelihood ratio...
Monte Carlo simulations for plasma physics
Energy Technology Data Exchange (ETDEWEB)
Okamoto, M.; Murakami, S.; Nakajima, N.; Wang, W.X. [National Inst. for Fusion Science, Toki, Gifu (Japan)
2000-07-01
Plasma behaviours are very complicated and the analyses are generally difficult. However, when the collisional processes play an important role in the plasma behaviour, the Monte Carlo method is often employed as a useful tool. For examples, in neutral particle injection heating (NBI heating), electron or ion cyclotron heating, and alpha heating, Coulomb collisions slow down high energetic particles and pitch angle scatter them. These processes are often studied by the Monte Carlo technique and good agreements can be obtained with the experimental results. Recently, Monte Carlo Method has been developed to study fast particle transports associated with heating and generating the radial electric field. Further it is applied to investigating the neoclassical transport in the plasma with steep gradients of density and temperatures which is beyong the conventional neoclassical theory. In this report, we briefly summarize the researches done by the present authors utilizing the Monte Carlo method. (author)
Monte Carlo methods for particle transport
Haghighat, Alireza
2015-01-01
The Monte Carlo method has become the de facto standard in radiation transport. Although powerful, if not understood and used appropriately, the method can give misleading results. Monte Carlo Methods for Particle Transport teaches appropriate use of the Monte Carlo method, explaining the method's fundamental concepts as well as its limitations. Concise yet comprehensive, this well-organized text: * Introduces the particle importance equation and its use for variance reduction * Describes general and particle-transport-specific variance reduction techniques * Presents particle transport eigenvalue issues and methodologies to address these issues * Explores advanced formulations based on the author's research activities * Discusses parallel processing concepts and factors affecting parallel performance Featuring illustrative examples, mathematical derivations, computer algorithms, and homework problems, Monte Carlo Methods for Particle Transport provides nuclear engineers and scientists with a practical guide ...
Hybrid Monte Carlo methods in computational finance
Leitao Rodriguez, A.
2017-01-01
Monte Carlo methods are highly appreciated and intensively employed in computational finance in the context of financial derivatives valuation or risk management. The method offers valuable advantages like flexibility, easy interpretation and straightforward implementation. Furthermore, the
Avariide kiuste Monte Carlosse / Aare Arula
Arula, Aare
2007-01-01
Vt. ka Tehnika dlja Vsehh nr. 3, lk. 26-27. 26. jaanuaril 1937 Tallinnast Monte Carlo tähesõidule startinud Karl Siitanit ja tema meeskonda ootasid ees seiklused, mis oleksid neile peaaegu elu maksnud
Quantum Monte Carlo approaches for correlated systems
Becca, Federico
2017-01-01
Over the past several decades, computational approaches to studying strongly-interacting systems have become increasingly varied and sophisticated. This book provides a comprehensive introduction to state-of-the-art quantum Monte Carlo techniques relevant for applications in correlated systems. Providing a clear overview of variational wave functions, and featuring a detailed presentation of stochastic samplings including Markov chains and Langevin dynamics, which are developed into a discussion of Monte Carlo methods. The variational technique is described, from foundations to a detailed description of its algorithms. Further topics discussed include optimisation techniques, real-time dynamics and projection methods, including Green's function, reptation and auxiliary-field Monte Carlo, from basic definitions to advanced algorithms for efficient codes, and the book concludes with recent developments on the continuum space. Quantum Monte Carlo Approaches for Correlated Systems provides an extensive reference ...
Pavlov, Alexander S; Khalatur, Pavel G
2016-06-28
Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more
Multilevel Monte Carlo in Approximate Bayesian Computation
Jasra, Ajay
2017-02-13
In the following article we consider approximate Bayesian computation (ABC) inference. We introduce a method for numerically approximating ABC posteriors using the multilevel Monte Carlo (MLMC). A sequential Monte Carlo version of the approach is developed and it is shown under some assumptions that for a given level of mean square error, this method for ABC has a lower cost than i.i.d. sampling from the most accurate ABC approximation. Several numerical examples are given.
Monte Carlo Simulation Investigating Threading of Poly(ethylene oxide) in the Melt
Helfer, Carin; Xu, Guoqiang; Mattice, Wayne; Pugh, Coleen
2003-03-01
Polyrotaxanes are composed of multiple cyclic compounds threaded with a linear polymer. The predicted unusual physical and chemical properties resulting from the lack of covalent bonds between their cyclic and linear components have caused interest in synthesizing polyrotaxanes. In the current study, a coarse-grained Monte Carlo method on the second nearest neighbor diamond lattice (2nnd lattice) is established to investigate the threading of cyclic PEO molecules by linear PEO chains in the melt. This method allows for reverse-mapping of the coarse-grained chains to the fully atomistic detail in continuous space at any interval of the simulation. The short-range interactions that result from the local chain conformation are based on the Rotational Isomeric State model. A discretized Lennard-Jones (LJ) potential energy function is used to describe the long-range interactions with LJ parameters estimated since the experimental values are not available. The construction and validation of the simulation will be presented. Results of the fraction of cyclics threaded as a function of either Xc, the mass fraction of cyclics, or Nc, the size of the cyclics, will be discussed. * Supported by funds from NASA John H. Glenn research center.
Efficient Bayesian inference in stochastic chemical kinetic models using graphical processing units
Niemi, Jarad; Wheeler, Matthew
2011-01-01
A goal of systems biology is to understand the dynamics of intracellular systems. Stochastic chemical kinetic models are often utilized to accurately capture the stochastic nature of these systems due to low numbers of molecules. Collecting system data allows for estimation of stochastic chemical kinetic rate parameters. We describe a well-known, but typically impractical data augmentation Markov chain Monte Carlo algorithm for estimating these parameters. The impracticality is due to the use...
Simulating RNA folding kinetics on approximated energy landscapes.
Tang, Xinyu; Thomas, Shawna; Tapia, Lydia; Giedroc, David P; Amato, Nancy M
2008-09-12
We present a general computational approach to simulate RNA folding kinetics that can be used to extract population kinetics, folding rates and the formation of particular substructures that might be intermediates in the folding process. Simulating RNA folding kinetics can provide unique insight into RNA whose functions are dictated by folding kinetics and not always by nucleotide sequence or the structure of the lowest free-energy state. The method first builds an approximate map (or model) of the folding energy landscape from which the population kinetics are analyzed by solving the master equation on the map. We present results obtained using an analysis technique, map-based Monte Carlo simulation, which stochastically extracts folding pathways from the map. Our method compares favorably with other computational methods that begin with a comprehensive free-energy landscape, illustrating that the smaller, approximate map captures the major features of the complete energy landscape. As a result, our method scales to larger RNAs. For example, here we validate kinetics of RNA of more than 200 nucleotides. Our method accurately computes the kinetics-based functional rates of wild-type and mutant ColE1 RNAII and MS2 phage RNAs showing excellent agreement with experiment.
2017-02-13
AFRL-RV-PS- AFRL-RV-PS- TR-2016-0161 TR-2016-0161 ATOMISTIC- AND MESO-SCALE COMPUTATIONAL SIMULATIONS FOR DEVELOPING MULTI-TIMESCALE THEORY FOR...From - To) 18 Aug 2015 – 7 Dec 2016 4. TITLE AND SUBTITLE Atomistic- and Meso-Scale Computational Simulations for Developing Multi-Timescale Theory ...and knowledge gained from atomic- and meso-scale simulations will be input into rate-diffusion theory as initial conditions to calculate the steady
Principles of chemical kinetics
House, James E
2007-01-01
James House's revised Principles of Chemical Kinetics provides a clear and logical description of chemical kinetics in a manner unlike any other book of its kind. Clearly written with detailed derivations, the text allows students to move rapidly from theoretical concepts of rates of reaction to concrete applications. Unlike other texts, House presents a balanced treatment of kinetic reactions in gas, solution, and solid states. The entire text has been revised and includes many new sections and an additional chapter on applications of kinetics. The topics covered include quantitative rela
Introduction to chemical kinetics
Soustelle, Michel
2013-01-01
This book is a progressive presentation of kinetics of the chemical reactions. It provides complete coverage of the domain of chemical kinetics, which is necessary for the various future users in the fields of Chemistry, Physical Chemistry, Materials Science, Chemical Engineering, Macromolecular Chemistry and Combustion. It will help them to understand the most sophisticated knowledge of their future job area. Over 15 chapters, this book present the fundamentals of chemical kinetics, its relations with reaction mechanisms and kinetic properties. Two chapters are then devoted to experimental re
A novel approach to tracer-kinetic modeling for (macromolecular) dynamic contrast-enhanced MRI
Jacobs, Igor; Strijkers, Gustav J.; Keizer, Henk M.; Janssen, Henk M.; Nicolay, Klaas; Schabel, Matthias C.
2016-01-01
To develop a novel tracer-kinetic modeling approach for multi-agent dynamic contrast-enhanced MRI (DCE-MRI) that facilitates separate estimation of parameters characterizing blood flow and microvascular permeability within one individual. Monte Carlo simulations were performed to investigate the
Approaching Chemical Accuracy with Quantum Monte Carlo
Petruzielo, F R; Umrigar, C J
2012-01-01
A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space.
Calculating alpha Eigenvalues in a Continuous-Energy Infinite Medium with Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Betzler, Benjamin R. [Los Alamos National Laboratory; Kiedrowski, Brian C. [Los Alamos National Laboratory; Brown, Forrest B. [Los Alamos National Laboratory; Martin, William R. [Los Alamos National Laboratory
2012-09-04
The {alpha} eigenvalue has implications for time-dependent problems where the system is sub- or supercritical. We present methods and results from calculating the {alpha}-eigenvalue spectrum for a continuous-energy infinite medium with a simplified Monte Carlo transport code. We formulate the {alpha}-eigenvalue problem, detail the Monte Carlo code physics, and provide verification and results. We have a method for calculating the {alpha}-eigenvalue spectrum in a continuous-energy infinite-medium. The continuous-time Markov process described by the transition rate matrix provides a way of obtaining the {alpha}-eigenvalue spectrum and kinetic modes. These are useful for the approximation of the time dependence of the system.
Monte Carlo wave packet approach to dissociative multiple ionization in diatomic molecules
DEFF Research Database (Denmark)
Leth, Henriette Astrup; Madsen, Lars Bojer; Mølmer, Klaus
2010-01-01
separately for each molecular charge state. Our model circumvents the solution of a multiparticle Schrödinger equation and makes it possible to extract the kinetic energy release spectrum via the Coulomb explosion channel as well as the physical origin of the different structures in the spectrum......A detailed description of the Monte Carlo wave packet technique applied to dissociative multiple ionization of diatomic molecules in short intense laser pulses is presented. The Monte Carlo wave packet technique relies on the Born-Oppenheimer separation of electronic and nuclear dynamics...... and provides a consistent theoretical framework for treating simultaneously both ionization and dissociation. By simulating the detection of continuum electrons and collapsing the system onto either the neutral, singly ionized or doubly ionized states in every time step the nuclear dynamics can be solved...
Wieggers, R. C.; W. J. Goedheer,; M.R. Akdim,; F. Bijkerk,; Zegeling, P. A.
2008-01-01
We present a kinetic simulation of the plasma formed by photoionization in the intense flux of an extreme ultraviolet lithography (EUVL) light source. The model is based on the particle-in-cell plus Monte Carlo approach. The photoelectric effect and ionization by electron collisions are included.
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.
Composition manipulation of near infrared InAsxSb1-x nanocrystals: Atomistic tight-binding theory
Sukkabot, Worasak
2017-05-01
Based on a successful atomistic tight-binding model in the conjunction with an empirical bowing parameter and the widely used virtual crystal approximation, the theoretical investigations of near infrared InAsxSb1-x nanocrystals with the experimentally synthesized sizes and As compositions (x) are reported. Under various experimental As compositions (x), the single-particle spectra, charge densities, density of states (DOS), overlaps of ground electron and hole wave functions, optical spectra, atomistic electron-hole interactions and stokes shift are numerically computed. I report the correlation of the structural and optical properties of InAsxSb1-x nanocrystals with different alloy compositions (x). With the increasing compositions (x), the single-electron energies are increased, while the single-hole energies are reduced, thus introducing the wider optical band gaps. The atomistic tight-binding model reproduces very well the change in the band gap values with the compositions observed in the experimental reports. The As compositions (x) of alloy InAsxSb1-x nanocrystals are used to propel photonic and optoelectronic device performance in a broad range of the near infrared spectrum with the wave length from 825 to 990 nm. With the increasing content (x), the optical intensities are reduced, whereas atomistic electron-hole interactions and stokes shift are progressively increased. Finally, the present systematic study of alloy InAsxSb1-x nanocrystals is one of the most important milestones on the road to provide the understanding of the composition-dependent structural and optical properties and a complete tactic to design a facile band gap modulation method of preparing the interesting near infrared emitting devices and detectors.
Condon, Joshua E; Martin, Tyler B; Jayaraman, Arthi
2017-04-19
Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state". In agreement with past experimental observations of Luo and Kiick, upon anchoring ELP oligomers to a point to mimic ELP oligomers conjugated to another macromolecule, there is an apparent slight shift in the transition temperature to lower values compared to free (unconjugated) ELP oligomers. However, these atomistic simulations are limited to small systems of short ELPs, and as such do not capture the multiple chain aggregation/phase separation observed in experiments of ELPs. Therefore, we utilize phenomenological coarse-grained (CG) MD simulations to probe how conjugating a block of generic-LCST polymer to another rigid unresponsive macromolecular block impacts the transition temperatures at concentrations and length scales larger than atomistic simulations. We find that when multiple LCST polymer chains are conjugated to a rigid unresponsive polymer block, the increased local crowding of the LCST polymers shifts the transition marked by onset of chain aggregation to smaller effective polymer-polymer attraction energies compared to the free LCST polymer chains. The driving force needed for aggregation is reduced in the conjugates compared to free LCST polymer due to reduction in the loss of polymer configurational entropy upon aggregation.
Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.
2011-01-01
Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.
Hybrid Multilevel Monte Carlo Simulation of Stochastic Reaction Networks
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.
Atomistic simulations to micro-mechanisms of adhesion in automotive applications
Sen, Fatih Gurcag
This study aimed at depicting atomistic and microstructural aspects of adhesion and friction that appear in different automotive applications and manufacturing processes using atomistic simulations coupled with tribological tests and surface characterization experiments. Thin films that form at the contact interfaces due to chemical reactions and coatings that are developed to mitigate or enhance adhesion were studied in detail. The adhesion and friction experiments conducted on diamond-like carbon (DLC) coatings against Al indicated that F incorporation into DLC decreased the coefficient of friction (COF) by 30% -with respect to H-DLC that is known to have low COF and anti-adhesion properties against Al- to 0.14 owing to formation of repulsive F-F interactions at the sliding interface as shown by density functional theory (DFT) calculations. F atoms transferred to the Al surface with an increase in the contact pressure, and this F transfer led to the formation of a stable AlF3 compound at the Al surface as confirmed by XPS and cross-sectional FIB-TEM. The incorporation of Si and O in a F-containing DLC resulted in humidity independent low COF of 0.08 due to the hydration effect of the Si-O-Si chains in the carbonaceous tribolayers that resulted in repulsive OH-OH interactions at the contact interface. At high temperatures, adhesion of Al was found to be enhanced as a result of superplastic oxide fibers on the Al surface. Molecular dynamics (MD) simulations of tensile deformation of Al nanowires in oxygen carried out with ReaxFF showed that native oxide of Al has an oxygen deficient, low density structure and in O2, the oxygen diffusion in amorphous oxide healed the broken Al-O bonds during applied strain and resulted in the superplasticity. The oxide shell also provided nucleation sites for dislocations in Al crystal. In fuel cell applications, where low Pt/carbon adhesion is causing durability problems, spin-polarized DFT showed that metals with unfilled d
Atomistic methodologies for material properties of 2D materials at the nanoscale
Zhang, Zhen
Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our
Shih, Cheng-Yu; Wu, Chengping; Shugaev, Maxim V; Zhigilei, Leonid V
2017-03-01
Laser ablation in liquids is actively used for generation of clean colloidal nanoparticles with unique shapes and functionalities. The fundamental mechanisms of the laser ablation in liquids and the key processes that control the nanoparticle structure, composition, and size distribution, however, are not yet fully understood. In this paper, we report the results of first atomistic simulations of laser ablation of metal targets in liquid environment. A model combining a coarse-grained representation of the liquid environment (parameterized for water), a fully atomistic description of laser interactions with metal targets, and acoustic impedance matching boundary conditions is developed and applied for simulation of laser ablation of a thin silver film deposited on a silica substrate. The simulations, performed at two laser fluences in the regime of phase explosion, predict a rapid deceleration of the ejected ablation plume and the formation of a dense superheated molten layer at the water-plume interface. The water in contact with the hot metal layer is brought to the supercritical state and transforms into an expanding low density metal-water mixing region that serves as a precursor for the formation of a cavitation bubble. Two distinct mechanisms of the nanoparticle formation are predicted in the simulations: (1) the nucleation and growth of small (mostly ⩽10nm) nanoparticles in the metal-water mixing region and (2) the formation of larger (tens of nm) nanoparticles through the breakup of the superheated molten metal layer triggered by the emergence of complex morphological features attributed to the Rayleigh-Taylor instability of the interface between at the superheated metal layer and the supercritical water. The first mechanism is facilitated by the rapid cooling of the growing nanoparticles in the supercritical water environment, resulting in solidification of the nanoparticles located in the upper part of the mixing region on the timescale of nanoseconds
Jones, R. E.; Criscenti, L. J.; Rimsza, J.
2016-12-01
Predicting fracture initiation and propagation in low-permeability geomaterials is a critical yet un- solved problem crucial to assessing shale caprocks at carbon dioxide sequestration sites, and controlling fracturing for gas and oil extraction. Experiments indicate that chemical reactions at fluid-geomaterial interfaces play a major role in subcritical crack growth by weakening the material and altering crack nu- cleation and growth rates. Engineering the subsurface fracture environment, however, has been hindered by a lack of understanding of the mechanisms relating chemical environment to mechanical outcome, and a lack of capability directly linking atomistic insight to macroscale observables. We have developed a fundamental atomic-level understanding of the chemical-mechanical mecha- nisms that control subcritical cracks through coarse-graining data from reactive molecular simulations. Previous studies of fracture at the atomic level have typically been limited to producing stress-strain curves, quantifying either the system-level stress or energy at which fracture propagation occurs. As such, these curves are neither characteristic of nor insightful regarding fracture features local to the crack tip. In contrast, configurational forces, such as the J-integral, are specific to the crack in that they measure the energy available to move the crack and truly quantify fracture resistance. By development and use of field estimators consistent with the continuum conservation properties we are able to connect the data produced by atomistic simulation to the continuum-level theory of fracture mechanics and thus inform engineering decisions. In order to trust this connection we have performed theoretical consistency tests and validation with experimental data. Although we have targeted geomaterials, this capability can have direct impact on other unsolved technological problems such as predicting the corrosion and embrittlement of metals and ceramics. Sandia National
Energy Technology Data Exchange (ETDEWEB)
Dunn, Martin L. [Univ. of Colorado, Boulder, CO (United States); Talmage, Mellisa J. [Univ. of Colorado, Boulder, CO (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); West, Neil [Univ. of Colorado, Boulder, CO (United States); Gullett, Philip Michael [Mississippi State Univ., Mississippi State, MS (United States); Miller, David C. [Univ. of Colorado, Boulder, CO (United States); Spark, Kevin [Univ. of Colorado, Boulder, CO (United States); Diao, Jiankuai [Univ. of Colorado, Boulder, CO (United States); Horstemeyer, Mark F. [Mississippi State Univ., Mississippi State, MS (United States); Zimmerman, Jonathan A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gall, K. [Georgia Inst. of Technology, Atlanta, GA (United States)
2006-10-01
Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project
Self-learning Monte Carlo method
Liu, Junwei; Qi, Yang; Meng, Zi Yang; Fu, Liang
2017-01-01
Monte Carlo simulation is an unbiased numerical tool for studying classical and quantum many-body systems. One of its bottlenecks is the lack of a general and efficient update algorithm for large size systems close to the phase transition, for which local updates perform badly. In this Rapid Communication, we propose a general-purpose Monte Carlo method, dubbed self-learning Monte Carlo (SLMC), in which an efficient update algorithm is first learned from the training data generated in trial simulations and then used to speed up the actual simulation. We demonstrate the efficiency of SLMC in a spin model at the phase transition point, achieving a 10-20 times speedup.
Monte Carlo strategies in scientific computing
Liu, Jun S
2008-01-01
This paperback edition is a reprint of the 2001 Springer edition This book provides a self-contained and up-to-date treatment of the Monte Carlo method and develops a common framework under which various Monte Carlo techniques can be "standardized" and compared Given the interdisciplinary nature of the topics and a moderate prerequisite for the reader, this book should be of interest to a broad audience of quantitative researchers such as computational biologists, computer scientists, econometricians, engineers, probabilists, and statisticians It can also be used as the textbook for a graduate-level course on Monte Carlo methods Many problems discussed in the alter chapters can be potential thesis topics for masters’ or PhD students in statistics or computer science departments Jun Liu is Professor of Statistics at Harvard University, with a courtesy Professor appointment at Harvard Biostatistics Department Professor Liu was the recipient of the 2002 COPSS Presidents' Award, the most prestigious one for sta...
Off-diagonal expansion quantum Monte Carlo.
Albash, Tameem; Wagenbreth, Gene; Hen, Itay
2017-12-01
We propose a Monte Carlo algorithm designed to simulate quantum as well as classical systems at equilibrium, bridging the algorithmic gap between quantum and classical thermal simulation algorithms. The method is based on a decomposition of the quantum partition function that can be viewed as a series expansion about its classical part. We argue that the algorithm not only provides a theoretical advancement in the field of quantum Monte Carlo simulations, but is optimally suited to tackle quantum many-body systems that exhibit a range of behaviors from "fully quantum" to "fully classical," in contrast to many existing methods. We demonstrate the advantages, sometimes by orders of magnitude, of the technique by comparing it against existing state-of-the-art schemes such as path integral quantum Monte Carlo and stochastic series expansion. We also illustrate how our method allows for the unification of quantum and classical thermal parallel tempering techniques into a single algorithm and discuss its practical significance.
Off-diagonal expansion quantum Monte Carlo
Albash, Tameem; Wagenbreth, Gene; Hen, Itay
2017-12-01
We propose a Monte Carlo algorithm designed to simulate quantum as well as classical systems at equilibrium, bridging the algorithmic gap between quantum and classical thermal simulation algorithms. The method is based on a decomposition of the quantum partition function that can be viewed as a series expansion about its classical part. We argue that the algorithm not only provides a theoretical advancement in the field of quantum Monte Carlo simulations, but is optimally suited to tackle quantum many-body systems that exhibit a range of behaviors from "fully quantum" to "fully classical," in contrast to many existing methods. We demonstrate the advantages, sometimes by orders of magnitude, of the technique by comparing it against existing state-of-the-art schemes such as path integral quantum Monte Carlo and stochastic series expansion. We also illustrate how our method allows for the unification of quantum and classical thermal parallel tempering techniques into a single algorithm and discuss its practical significance.
1D to 3D diffusion-reaction kinetics of defects in crystals
DEFF Research Database (Denmark)
Trinkaus, H.; Heinisch, H.L.; Barashev, A.V.
2002-01-01
Microstructural features evolving in crystalline solids from diffusion-reaction kinetics of mobile components depend crucially on the dimension of the underlying diffusion process which is commonly assumed to be three-dimensional (3D). In metals, irradiation-induced displacement cascades produce...... clusters of self-interstitials performing 1D diffusion. Changes between equivalent 1D diffusion paths and transversal diffusion result in diffusion-reaction kinetics between one and three dimensions. An analytical approach suggests a single-variable function (master curve) interpolating between the 1D...... and 3D limiting cases. The analytical result is fully confirmed by kinetic Monte Carlo simulations....
Monte Carlo sampling for stochastic weight functions.
Frenkel, Daan; Schrenk, K Julian; Martiniani, Stefano
2017-07-03
Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here, we consider the case that the weight determining the acceptance probability itself is fluctuating. This situation is common in many numerical studies. We show that it is possible to construct a rigorous Monte Carlo algorithm that visits points in state space with a probability proportional to their average weight. The same approach may have applications for certain classes of high-throughput experiments and the analysis of noisy datasets.
Monte Carlo Treatment Planning for Advanced Radiotherapy
DEFF Research Database (Denmark)
Cronholm, Rickard
This Ph.d. project describes the development of a workflow for Monte Carlo Treatment Planning for clinical radiotherapy plans. The workflow may be utilized to perform an independent dose verification of treatment plans. Modern radiotherapy treatment delivery is often conducted by dynamically...... modulating the intensity of the field during the irradiation. The workflow described has the potential to fully model the dynamic delivery, including gantry rotation during irradiation, of modern radiotherapy. Three corner stones of Monte Carlo Treatment Planning are identified: Building, commissioning...
AlphaGo ja Monte Carlo -puuhaku
Kumpulainen, Samu
2017-01-01
Tässä tutkielmassa käsittelen Monte Carlo -puuhakualgoritmia sekä sen roolia hyvin menestyneessä AlphaGo-tekoälyssä. Tavoitteena oli muodostaa kokonaiskuva AlphaGo:n toiminnasta, painottuen etenkin Monte Carlo -puuhaun näkökulmaan. Tutkimuksen perusteella selvisi miten ohjelma hyödyntää omassa hakualgoritmissään kyseistä puuhakua, jota se parantaa hyödyntäen koneoppimista ja useita eri tarkoituksiin opetettuja neuroverkkoja. AlphaGo saavutti näin tehokkuuden, johon muut go-ohjelmat eivä...
Fast sequential Monte Carlo methods for counting and optimization
Rubinstein, Reuven Y; Vaisman, Radislav
2013-01-01
A comprehensive account of the theory and application of Monte Carlo methods Based on years of research in efficient Monte Carlo methods for estimation of rare-event probabilities, counting problems, and combinatorial optimization, Fast Sequential Monte Carlo Methods for Counting and Optimization is a complete illustration of fast sequential Monte Carlo techniques. The book provides an accessible overview of current work in the field of Monte Carlo methods, specifically sequential Monte Carlo techniques, for solving abstract counting and optimization problems. Written by authorities in the
Atomistic Model for the Polyamide Formation from β-Lactam Catalyzed by Candida Antarctica Lipase B
Energy Technology Data Exchange (ETDEWEB)
Baum, Iris; Elsasser, Brigitta M.; Schwab, Leendert; Loos, Katja; Fels, Gregor
2011-04-01
Candida antarctica lipase B (CALB) is an established biocatalyst for a variety of transesterification, amidation, and polymerization reactions. In contrast to polyesters, polyamides are not yet generally accessible via enzymatic polymerization. In this regard, an enzyme-catalyzed ring-opening polymerization of {beta}-lactam (2-azetidinone) using CALB is the first example of an enzymatic polyamide formation yielding unbranched poly({beta}-alanine), nylon 3. The performance of this polymerization, however, is poor, considering the maximum chain length of 18 monomer units with an average length of 8, and the molecular basis of the reaction so far is not understood. We have employed molecular modeling techniques using docking tools, molecular dynamics, and QM/MM procedures to gain insight into the mechanistic details of the various reaction steps involved. As a result, we propose a catalytic cycle for the oligomerization of {beta}-lactam that rationalizes the activation of the monomer, the chain elongation by additional {beta}-lactam molecules, and the termination of the polymer chain. In addition, the processes leading to a premature chain termination are studied. Particularly, the QM/MM calculation enables an atomistic description of all eight steps involved in the catalytic cycle, which features an in situ-generated {beta}-alanine as the elongating monomer and which is compatible with the experimental findings.
Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael
2016-01-01
Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646
Ash'arite's atomistic conception of the physical world: A restatement
Energy Technology Data Exchange (ETDEWEB)
Pozi, Firdaus; Othman, Mohd Yusof [School of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia and Institute of Islam Hadhari, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan (Malaysia); Mohamed, Faizal [School of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan (Malaysia)
2013-11-27
Atomism plays an important role in the history of human thought. It can be traced back from Democritus atomos in the 500 BC to particle physics and quantum theory in the 21{sup st} century. However, as it being rejected and developed in the course of history of science, it still brings the fundamental question that perplexes physicists. It gives the views that the world is eternal; that the laws of nature is immutable and eternal therefore all phenomena can be determined through the laws and that there is no reality behind the quantum world. In this paper, we shall briefly describe all these three views on the nature of the physical world or universe and this include on the nature of matter. Then, we shall explain our stand on those conceptions based on the Ash'arites atomistic conception of the physical world. We hope this paper can shed a light on several fundamental issues in the conception of the universe and gives the proper response to them.
Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers
Hong, Bingbing
2013-10-02
We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH 2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henrys constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henrys constant. Dependence of the calculated Henrys constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. © 2013 Taylor & Francis.
Features of structure and phase transitions in pure uranium and U-Mo alloys: atomistic simulation
Kolotova, L. N.; Kuksin, A. Yu; Smirnova, D. E.; Starikov, S. V.; Tseplyaev, V. I.
2016-11-01
We study structural properties of cubic and tetragonal phases of U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. For pure uranium and U-Mo alloys at low temperatures we observe body-centered tetragonal (bct) structure, which is similar to the metastable γ°-phase found in the experiments. At higher temperatures bct structure transforms to a quasi body-centered cubic (q-bcc) phase that exhibits cubic symmetry just on the scale of several interatomic spacings or when averaged over time. Instantaneous pair distribution function (PDF) differs from PDF for the time-averaged atomic coordinates corresponding to the bcc lattice. The local positions of uranium atoms in q-bcc lattice correspond to the bct structure, which is energetically favourable due to formation of short U-U bonds. Transition from bct to q-bcc could be considered as ferro-to paraelastic transition of order-disorder type. The temperature of transition depends on Mo concentration. For pure uranium it is equal to about 700 K, which is well below than the upper boundary of the stability region of the α-U phase. Due to this reason, bct phase is observed only in uranium alloys containing metals with low solubility in α-U.
Atomistic simulations of highly conductive molecular transport junctions under realistic conditions
French, William R.
2013-01-01
We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.
Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state
Energy Technology Data Exchange (ETDEWEB)
Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D., E-mail: alejandro.rey@mcgill.ca [Department of Chemical Engineering, McGill University, Montreal H3A 0C5 (Canada)
2016-08-15
This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.
Machine learning of correlated dihedral potentials for atomistic molecular force fields.
Friederich, Pascal; Konrad, Manuel; Strunk, Timo; Wenzel, Wolfgang
2018-02-07
Computer simulation increasingly complements experimental efforts to describe nanoscale structure formation. Molecular mechanics simulations and related computational methods fundamentally rely on the accuracy of classical atomistic force fields for the evaluation of inter- and intramolecular energies. One indispensable component of such force fields, in particular for large organic molecules, is the accuracy of molecule-specific dihedral potentials which are the key determinants of molecular flexibility. We show in this work that non-local correlations of dihedral potentials play a decisive role in the description of the total molecular energy-an effect which is neglected in most state-of-the-art dihedral force fields. We furthermore present an efficient machine learning approach to compute intramolecular conformational energies. We demonstrate with the example of α-NPD, a molecule frequently used in organic electronics, that this approach outperforms traditional force fields by decreasing the mean absolute deviations by one order of magnitude to values smaller than 0.37 kcal/mol (16.0 meV) per dihedral angle.
Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state
Directory of Open Access Journals (Sweden)
Thomas M. Vlasic
2016-08-01
Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.
Phonon-eigenspectrum-based formulation of the atomistic Green's function method
Sadasivam, Sridhar; Waghmare, Umesh V.; Fisher, Timothy S.
2017-11-01
While the atomistic Green's function (AGF) method has the potential to compute spectrally resolved phonon transport across interfaces, most prior formulations of the AGF method provide only the total phonon transmission function that includes contributions from all phonon branches or channels. In this work, we present a formulation of the conventional AGF technique in terms of phonon eigenspectra that provides a natural decomposition of the total transmission function into contributions from various phonon modes. The method involves the use of Dyson and Lippmann-Schwinger equations to determine surface Green's functions from the phonon eigenspectrum of the bulk, and establishes a direct connection between the transmission function and the bulk phonon spectra of the materials forming the interface. We elucidate our formulation of the AGF technique through its application to a microscopic picture of phonon mode conversion at Si-Ge interfaces with atomic intermixing. Intermixing of atoms near the interface is shown to increase the phase space available for phonon mode conversion and to enhance thermal interface conductance at moderate levels of atomic mixing. The eigenspectrum-based AGF method should be useful in determination of microscopic mechanisms of phonon scattering and identification of the specific modes that dominate thermal transport across an interface.
Mapping the Atomistic Structure of Graded Core/Shell Colloidal Nanocrystals.
Yarema, Maksym; Xing, Yunhua; Lechner, Rainer T; Ludescher, Lukas; Dordevic, Nikola; Lin, Weyde M M; Yarema, Olesya; Wood, Vanessa
2017-09-15
Engineering the compositional gradient for core/shell semiconductor nanocrystals improves their optical properties. To date, however, the structure of graded core/shell nanocrystal emitters has only been qualitatively described. In this paper, we demonstrate an approach to quantify nanocrystal structure, selecting graded Ag-In-Se/ZnSe core/shell nanocrystals as a proof-of-concept material. A combination of multi-energy small-angle X-ray scattering and electron microscopy techniques enables us to establish the radial distribution of ZnSe with sub-nanometer resolution. Using ab initio shape-retrieval analysis of X-ray scattering spectra, we further determine the average shape of nanocrystals. These results allow us to generate three-dimensional, atomistic reconstructions of graded core/shell nanocrystals. We use these reconstructions to calculate solid-state Zn diffusion in the Ag-In-Se nanocrystals and the lattice mismatch between nanocrystal monolayers. Finally, we apply these findings to propose design rules for optimal shell structure and record-luminescent core/shell nanocrystals.
Prediction of TF target sites based on atomistic models of protein-DNA complexes
Directory of Open Access Journals (Sweden)
Collado-Vides Julio
2008-10-01
Full Text Available Abstract Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.
Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling.
Lupala, Cecylia S; Rasaeifar, Bahareh; Gomez-Gutierrez, Patricia; Perez, Juan J
2017-08-14
Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.
Development and assessment of atomistic models for predicting static friction coefficients
Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.
2016-08-01
The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.
Ash'arite's atomistic conception of the physical world: A restatement
Pozi, Firdaus; Mohamed, Faizal; Othman, Mohd Yusof
2013-11-01
Atomism plays an important role in the history of human thought. It can be traced back from Democritus atomos in the 500 BC to particle physics and quantum theory in the 21st century. However, as it being rejected and developed in the course of history of science, it still brings the fundamental question that perplexes physicists. It gives the views that the world is eternal; that the laws of nature is immutable and eternal therefore all phenomena can be determined through the laws and that there is no reality behind the quantum world. In this paper, we shall briefly describe all these three views on the nature of the physical world or universe and this include on the nature of matter. Then, we shall explain our stand on those conceptions based on the Ash'arites atomistic conception of the physical world. We hope this paper can shed a light on several fundamental issues in the conception of the universe and gives the proper response to them.
Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.
2017-05-01
Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.
Atomistic study on dopant-distributions in realistically sized, highly P-doped Si nanowires.
Ryu, Hoon; Kim, Jongseob; Hong, Ki-Ha
2015-01-14
The dependency of dopant-distributions on channel diameters in realistically sized, highly phosphorus-doped silicon nanowires is investigated with an atomistic tight-binding approach coupled to self-consistent Schrödinger-Poisson simulations. By overcoming the limit in channel sizes and doping densities of previous studies, this work examines electronic structures and electrostatics of free-standing circular silicon nanowires that are phosphorus-doped with a high density of ∼ 2 × 10(19) cm(-3) and have 12 nm-28 nm cross-sections. Results of analysis on the channel energy indicate that the uniformly distributed dopant profile would be hardly obtained when the nanowire cross-section is smaller than 20 nm. Insufficient room to screen donor ions and shallower impurity bands are the primary reasons of the nonuniform dopant-distributions in smaller nanowires. Being firmly connected to the recent experimental study (Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 15254-15258), this work establishes the first theoretical framework for understanding dopant-distributions in over-10 nm highly doped silicon nanowires.
Tseng, Frank; Simsek, Ergun; Gunlycke, Daniel
2015-03-01
Monolayer transition-metal dichalcogenides form a direct bandgap predicted in the visible regime making them attractive host materials for various electronic and optoelectronic applications. Due to a weak dielectric screening in these materials, strongly bound electron-hole pairs or excitons have binding energies up to at least several hundred meV's. While the conventional wisdom is to think of excitons as hydrogen-like quasi-particles, we show that the hydrogen model breaks down for these experimentally observed strongly bound, room-temperature excitons. To capture these non-hydrogen-like photo-excitations, we introduce an atomistic model for excitons that predicts both bright excitons and dark excitons, and their broken degeneracy in these two-dimensional materials. For strongly bound exciton states, the lattice potential significantly distorts the envelope wave functions, which affects predicted exciton peak energies. The combination of large binding energies and non-degeneracy of exciton states in monolayer transition metal dichalogendies may furthermore be exploited in room temperature applications where prolonged exciton lifetimes are necessary. This work has been funded by the Office of Naval Research (ONR), directly and through the Naval Research Laboratory (NRL). F.T and E.S acknowledge support from NRL through the NRC Research Associateship Program and ONR Summer Faculty Program, respectively.
Atomistic Modeling of Mechanical Loss in Pure and Doped Amorphous Oxides
Trinastic, Jonathan; Hamdan, Rashid; Cheng, Hai-Ping
2014-03-01
The mechanical dissipation in the oxide coatings of many precision measurement systems is a major source of thermal noise that limits the performance of such devices. A good candidate for a coating material to reduce the mechanical loss is tantala (Ta2O5) doped with titania (TiO2). Here, we numerically calculate the mechanical loss (internal friction) in these and other promising oxides based on the double well model. Using classical, atomistic molecular dynamics simulations, we estimate the density of double wells in the energy landscape of the amorphous oxides and the distribution of barrier heights, in addition to the deformation potentials, the elastic constants and vibrational frequencies at both the bottom of the potential wells and at the saddle points, all of which are relevant to the internal friction calculation. We use two versions of the bisection method to find the double well densities and distributions. All methods used in these calculations are implemented in DL-POLY molecular dynamics simulation software. These calculations will provide experimentalists with a better guide into which material combinations might be better choice for reducing the mechanical loss.
Bondi, Robert J.; Fox, Brian P.; Marinella, Matthew J.
2016-03-01
First-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influence on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.
Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2
Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.
2012-01-01
Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.
The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.
Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele
2017-09-14
In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.
Directory of Open Access Journals (Sweden)
Michael J. Leamy
2011-12-01
Full Text Available Dispersion calculations are presented for cylindrical carbon nanotubes using a manifold-based continuum-atomistic finite element formulation combined with Bloch analysis. The formulated finite elements allow any (n,m chiral nanotube, or mixed tubes formed by periodically-repeating heterojunctions, to be examined quickly and accurately using only three input parameters (radius, chiral angle, and unit cell length and a trivial structured mesh, thus avoiding the tedious geometry generation and energy minimization tasks associated with ab initio and lattice dynamics-based techniques. A critical assessment of the technique is pursued to determine the validity range of the resulting dispersion calculations, and to identify any dispersion anomalies. Two small anomalies in the dispersion curves are documented, which can be easily identified and therefore rectified. They include difficulty in achieving a zero energy point for the acoustic twisting phonon, and a branch veering in nanotubes with nonzero chiral angle. The twisting mode quickly restores its correct group velocity as wavenumber increases, while the branch veering is associated with a rapid exchange of eigenvectors at the veering point, which also lessens its impact. By taking into account the two noted anomalies, accurate predictions of acoustic and low-frequency optical branches can be achieved out to the midpoint of the first Brillouin zone.
Mukherjee, Sushovan; Gopalakrishnan, S.
2017-04-01
Grapahene is a two dimensional allotrope of carbon. Since the onset of current century, particularly, upon successful exfoliation of single layer graphene, it has received significant research attention because of some of the extreme mechanical, thermal, electromagnetic and optical properties it exhibits. As various applications of graphene have been envisioned and their realizations attempted, dynamic characteristics of graphene also became an extremely important field of study. Based on solid state physics and first principle analysis, dispersion relationship of graphene has been computed using various methods. Some of these methods rely on various inter atomic potentials and force-fields. An approximate technique of mechanical characterization involves atomisticcontinuum modeling of carbon carbon bonds in graphene and its rolled 1D form carbon nanotube. In this technique, the carbon-carbon bonds are modeled as 1D frame elements. The equivalence of energies in various modes of the actual structure and the equivalent mechanical system has led to specification of various model parameters. Here, based on atomistic continuum method, we attempt to compute the dispersion relationship accounting for the bonded interactions and the next nearest non-bonded interactions. For that purpose we use frequency domain spectral finite element method with pointed inertial components. It has been shown that it is possible to obtain the dispersion relationship close to the one computed using ab-initio method.
Atomistic simulations of CO2 and N2 within cage-type silica zeolites.
Madison, Lindsey; Heitzer, Henry; Russell, Colin; Kohen, Daniela
2011-03-01
The behavior of CO(2) and N(2), both as single components and as binary mixtures, in two cage-type silica zeolites was studied using atomistic simulations. The zeolites considered, ITQ-3 and paradigm cage-type zeolite ZK4 (the all-silica analog of LTA), were chosen so that the principles illustrated can be generalized to other adsorbent/adsorbate systems with similar topology and types of interactions. N(2) was chosen both because of the potential uses of N(2)/CO(2) separations and because it differs from CO(2) most significantly in the magnitude of its Coulombic interactions with zeolites. Despite similarities between N(2) and CO(2) diffusion in other materials, we show here that the diffusion of CO(2) within cage-type zeolites is dominated by an energy barrier to diffusion located at the entrance to the narrow channels connecting larger cages. This barrier originates in Coulombic interactions between zeolites and CO(2)'s quadrupole and results in well-defined orientations for the diffusing molecules. Furthermore, CO(2)'s favorable electrostatic interactions with the zeolite framework result in preferential binding in the windows between cages. N(2)'s behavior, in contrast, is more consistent with that of molecules previously studied. Our analysis suggests that CO(2)'s behavior might be common for adsorbates with quadrupoles that interact strongly with a material that has narrow windows between cages.
Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.
2016-01-01
DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.
Atomistic investigation on the detachment of oil molecules from defective alumina surface
Xie, W. K.; Sun, Y. Z.; Liu, H. T.
2017-12-01
The mechanism of oil detachment from defective alumina surface in aqueous solution was investigated via atomistic molecular dynamics (MD) simulations. Special attention was focused on the effect of surface defect on the oil detachment. Our simulation results suggest that compared with perfect Al2O3 surface, defective substrate surface provides much more sites for the adsorption of oil molecules, thus it has higher oil adsorption energy. However, higher oil-solid adsorption energy does not mean that oil contaminants are much more difficult to be detached. It is found that surface defect could induce the spontaneous imbibition of water molecules, effectively promoting the detachment of oil molecules. Thus, compared with perfect alumina surface, the detachment of oil molecules from defective alumina surface tends to be much easier. Moreover, surface defect could lead to the oil residues inside surface defect. In water solution, the entire detachment process of oil molecules on defective surface consists of following stages, including the early detachment of oil molecules inside surface defect induced by capillary-driven spontaneous imbibition of water molecules, the following conformational change of oil molecules on topmost surface and the final migration of detached oil molecules from solid surface. These findings may help to sufficiently enrich the removal mechanism of oil molecules adhered onto defective solid surface.
Use of Monte Carlo Methods in brachytherapy; Uso del metodo de Monte Carlo en braquiterapia
Energy Technology Data Exchange (ETDEWEB)
Granero Cabanero, D.
2015-07-01
The Monte Carlo method has become a fundamental tool for brachytherapy dosimetry mainly because no difficulties associated with experimental dosimetry. In brachytherapy the main handicap of experimental dosimetry is the high dose gradient near the present sources making small uncertainties in the positioning of the detectors lead to large uncertainties in the dose. This presentation will review mainly the procedure for calculating dose distributions around a fountain using the Monte Carlo method showing the difficulties inherent in these calculations. In addition we will briefly review other applications of the method of Monte Carlo in brachytherapy dosimetry, as its use in advanced calculation algorithms, calculating barriers or obtaining dose applicators around. (Author)
Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules
Lester, William A; Reynolds, PJ
1994-01-01
This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n
On the use of stochastic approximation Monte Carlo for Monte Carlo integration
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.
Solid 4He and the diffusion Monte Carlo method: A study of their properties
Rugeles, E. J.; Ujevic, Sebastian; Vitiello, S. A.
2017-10-01
Properties of helium atoms in the solid phase are investigated using the multiweight diffusion Monte Carlo method. Two different importance function transformations are used in two series of independent calculations. The kinetic energy is estimated for both the solid and liquid phases of 4He. We estimate the melting and freezing densities, among other properties of interest. Our estimates are compared with experimental values. We discuss why walkers biased by two distinctly different guiding functions do not lead to noticeable changes in the reported results. Criticisms concerning the bias introduced into our estimates by population control and system size effects are considered.
About implementing a Monte Carlo simulation algorithm for enzymatic reactions in crowded media
Directory of Open Access Journals (Sweden)
ADRIANA ISVORAN
2006-01-01
Full Text Available In this paper, several aspects of implementing a Monte Carlo simulation algorithm for studying the Michaelis–Menten mechanism of enzymatic reactions in crowded media are presented. Using a two dimensional lattice with obstacles, it is shown how the initial distribution of the reactants and obstacles on the lattice affects the values of the rate coefficients and the concentration of the reactants. The influence of the number of considered nearest neighbours and of the obstacle concentration on the values of the rate coefficients is also demonstrated. The results strongly suggest fractal kinetics for enzyme reactions in crowded media.
A kinetic theory of micromagnetic time evolution
Energy Technology Data Exchange (ETDEWEB)
Parker, G.J., E-mail: gregory.parker@hgst.com [HGST, 3904 Yueba Buena Rd., San Jose, CA 95135 (United States); Hitchon, W.N.G. [Department of Electrical and Computer Engineering, University of Wisconsin–Madison, Madison, WI 53706 (United States)
2013-11-08
A semi-analytic description of recording media grains' magnetization flipping in a magnetic field provides hysteresis loops, efficiently, with all parameters found by following orbits, and in close agreement with existing results. Integrating the Landau–Lifshitz–Gilbert (LLG) equations numerically gives the average energy diffusion coefficient D{sub ϵ}, energy loss rate a{sub ϵ} and the barrier height which must be overcome. These allow solution of the kinetic equation for the probability density f and the escape rate γ of a grain trapped in an energy well, as well as other, similar, very stiff systems. γ is used in Monte Carlo simulation of hysteresis. The essential physics governing the grains' behavior is outlined.
A kinetic theory of micromagnetic time evolution
Parker, G. J.; Hitchon, W. N. G.
2013-11-01
A semi-analytic description of recording media grains' magnetization flipping in a magnetic field provides hysteresis loops, efficiently, with all parameters found by following orbits, and in close agreement with existing results. Integrating the Landau-Lifshitz-Gilbert (LLG) equations numerically gives the average energy diffusion coefficient Dɛ, energy loss rate aɛ and the barrier height which must be overcome. These allow solution of the kinetic equation for the probability density f and the escape rate γ of a grain trapped in an energy well, as well as other, similar, very stiff systems. γ is used in Monte Carlo simulation of hysteresis. The essential physics governing the grains' behavior is outlined.
Scalable Domain Decomposed Monte Carlo Particle Transport
Energy Technology Data Exchange (ETDEWEB)
O' Brien, Matthew Joseph [Univ. of California, Davis, CA (United States)
2013-12-05
In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation.
Monte Carlo studies of uranium calorimetry
Energy Technology Data Exchange (ETDEWEB)
Brau, J.; Hargis, H.J.; Gabriel, T.A.; Bishop, B.L.
1985-01-01
Detailed Monte Carlo calculations of uranium calorimetry are presented which reveal a significant difference in the responses of liquid argon and plastic scintillator in uranium calorimeters. Due to saturation effects, neutrons from the uranium are found to contribute only weakly to the liquid argon signal. Electromagnetic sampling inefficiencies are significant and contribute substantially to compensation in both systems. 17 references.
Quantum algorithm for exact Monte Carlo sampling
Destainville, Nicolas; Georgeot, Bertrand; Giraud, Olivier
2010-01-01
We build a quantum algorithm which uses the Grover quantum search procedure in order to sample the exact equilibrium distribution of a wide range of classical statistical mechanics systems. The algorithm is based on recently developed exact Monte Carlo sampling methods, and yields a polynomial gain compared to classical procedures.
Monte Carlo calculations of atoms and molecules
Schmidt, K. E.; Moskowitz, J. W.
1986-06-01
The variational and Green's function Monte Carlo (GFMC) methods can treat many interesting atomic and molecular problems. These methods can give chemical accuracy for up to 10 or so electrons. The various implementations of the GFMC method, including the domain Green's function method and the short-time approximation, are discussed. Results are presented for several representative atoms and molecules.
Dynamic bounds coupled with Monte Carlo simulations
Rajabali Nejad, Mohammadreza; Meester, L.E.; van Gelder, P.H.A.J.M.; Vrijling, J.K.
2011-01-01
For the reliability analysis of engineering structures a variety of methods is known, of which Monte Carlo (MC) simulation is widely considered to be among the most robust and most generally applicable. To reduce simulation cost of the MC method, variance reduction methods are applied. This paper
An analysis of Monte Carlo tree search
CSIR Research Space (South Africa)
James, S
2017-02-01
Full Text Available Monte Carlo Tree Search (MCTS) is a family of directed search algorithms that has gained widespread attention in recent years. Despite the vast amount of research into MCTS, the effect of modifications on the algorithm, as well as the manner...
Irreversible processes kinetic theory
Brush, Stephen G
2013-01-01
Kinetic Theory, Volume 2: Irreversible Processes deals with the kinetic theory of gases and the irreversible processes they undergo. It includes the two papers by James Clerk Maxwell and Ludwig Boltzmann in which the basic equations for transport processes in gases are formulated, together with the first derivation of Boltzmann's ""H-theorem"" and a discussion of this theorem, along with the problem of irreversibility.Comprised of 10 chapters, this volume begins with an introduction to the fundamental nature of heat and of gases, along with Boltzmann's work on the kinetic theory of gases and s
National Research Council Canada - National Science Library
Fahmel Beyer, Bernd
2017-01-01
Oaxaca; Monte Albán V; Zapotecos; Mixtecos Abstract This paper focuses on the archaeology of period V at Monte Alban and the material culture associated with the Mixtecs in the central valleys of Oaxaca...
Shneidman, V. A.; Jackson, K. A.; Beatty, K. M.
2000-08-01
Large scale Monte Carlo simulations and theoretical analysis of thermodynamic properties of small clusters and large nuclei on two-dimensional Ising lattices were performed in order to test the kinetic and thermodynamic aspects of several mainstream nucleation approaches. The kinetics predicted by the classical theory (i.e. the time evolution of cluster distributions) is accurate at intermediate temperatures as long as the description relies on measured (not calculated!) equilibrium distributions and as long as coagulation between clusters can be neglected. However, the classical theory seriously overestimates the equilibrium cluster populations—this can be unambiguously demonstrated since the interfacial tensions for two-dimensional Ising systems are known exactly from the Onsager solution and from later developments. Alternatives to classical description are also considered, and ways to improve the correspondence between theory and simulations are discussed.
Directory of Open Access Journals (Sweden)
Laureau Axel
2017-01-01
Full Text Available The studies presented in this paper are performed in the general framework of transient coupled calculations with accurate neutron kinetics models able to characterize spatial decoupling in the core. An innovative fission matrix interpolation model has been developed with a correlated sampling technique associated to the Transient Fission Matrix (TFM approach. This paper presents a validation of this Monte Carlo based kinetic approach on sodium fast reactors. An application case representative of an assembly of the low void effect sodium fast reactor ASTRID is used to study the physics of this kind of system and to illustrate the capabilities provided by this approach. To validate the interpolation model developed, different comparisons have been performed with direct Monte Carlo and ERANOS deterministic S N calculations on spatial kinetics parameters (flux redistribution, reactivity estimation, etc. together with point kinetics feedback estimations.
SRD 17 NIST Chemical Kinetics Database (Web, free access) The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.
Thermal kinetic inductance detector
Cecil, Thomas; Gades, Lisa; Miceli, Antonio; Quaranta, Orlando
2016-12-20
A microcalorimeter for radiation detection that uses superconducting kinetic inductance resonators as the thermometers. The detector is frequency-multiplexed which enables detector systems with a large number of pixels.
Bénichou, O; Chevalier, C; Klafter, J; Meyer, B; Voituriez, R
2010-06-01
It has long been appreciated that the transport properties of molecules can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target-the first-passage time (FPT). Determining the FPT distribution in realistic confined geometries has until now, however, seemed intractable. Here, we calculate this FPT distribution analytically and show that transport processes as varied as regular diffusion, anomalous diffusion, and diffusion in disordered media and fractals, fall into the same universality classes. Beyond the theoretical aspect, this result changes our views on standard reaction kinetics and we introduce the concept of 'geometry-controlled kinetics'. More precisely, we argue that geometry-and in particular the initial distance between reactants in 'compact' systems-can become a key parameter. These findings could help explain the crucial role that the spatial organization of genes has in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.
Fundamentals of enzyme kinetics.
Seibert, Eleanore; Tracy, Timothy S
2014-01-01
This chapter provides a general introduction to the kinetics of enzyme-catalyzed reactions, with a focus on drug-metabolizing enzymes. A prerequisite to understanding enzyme kinetics is having a clear grasp of the meanings of "enzyme" and "catalysis." Catalysts are reagents that can increase the rate of a chemical reaction without being consumed in the reaction. Enzymes are proteins that form a subset of catalysts. These concepts are further explored below.
Electrochemical kinetics theoretical aspects
Vetter, Klaus J
1967-01-01
Electrochemical Kinetics: Theoretical Aspects focuses on the processes, methodologies, reactions, and transformations in electrochemical kinetics. The book first offers information on electrochemical thermodynamics and the theory of overvoltage. Topics include equilibrium potentials, concepts and definitions, electrical double layer and electrocapillarity, and charge-transfer, diffusion, and reaction overvoltage. Crystallization overvoltage, total overvoltage, and resistance polarization are also discussed. The text then examines the methods of determining electrochemical reaction mechanisms
Evaluation of Monte Carlo tools for high energy atmospheric physics
Rutjes, Casper; Sarria, David; Broberg Skeltved, Alexander; Luque, Alejandro; Diniz, Gabriel; Østgaard, Nikolai; Ebert, Ute
2016-11-01
The emerging field of high energy atmospheric physics (HEAP) includes terrestrial gamma-ray flashes, electron-positron beams and gamma-ray glows from thunderstorms. Similar emissions of high energy particles occur in pulsed high voltage discharges. Understanding these phenomena requires appropriate models for the interaction of electrons, positrons and photons of up to 40 MeV energy with atmospheric air. In this paper, we benchmark the performance of the Monte Carlo codes Geant4, EGS5 and FLUKA developed in other fields of physics and of the custom-made codes GRRR and MC-PEPTITA against each other within the parameter regime relevant for high energy atmospheric physics. We focus on basic tests, namely on the evolution of monoenergetic and directed beams of electrons, positrons and photons with kinetic energies between 100 keV and 40 MeV through homogeneous air in the absence of electric and magnetic fields, using a low energy cutoff of 50 keV. We discuss important differences between the results of the different codes and provide plausible explanations. We also test the computational performance of the codes. The Supplement contains all results, providing a first benchmark for present and future custom-made codes that are more flexible in including electrodynamic interactions.
Evaluation of Monte Carlo tools for high energy atmospheric physics
Directory of Open Access Journals (Sweden)
C. Rutjes
2016-11-01
Full Text Available The emerging field of high energy atmospheric physics (HEAP includes terrestrial gamma-ray flashes, electron–positron beams and gamma-ray glows from thunderstorms. Similar emissions of high energy particles occur in pulsed high voltage discharges. Understanding these phenomena requires appropriate models for the interaction of electrons, positrons and photons of up to 40 MeV energy with atmospheric air. In this paper, we benchmark the performance of the Monte Carlo codes Geant4, EGS5 and FLUKA developed in other fields of physics and of the custom-made codes GRRR and MC-PEPTITA against each other within the parameter regime relevant for high energy atmospheric physics. We focus on basic tests, namely on the evolution of monoenergetic and directed beams of electrons, positrons and photons with kinetic energies between 100 keV and 40 MeV through homogeneous air in the absence of electric and magnetic fields, using a low energy cutoff of 50 keV. We discuss important differences between the results of the different codes and provide plausible explanations. We also test the computational performance of the codes. The Supplement contains all results, providing a first benchmark for present and future custom-made codes that are more flexible in including electrodynamic interactions.
Estimation of overland flow metrics at semiarid condition: Patagonian Monte
Rossi, M. J.; Ares, J. O.
2012-05-01
Water infiltration and overland flow (WIOF) processes are relevant in considering water partition among plant life forms, the sustainability of vegetation and the design of sustainable hydrological management. WIOF processes in arid and semiarid regions present regional characteristic trends imposed by the prevailing physical conditions of the upper soil as evolved under water-limited climate. A set of plot-scale field experiments at the semi-arid Patagonian Monte (Argentina) was performed in order to estimate infiltration-overland descriptive flow parameters. The micro-relief of undisturbed field plots at z-scale depression storage intensity. The experimental procedure presented supplies plot-scale estimates of overland flow and infiltration intensities at various intensities of water input which can be incorporated in larger-scale hydrological grid-models of arid regions. Findings were: (1) Overland flow velocities as well as infiltration-overland flow mass balances are consistently modelled by considering variable infiltration rates corresponding to depression storage and/or non-ponded areas. (2) The statistical relations presented allow the estimation of theoretical hydrodynamic parameters (Chezy's frictional C, average overland flow depth d*) through measurable characteristics of the surface soil and overland flow kinetics. (3) A protocol of field experiments and coupled time-distributed modelling to 1-2 above is described. The methodology and results obtained in this study are probably relevant to similar arid-semiarid areas of the world.
Monte Carlo simulation of three-dimensional islands
Tan, Sovirith; Lam, Pui-Man
1999-09-01
The usual kinetic Monte Carlo method is adapted, to treat off-lattice problems of multilayer growth (coverage θ>1) by molecular-beam epitaxy. This method takes into account the Schwoebel barrier, which comes out as a result of the choice of the potential interaction between the atoms. This method allows a free choice of the lattice mismatch, temperature, deposition flux rate, and interfacial energies. A particular choice of these parameters leads to the three-dimensional (3D) (Volmer-Weber) growth mode, whereas another choice of these parameters leads to the 2D-3D growth mode (Stranski-Krastanov). The 3D islands seem to obey scaling only approximately. Using this method, the surface stress inside a substrate and a (pyramidal) coherent 3D island is computed. Strong relaxations appear, not only at the edges of the 3D island (which is expected), but also in the proximity of the edges, and inside the 3D island. These particular sites inside the 3D island are located just beneath a step site of the upper layer. Moreover, these particular sites develop strong corrugations, which later are propagating along the layer. Strain-induced modulation of layers is thermally activated, so the steps could act as defects and nucleation sites for propagating roughness, in agreement with some theories and experimental facts.
Decohesion Kinetics of PEDOT:PSS Conducting Polymer Films
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.
Quantum instanton evaluation of the kinetic isotope effects
Energy Technology Data Exchange (ETDEWEB)
Vanicek, Jiri; Miller, William H.; Castillo, Jesus F.; Aoiz, F.Javier
2005-04-19
A general quantum-mechanical method for computing kinetic isotope effects is presented. The method is based on the quantum instanton approximation for the rate constant and on the path integral Metropolis Monte-Carlo evaluation of the Boltzmann operator matrix elements. It computes the kinetic isotope effect directly, using a thermodynamic integration with respect to the mass of the isotope, thus avoiding the more computationally expensive process of computing the individual rate constants. The method is more accurate than variational transition-state theories or the semiclassical instanton method since it does not assume a single reaction path and does not use a semiclassical approximation of the Boltzmann operator. While the general Monte-Carlo implementation makes the method accessible to systems with a large number of atoms, we present numerical results for the Eckart barrier and for the collinear and full three-dimensional isotope variants of the hydrogen exchange reaction H+H{sub 2} {yields} H{sub 2}+H. In all seven test cases, for temperatures between 250 K and 600 K, the error of the quantum instanton approximation for the kinetic isotope effects is less than {approx}10%.
Gowdy, James; Batchelor, Matthew; Neelov, Igor; Paci, Emanuele
2017-10-19
The kinetics of loop formation, i.e., the occurrence of contact between two atoms of a polypeptide, remains the focus of continuing interest. One of the reasons is that contact formation is the elementary event underlying processes such as folding and binding. More importantly, it is experimentally measurable and can be predicted theoretically for ideal polymers. Deviations from single exponential kinetics have sometimes been interpreted as a signature of rugged, protein-like, free energy landscapes. Here we present simulations, with different atomistic models, of short peptides with varied structural propensity, and of a structured protein. Results show exponential contact formation kinetics (or relaxation) at long times, and a power law relaxation at very short times. At intermediate times, a deviation from either power law or simple exponential kinetics is observed that appears to be characteristic of polypeptides with either specific or nonspecific attractive interactions but disappears if attractive interactions are absent. Our results agree with recent experimental measurements on peptides and proteins and offer a comprehensive interpretation for them.
Varga, Matthew; Schwartz, Steven
2015-03-01
The experimental determination of kinetic isotope effects in enzymatic systems can be a difficult, time-consuming, and expensive process. In this study, we use the Chandler-Bolhius method for the determination of reaction rates within transition path sampling (rTPS) to determine the primary kinetic isotope effect in yeast alcohol dehydrogenase (YADH). In this study, normal mode centroid molecular dynamics (CMD) was applied to the transferring hydride/deuteride in order to correctly incorporate quantum effects into the molecular simulations. Though previous studies have used rTPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. Due to the fact that particle transfer is not wholly indicative of the chemical step, this method cannot be used to determine reaction rate constants in YADH. However, it is possible to determine the transition rate constant of the particle transfer, and the kinetic isotope effect of that step. This method provides a set of tools to determine kinetic isotope effects with the atomistic detail of molecular simulations.
Atomistic tensile deformation mechanisms of Fe with gradient nano-grained structure
Directory of Open Access Journals (Sweden)
Wenbin Li
2015-08-01
Full Text Available Large-scale molecular dynamics (MD simulations have been performed to investigate the tensile properties and the related atomistic deformation mechanisms of the gradient nano-grained (GNG structure of bcc Fe (gradient grains with d from 25 nm to 105 nm, and comparisons were made with the uniform nano-grained (NG structure of bcc Fe (grains with d = 25 nm. The grain size gradient in the nano-scale converts the applied uniaxial stress to multi-axial stresses and promotes the dislocation behaviors in the GNG structure, which results in extra hardening and flow strength. Thus, the GNG structure shows slightly higher flow stress at the early plastic deformation stage when compared to the uniform NG structure (even with smaller grain size. In the GNG structure, the dominant deformation mechanisms are closely related to the grain sizes. For grains with d = 25 nm, the deformation mechanisms are dominated by GB migration, grain rotation and grain coalescence although a few dislocations are observed. For grains with d = 54 nm, dislocation nucleation, propagation and formation of dislocation wall near GBs are observed. Moreover, formation of dislocation wall and dislocation pile-up near GBs are observed for grains with d = 105 nm, which is the first observation by MD simulations to our best knowledge. The strain compatibility among different layers with various grain sizes in the GNG structure should promote the dislocation behaviors and the flow stress of the whole structure, and the present results should provide insights to design the microstructures for developing strong-and-ductile metals.
Directory of Open Access Journals (Sweden)
Tarja Äijänen
2014-11-01
Full Text Available Cholesteryl ester transfer protein (CETP mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity and thereby raise high density lipoprotein (HDL-cholesterol and decrease low density lipoprotein (LDL-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site of anacetrapib turns out to reside in the tunnel inside CETP, near the residues surrounding the N-terminal opening. Free energy calculations show that when anacetrapib resides in this area, it hinders the ability of cholesteryl ester to diffuse out from CETP. The simulations further bring out the ability of anacetrapib to regulate the structure-function relationships of phospholipids and helix X, the latter representing the structural region of CETP important to the process of neutral lipid exchange with lipoproteins. Altogether, the simulations propose CETP inhibition to be realized when anacetrapib is transferred into the lipid binding pocket. The novel insight gained in this study has potential use in the development of new molecular agents capable of preventing the progression of cardiovascular diseases.
Directory of Open Access Journals (Sweden)
Victor M. Nazarychev
2017-10-01
Full Text Available Crystallization of all-aromatic heterocyclic polymers typically results in an improvement of their thermo-mechanical properties. Nucleation agents may be used to promote crystallization, and it is well known that the incorporation of nanoparticles, and in particular carbon-based nanofillers, may induce or accelerate crystallization through nucleation. The present study addresses the structural properties of polyetherimide-based nanocomposites and the initial stages of polyetherimide crystallization as a result of single-walled carbon nanotube (SWCNT incorporation. We selected two amorphous thermoplastic polyetherimides ODPA-P3 and aBPDA-P3 based on 3,3′,4,4′-oxydiphthalic dianhydride (ODPA, 2,3′,3,4′-biphenyltetracarboxylic dianhydride (aBPDA and diamine 1,4-bis[4-(4-aminophenoxyphenoxy]benzene (P3 and simulated the onset of crystallization in the presence of SWCNTs using atomistic molecular dynamics. For ODPA-P3, we found that the planar phthalimide and phenylene moieties show pronounced ordering near the CNT (carbon nanotube surface, which can be regarded as the initial stage of crystallization. We will discuss two possible mechanisms for ODPA-P3 crystallization in the presence of SWCNTs: the spatial confinement caused by the CNTs and π–π interactions at the CNT-polymer matrix interface. Based on our simulation results, we propose that ODPA-P3 crystallization is most likely initiated by favorable π–π interactions between the carbon nanofiller surface and the planar ODPA-P3 phthalimide and phenylene moieties.
Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank
2017-10-01
Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.
Mechanics of low-dimensional carbon nanostructures: Atomistic, continuum, and multi-scale approaches
Mahdavi, Arash
A new multiscale modeling technique called the Consistent Atomic-scale Finite Element (CAFE) method is introduced. Unlike traditional approaches for linking the atomic structure to its equivalent continuum, this method directly connects the atomic degrees of freedom to a reduced set of finite element degrees of freedom without passing through an intermediate homogenized continuum. As a result, there is no need to introduce stress and strain measures at the atomic level. The Tersoff-Brenner interatomic potential is used to calculate the consistent tangent stiffness matrix of the structure. In this finite element formulation, all local and non-local interactions between carbon atoms are taken into account using overlapping finite elements. In addition, a consistent hierarchical finite element modeling technique is developed for adaptively coarsening and refining the mesh over different parts of the model. This process is consistent with the underlying atomic structure and, by refining the mesh to the scale of atomic spacing, molecular dynamic results can be recovered. This method is valid across the scales and can be used to concurrently model atomistic and continuum phenomena so, in contrast with most other multi-scale methods, there is no need to introduce artificial boundaries for coupling atomistic and continuum regions. Effect of the length scale of the nanostructure is also included in the model by building the hierarchy of elements from bottom up using a finite size atom cluster as the building block. To be consistent with the bravais multi-lattice structure of sp2-bonded carbon, two independent displacement fields are used for reducing the order of the model. Sparse structure of the stiffness matrix of these nanostructures is exploited to reduce the memory requirement and to speed up the formation of the system matrices and solution of the equilibrium equations. Applicability of the method is shown with several examples of the nonlinear mechanics of carbon
Calculation of the Effective Delayed Neutron Fraction by Deterministic and Monte Carlo Methods
Directory of Open Access Journals (Sweden)
M. Carta
2011-01-01
Full Text Available The studies on Accelerator-Driven Systems (ADSs have renewed the interest in the theoretical and computational evaluation of the main integral parameters characterizing subcritical systems (e.g., reactivity, effective delayed neutron fraction βeff, and mean prompt neutron generation time. In particular, some kinetic parameters, as the effective delayed neutron fraction, are evaluated in Monte Carlo codes by formulations which do not require the calculation of the adjoint flux. This paper is focused on a theoretical and computational analysis about how the different βeff definitions are connected and which are the approximations inherent to the Monte Carlo definition with respect to the standard definition involving weighted integrals. By means of a refined transport computational analysis carried out in a coherent and consistent way, that is, using the same deterministic code and neutron data library for the βeff evaluation in different ways, the theoretical analysis is numerically confirmed. Both theoretical and numerical results confirm the effectiveness of the Monte Carlo βeff evaluation, at least in cases where spectral differences between total and prompt fluxes are negligible with respect to the value of the functionals entering the classical βeff formulation.
CPMC-Lab: A MATLAB package for Constrained Path Monte Carlo calculations
Nguyen, Huy; Shi, Hao; Xu, Jie; Zhang, Shiwei
2014-12-01
We describe CPMC-Lab, a MATLAB program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to ab initio calculations in molecules and solids. The present package implements the full ground-state constrained-path Monte Carlo (CPMC) method in MATLAB with a graphical interface, using the Hubbard model as an example. The package can perform calculations in finite supercells in any dimensions, under periodic or twist boundary conditions. Importance sampling and all other algorithmic details of a total energy calculation are included and illustrated. This open-source tool allows users to experiment with various model and run parameters and visualize the results. It provides a direct and interactive environment to learn the method and study the code with minimal overhead for setup. Furthermore, the package can be easily generalized for auxiliary-field quantum Monte Carlo (AFQMC) calculations in many other models for correlated electron systems, and can serve as a template for developing a production code for AFQMC total energy calculations in real materials. Several illustrative studies are carried out in one- and two-dimensional lattices on total energy, kinetic energy, potential energy, and charge- and spin-gaps.
Hypothesis testing of scientific Monte Carlo calculations
Wallerberger, Markus; Gull, Emanuel
2017-11-01
The steadily increasing size of scientific Monte Carlo simulations and the desire for robust, correct, and reproducible results necessitates rigorous testing procedures for scientific simulations in order to detect numerical problems and programming bugs. However, the testing paradigms developed for deterministic algorithms have proven to be ill suited for stochastic algorithms. In this paper we demonstrate explicitly how the technique of statistical hypothesis testing, which is in wide use in other fields of science, can be used to devise automatic and reliable tests for Monte Carlo methods, and we show that these tests are able to detect some of the common problems encountered in stochastic scientific simulations. We argue that hypothesis testing should become part of the standard testing toolkit for scientific simulations.
No-compromise reptation quantum Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Yuen, W K [Department of Mathematics, Brock University, St. Catharines, ON L2S 3A1 (Canada); Farrar, Thomas J [Department of Mathematics, Brock University, St. Catharines, ON L2S 3A1 (Canada); Rothstein, Stuart M [Departments of Chemistry and Physics, Brock University, St. Catharines, ON L2S 3A1 (Canada)
2007-07-06
Since its publication, the reptation quantum Monte Carlo algorithm of Baroni and Moroni (1999 Phys. Rev. Lett. 82 4745) has been applied to several important problems in physics, but its mathematical foundations are not well understood. We show that their algorithm is not of typical Metropolis-Hastings type, and we specify conditions required for the generated Markov chain to be stationary and to converge to the intended distribution. The time-step bias may add up, and in many applications it is only the middle of a reptile that is the most important. Therefore, we propose an alternative, 'no-compromise reptation quantum Monte Carlo' to stabilize the middle of the reptile. (fast track communication)
Multilevel sequential Monte-Carlo samplers
Jasra, Ajay
2016-01-05
Multilevel Monte-Carlo methods provide a powerful computational technique for reducing the computational cost of estimating expectations for a given computational effort. They are particularly relevant for computational problems when approximate distributions are determined via a resolution parameter h, with h=0 giving the theoretical exact distribution (e.g. SDEs or inverse problems with PDEs). The method provides a benefit by coupling samples from successive resolutions, and estimating differences of successive expectations. We develop a methodology that brings Sequential Monte-Carlo (SMC) algorithms within the framework of the Multilevel idea, as SMC provides a natural set-up for coupling samples over different resolutions. We prove that the new algorithm indeed preserves the benefits of the multilevel principle, even if samples at all resolutions are now correlated.
Multilevel Monte Carlo Approaches for Numerical Homogenization
Efendiev, Yalchin R.
2015-10-01
In this article, we study the application of multilevel Monte Carlo (MLMC) approaches to numerical random homogenization. Our objective is to compute the expectation of some functionals of the homogenized coefficients, or of the homogenized solutions. This is accomplished within MLMC by considering different sizes of representative volumes (RVEs). Many inexpensive computations with the smallest RVE size are combined with fewer expensive computations performed on larger RVEs. Likewise, when it comes to homogenized solutions, different levels of coarse-grid meshes are used to solve the homogenized equation. We show that, by carefully selecting the number of realizations at each level, we can achieve a speed-up in the computations in comparison to a standard Monte Carlo method. Numerical results are presented for both one-dimensional and two-dimensional test-cases that illustrate the efficiency of the approach.
Evaluation Function Based Monte-Carlo LOA
Winands, Mark H. M.; Björnsson, Yngvi
Recently, Monte-Carlo Tree Search (MCTS) has advanced the field of computer Go substantially. Also in the game of Lines of Action (LOA), which has been dominated so far by αβ, MCTS is making an inroad. In this paper we investigate how to use a positional evaluation function in a Monte-Carlo simulation-based LOA program (MC-LOA). Four different simulation strategies are designed, called Evaluation Cut-Off, Corrective, Greedy, and Mixed. They use an evaluation function in several ways. Experimental results reveal that the Mixed strategy is the best among them. This strategy draws the moves randomly based on their transition probabilities in the first part of a simulation, but selects them based on their evaluation score in the second part of a simulation. Using this simulation strategy the MC-LOA program plays at the same level as the αβ program MIA, the best LOA-playing entity in the world.
Adaptive Monte Carlo for nuclear data evaluation
Directory of Open Access Journals (Sweden)
Schnabel Georg
2017-01-01
Full Text Available An adaptive Monte Carlo method for nuclear data evaluation is presented. A fast evaluation method based on the linearization of the nuclear model guides the adaptation of the sampling distribution towards the posterior distribution. The method is suited for parallel computation and provides detailed uncertainty information about nuclear model parameters. Especially, the posterior distribution of the model parameters is not restricted to be multivariate normal. The method is demonstrated in an evaluation of the 181Ta total cross section for incident neutrons. Future applications are as an efficient sampling scheme in the Total Monte Carlo method, and the restriction of parameter uncertainties in nuclear models by both differential and integral data.
Monte Carlo Simulation for Particle Detectors
Pia, Maria Grazia
2012-01-01
Monte Carlo simulation is an essential component of experimental particle physics in all the phases of its life-cycle: the investigation of the physics reach of detector concepts, the design of facilities and detectors, the development and optimization of data reconstruction software, the data analysis for the production of physics results. This note briefly outlines some research topics related to Monte Carlo simulation, that are relevant to future experimental perspectives in particle physics. The focus is on physics aspects: conceptual progress beyond current particle transport schemes, the incorporation of materials science knowledge relevant to novel detection technologies, functionality to model radiation damage, the capability for multi-scale simulation, quantitative validation and uncertainty quantification to determine the predictive power of simulation. The R&D on simulation for future detectors would profit from cooperation within various components of the particle physics community, and synerg...
Optimal Bayesian Experimental Design for Combustion Kinetics
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.
Stephanou, Pavlos S; Baig, Chunggi; Tsolou, Georgia; Mavrantzas, Vlasis G; Kröger, Martin
2010-03-28
The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability psi(s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed psi(s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic
Energy Technology Data Exchange (ETDEWEB)
Vitek, Vaclav
1998-08-01
The overarching goal of the research supported by this grant was investigation of the structure and properties of interfaces in multicomponent systems by atomistic modeling. Initially, the research was devoted to studies of segregation to grain boundaries in binary disordered alloys. The next step was then studies of the structure and properties of grain boundaries in ordered compounds, specifically Ni3Al and NiAl, and grain boundary segregation in these compounds in the case of off-stoichiometry. Finally, the structure of Nb/sapphire interfaces, in particular the core configurations of the misfit dislocations, was studied.
Monte Carlo methods for preference learning
DEFF Research Database (Denmark)
Viappiani, P.
2012-01-01
Utility elicitation is an important component of many applications, such as decision support systems and recommender systems. Such systems query the users about their preferences and give recommendations based on the system’s belief about the utility function. Critical to these applications is th...... is the acquisition of prior distribution about the utility parameters and the possibility of real time Bayesian inference. In this paper we consider Monte Carlo methods for these problems....
INTELLECTUAL CAPITAL VALUATION USING MONTE CARLO SIMULATION
Tarnóczi Tibor; Tóth Réka; Fenyves Veronika
2010-01-01
We present a simulation model in this paper to determine the value of intellectual capital. In frame of the simulation model we have used the Baruch Lev’s intellectual capital valuation modell.We have built in the Baruch Lev model in a two-dimensional Monte Carlo simulation modell. We have determined the intellectual capital in case of some stock exchange company. The calculation are presented in case of a selected company.
INTELLECTUAL CAPITAL VALUATION USING MONTE CARLO SIMULATION
Directory of Open Access Journals (Sweden)
Tarnóczi Tibor
2010-07-01
Full Text Available We present a simulation model in this paper to determine the value of intellectual capital. In frame of the simulation model we have used the Baruch Lev’s intellectual capital valuation modell.We have built in the Baruch Lev model in a two-dimensional Monte Carlo simulation modell. We have determined the intellectual capital in case of some stock exchange company. The calculation are presented in case of a selected company.
Efficient Monte Carlo sampling by parallel marginalization
Weare, Jonathan
2007-01-01
Markov chain Monte Carlo sampling methods often suffer from long correlation times. Consequently, these methods must be run for many steps to generate an independent sample. In this paper, a method is proposed to overcome this difficulty. The method utilizes information from rapidly equilibrating coarse Markov chains that sample marginal distributions of the full system. This is accomplished through exchanges between the full chain and the auxiliary coarse chains. Results of numerical tests o...
Handbook of Markov chain Monte Carlo
Brooks, Steve
2011-01-01
""Handbook of Markov Chain Monte Carlo"" brings together the major advances that have occurred in recent years while incorporating enough introductory material for new users of MCMC. Along with thorough coverage of the theoretical foundations and algorithmic and computational methodology, this comprehensive handbook includes substantial realistic case studies from a variety of disciplines. These case studies demonstrate the application of MCMC methods and serve as a series of templates for the construction, implementation, and choice of MCMC methodology.
Applications of Maxent to quantum Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Silver, R.N.; Sivia, D.S.; Gubernatis, J.E. (Los Alamos National Lab., NM (USA)); Jarrell, M. (Ohio State Univ., Columbus, OH (USA). Dept. of Physics)
1990-01-01
We consider the application of maximum entropy methods to the analysis of data produced by computer simulations. The focus is the calculation of the dynamical properties of quantum many-body systems by Monte Carlo methods, which is termed the Analytical Continuation Problem.'' For the Anderson model of dilute magnetic impurities in metals, we obtain spectral functions and transport coefficients which obey Kondo Universality.'' 24 refs., 7 figs.
Conical Reflection in Direct Simulation Monte Carlo
Sampson, Andrew; Payne, Adam; Somers, William; Spencer, Ross
2006-10-01
Fenix is a particle-in-cell simulation, using a Direct Simulation Monte Carlo method, and is aimed to improve the accuracy of Inductively Coupled Plasma Mass Spectrometry (ICP-MS). It currently focuses on the ICP-MS first expansion region through a supersonic nozzle in cylindrical symmetry. Due to increased complexity in Fenix, it has become necessary to solve the general conical surface reflection problem. The previous method, the new solution, and results from the enhanced simulation will be presented.
Multiple alternative substrate kinetics.
Anderson, Vernon E
2015-11-01
The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.
Unified gas-kinetic simulation of slider air bearing
Directory of Open Access Journals (Sweden)
Ruijie Wang
2014-01-01
Full Text Available The unified gas-kinetic scheme (UGKS is presented and used in this letter to study the slider air bearing problem. The UGKS solutions are first validated by comparison with direct simulation Monte Carlo results. After validation, the UGKS is used to study the air-bearing problem under different non-equilibrium conditions. On the surface of the slider, the dependency of the gas pressure and normal force on the Mach and Knudsen numbers are fully evaluated. The non-equilibrium effect on the force loading in the whole transition regime up to the free molecular limit is also studied.
Sodium dopants in helium clusters: Structure, equilibrium and submersion kinetics
Energy Technology Data Exchange (ETDEWEB)
Calvo, F. [Laboratoire Interdisciplinaire de Physique, Rue de La Piscine, Campus Saint Martin d’Hères, 38000 Grenoble (France)
2015-12-31
Alkali impurities bind to helium nanodroplets very differently depending on their size and charge state, large neutral or charged dopants being wetted by the droplet whereas small neutral impurities prefer to reside aside. Using various computational modeling tools such as quantum Monte Carlo and path-integral molecular dynamics simulations, we have revisited some aspects of the physical chemistry of helium droplets interacting with sodium impurities, including the onset of snowball formation in presence of many-body polarization forces, the transition from non-wetted to wetted behavior in larger sodium clusters, and the kinetics of submersion of small dopants after sudden ionization.
Monte Carlo simulations of disorder in ZnSn N2 and the effects on the electronic structure
Lany, Stephan; Fioretti, Angela N.; Zawadzki, Paweł P.; Schelhas, Laura T.; Toberer, Eric S.; Zakutayev, Andriy; Tamboli, Adele C.
2017-08-01
In multinary compound semiconductors, cation disorder can decisively alter the electronic properties and impact potential applications. ZnSn N2 is a ternary nitride of interest for photovoltaics, which forms in a wurtzite-derived crystal structure. In the ground state, every N anion is coordinated by two Zn and two Sn cations, thereby observing the octet rule locally. Using a motif-based model Hamiltonian, we performed Monte Carlo simulations that provide atomistic representations of ZnSn N2 with varying degrees of cation disorder. Subsequent electronic structure calculations describe the evolution of band gaps, optical properties, and carrier localization effects as a function of the disorder. We find that octet-rule conserving disorder is practically impossible to avoid but perfectly benign, with hardly any effects on the electronic structure. In contrast, a fully random cation distribution would be very detrimental, but fortunately it is energetically highly unfavorable. A degree of disorder that can realistically be expected for nonequilibrium thin-film deposition leads to a moderate band-gap reduction and to moderate carrier localization effects. Comparing the simulated structures with experimental samples grown by sputtering, we find evidence that these samples indeed incorporate a certain degree of octet-rule violating disorder, which is reflected in the x-ray diffraction and in the optical absorption spectra. This study demonstrates that the electronic properties of ZnSn N2 are dominated by changes of the local coordination environments rather than long-range ordering effects.
Erbium hydride decomposition kinetics.
Energy Technology Data Exchange (ETDEWEB)
Ferrizz, Robert Matthew
2006-11-01
Thermal desorption spectroscopy (TDS) is used to study the decomposition kinetics of erbium hydride thin films. The TDS results presented in this report are analyzed quantitatively using Redhead's method to yield kinetic parameters (E{sub A} {approx} 54.2 kcal/mol), which are then utilized to predict hydrogen outgassing in vacuum for a variety of thermal treatments. Interestingly, it was found that the activation energy for desorption can vary by more than 7 kcal/mol (0.30 eV) for seemingly similar samples. In addition, small amounts of less-stable hydrogen were observed for all erbium dihydride films. A detailed explanation of several approaches for analyzing thermal desorption spectra to obtain kinetic information is included as an appendix.
Adeleke, Oluwatoyin A; Monama, Nkwe O; Tsai, Pei-Chin; Sithole, Happy M; Michniak-Kohn, Bozena B
2016-02-01
To date, effective treatment, prophylaxis, and control of tuberculosis (TB) infection is mainly dependent on the use of drugs. However, patient noncompliance with prescribed anti-TB treatment schemes remains a major problem confronting successful pharmacotherapeutic outcomes. Thus, the development of alternative delivery systems that can improve adherence for the existing anti-TB bioactives has been intensified in recent times. The aim of this investigation was to engineer an optimal, thermodynamically stable oral film (OF) formulation containing a key anti-TB agent, pyrazinamide (PYZ), employing molecular modeling and experimental tools. Four PYZ-loaded film variants (OF 1, OF 2, OF 3, OF 4) were constructed in silico and then prepared in vitro using the Accelrys Materials Studio software and solvent casting method, respectively. Screening and selection of the optimal OF was based on the computation of the total interaction energy (ET), kinetic energy (EK), solubility parameter (S), and cohesive energy density (CED) as well as determining mass, thickness, dissolution and disintegration times, dissolution pH, drug loading capacity, and surface morphology in vitro. OF 2 was selected as the optimal formulation as it displayed the lowest ET (-8006.28 kcal/mol), dissolution time (9.96 min), disintegration time (56.49 s), and weight (39.33 mg); moderate EK (1052.98 kcal/mol); highest S (44.55 (J/cm(3))(0.5)) and CED (1.99 × 10(9) J/m(3)), slim dimension (166 μm), good and unvarying drug loading capacity (98.04%), acceptable dissolution pH (6.70), and well-layered surface topography. The drug release behavior of the optimal OF 2 was best elucidated with the zero order (R(2) = 0.97) and Korsmeyer-Peppas (R(2) = 0.99) models. X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and differential scanning calorimetry (DSC) analyses showed that OF 2 was made of physically mixed multiple component polymeric and nonpolymeric compounds. OF 2 was
Tebuconazole photocatalytic degradation kinetics
Prestes, Thiago de Hermann; Gibbon, Danielle de Oliveira; Lansarin, Marla Azário; Moro, Celso Camilo
2010-01-01
The tebuconazole photocatalytic degradation kinetics was studied in a batch reactor using TiO2 (P25-Degussa) as catalyst and a high pressure mercury lamp. The photolysis, adsorption and irradiation effects in the reaction rate were evaluated. Afterward, the suspension catalyst concentration and initial pH to the maximum reaction rate was determined. It was observed that the reaction rate can be approached by a pseudo-first order, with a maximum kinetics constant at 260 mg L-1catalyst concentr...
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)
A kinetic Monte Carlo analysis for the production of singularly tethered carbon nanotubes
Energy Technology Data Exchange (ETDEWEB)
Hilmer, Andrew J; Strano, Michael S [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Nair, Nitish, E-mail: strano@mit.edu [Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309 (United States)
2010-12-10
Nanoparticles that possess a single covalent tether to either another particle or a surface play an increasingly important role in nanotechnology, serving as a foundation for aggregation-based plasmonic sensors, chemically assembled framework structures, and scanning probe tips. Using a theoretical approach, we explore the reaction conditions necessary to maximize singular tethering for several cases of homogeneously dispersed nanoparticles, with a particular focus on single-walled carbon nanotubes. In the limit of particles of monodisperse size and equal site reactivity, the number of tethers versus the reaction conversion is statistically described by the well-known binomial distribution, with a variance that is minimal for the single tether case. However, solutions of nanoparticles often deviate from this ideal, and reaction events can introduce steric hindrance to neighboring sites or alter particle electronic properties, both of which can influence local reactivity. In order to study these cases we use the electron transfer reactions of single-walled carbon nanotubes. We find that the distribution in the number of monofunctional tubes, as a function of conversion, is largely dependent on the distribution of nanotube rate constants, and therefore tube chiralities, in the initial solution. As a contemporary example, we examine the implications of this result on the metallic-semiconductor separation of carbon nanotubes using electron transfer chemistry.
Self-learning kinetic Monte Carlo simulations of diffusion in ferromagnetic α-Fe–Si alloys
Nandipati, Giridhar; Jiang, Xiujuan; Vemuri, Rama S.; Mathaudhu, Suveen; Rohatgi, Aashish
2018-01-01
Diffusion of Si atom and vacancy in the A2-phase of α-Fe–Si alloys in the ferromagnetic state, with and without magnetic order and in various temperature ranges, are studied using AKSOME, an on-lattice self-learning KMC code. Diffusion of the Si atom and the vacancy are studied in the dilute limit and up to 12 at.% Si, respectively, in the temperature range 350–700 K. Local Si neighborhood dependent activation energies for vacancy hops were calculated on-the-fly using a broken-bond model based on pairwise interaction. The migration barrier and prefactor for the Si diffusion in the dilute limit were obtained and found to agree with published data within the limits of uncertainty. Simulations results show that the prefactor and the migration barrier for the Si diffusion are approximately an order of magnitude higher, and a tenth of an electron-volt higher, respectively, in the magnetic disordered state than in the fully ordered state. However, the net result is that magnetic disorder does not have a significant effect on Si diffusivity within the range of parameters studied in this work. Nevertheless, with increasing temperature, the magnetic disorder increases and its effect on the Si diffusivity also increases. In the case of vacancy diffusion, with increasing Si concentration, its diffusion prefactor decreases while the migration barrier more or less remained constant and the effect of magnetic disorder increases with Si concentration. Important vacancy-Si/Fe atom exchange processes and their activation barriers were identified, and the effect of energetics on ordered phase formation in Fe–Si alloys are discussed.
2011-09-01
temperatures and stresses. Ide et al. joined two copper discs using silver metallo-organic nanoparticles [2]. The 11 nm silver nanoparticles produced an...into the Earth’s atmosphere, linings for friction brakes , turbine disks, and metallic glasses for high-strength films and ribbons to name a few...interfacial bond microstructure between the copper discs that was stronger and denser than that using fine 2 silver particles of 100 nm [2]. The
Efficient 3D Kinetic Monte Carlo Method for Modeling of Molecular Structure and Dynamics
DEFF Research Database (Denmark)
Panshenskov, Mikhail; Solov'yov, Ilia; Solov'yov, Andrey V.
2014-01-01
Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures...
Kinetic Monte Carlo of transport processes in Al/AlOx/Au-layers: Impact of defects
Directory of Open Access Journals (Sweden)
Benedikt Weiler
2016-09-01
Full Text Available Ultrathin films of alumina were investigated by a compact kMC-model. Experimental jV-curves from Al/AlOx/Au-junctions with plasma- and thermal-grown AlOx were fitted by simulated ones. We found dominant defects at 2.3-2.5 eV below CBM for AlOx with an effective mass mox∗=0.35 m0 and a barrier EB,Al/AlOx≈2.8 eV in agreement with literature. The parameterization is extended to varying defect levels, defect densities, injection barriers, effective masses and the thickness of AlOx. Thus, dominant charge transport processes and implications on the relevance of defects are derived and AlOx parameters are specified which are detrimental for the operation of devices.
A Kinetic Monte Carlo method for the simulation of heteroepitaxial growth
Much, F.; Ahr, M.; Biehl, M.; Kinzel, W.
2002-01-01
We introduce a simulation algorithm which allows the off-lattice simulation of various phenomena observed in heteroepitaxial growth like a critical layer thickness for the appearance of misfit dislocations, or self-assembled island formation in 1 + 1 dimensions. The only parameters of the model are
Atomistic Simulation of Dislocation Core Structures in b2 Nickel-Aluminum
Xie, Zhao-Yang
A systematic study of the core structures of , , and dislocations in B2 NiAl has been conducted using atomistic simulations with an embedded atom method (EAM) potential. New flexible boundary conditions and a new method of graphic representation of dislocation core structure have been employed. The main findings are the following: Core structures. There are no planar core structures of the dislocations found in B2 NiAl. The core spreading of dislocations in NiAl can occur along a variety of planes depending on dislocation slip plane and line orientation. Discrete lattice effects reduced the high strain levels from anisotropic elasticity solution at the dislocation core considerably and resulted in asymmetrical core structures. The core structure of the dislocations is mutilayered with spreading on the plane. The extent of the same strain level comparing with and dislocations is much larger. The complete dislocations in NiAl are also highly non-planar and are stable with respect to splitting into exact 1/2 partials as well as to alternative splittings that correspond to the stable fault in the vicinity of the antiphase boundary (APB), in both and planes. Peierls stresses. Peierls stresses of the dislocations have been calculated and have been compared for their relative ease of motion. Local disordering effects. The local disordering effects on the core structure are found to be significant only in the immediate vicinity of the point defect. Compositional deviation from stoichiometry. The simulation results of , , and dislocations in off stoichiometric NiAl show that the core structures became more extended than the ones in the stoichiometric NiAl. The core structures are not only dependent on the overall composition but also on their local atomic arrangement near the core region. When compositional deviation from stoichiometry is introduced, the response to the applied stress is different for the various slip systems. The Peierls stresses for the usually easiest
Atomistic simulations of deformation mechanisms in ultralight weight Mg-Li alloys
Karewar, Shivraj
Mg alloys have spurred a renewed academic and industrial interest because of their ultra-light-weight and high specific strength properties. Hexagonal close packed Mg has low deformability and a high plastic anisotropy between basal and non-basal slip systems at room temperature. Alloying with Li and other elements is believed to counter this deficiency by activating non-basal slip by reducing their nucleation stress. In this work I study how Li addition affects deformation mechanisms in Mg using atomistic simulations. In the first part, I create a reliable and transferable concentration dependent embedded atom method (CD-EAM) potential for my molecular dynamics study of deformation. This potential describes the Mg-Li phase diagram, which accurately describes the phase stability as a function of Li concentration and temperature. Also, it reproduces the heat of mixing, lattice parameters, and bulk moduli of the alloy as a function of Li concentration. Most importantly, our CD-EAM potential reproduces the variation of stacking fault energy for basal, prismatic, and pyramidal slip systems that in uences the deformation mechanisms as a function of Li concentration. This success of CD-EAM Mg-Li potential in reproducing different properties, as compared to literature data, shows its reliability and transferability. Next, I use this newly created potential to study the effect of Li addition on deformation mechanisms in Mg-Li nanocrystalline (NC) alloys. Mg-Li NC alloys show basal slip, pyramidal type-I slip, tension twinning, and two-compression twinning deformation modes. Li addition reduces the plastic anisotropy between basal and non-basal slip systems by modifying the energetics of Mg-Li alloys. This causes the solid solution softening. The inverse relationship between strength and ductility therefore suggests a concomitant increase in alloy ductility. A comparison of the NC results with single crystal deformation results helps to understand the qualitative and
Automated Algorithms for Quantum-Level Accuracy in Atomistic Simulations: LDRD Final Report.
Energy Technology Data Exchange (ETDEWEB)
Thompson, Aidan Patrick; Schultz, Peter Andrew; Crozier, Paul; Moore, Stan Gerald; Swiler, Laura Painton; Stephens, John Adam; Trott, Christian Robert; Foiles, Stephen Martin; Tucker, Garritt J. (Drexel University)
2014-09-01
This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel computers
Mirzaei Sichani, Mehrdad
The objective of this dissertation is to characterize the evolution of plastic deformation mechanisms in single crystal and nanocrystalline Cu models during shock by atomistic simulations. Molecular dynamics (MD) simulations are performed for a range of particle velocities from 0.5 to 1.7 km/s and initial temperatures of 5, 300 and 600 K for single crystal models as well as particle velocities from 1.5 to 3.4 km/s for nanocrystalline models with grain diameters of 6, 11, 16 and 26 nm. For single crystal models, four different shock directions are selected, , , and , and dislocation density behind the shock wave front generally increases with increasing particle velocity for all shock orientations. Plastic relaxation for shock in the , and directions is primarily due to a reduction in the Shockley partial dislocation density. In contrast, plastic relaxation is limited for shock in the orientation. This is partially due to the emergence of sessile stair-rod dislocations with Burgers vectors of 1/3 and 1/6 due to the reaction of Shockley partial dislocations with twin boundaries and stacking fault intersections. For shock, FCC Cu is uniaxially compressed towards the BCC structure behind the shock wave front; this process is more favorable at higher shock pressures and temperatures. For particle velocities above 0.9 km/s, regions of HCP crystal structure nucleate from uniaxially compressed Cu. Free energy calculations proves that the nucleation and growth of these HCP clusters are an artifact of the embedded-atom interatomic potential. In addition, simulated x-ray diffraction line profiles are created for shock models of single crystal Cu at the Hugoniot state. Generally, peak broadening in the x-ray diffraction line profiles increases with increasing particle velocity. For nanocrystalline models, the compression of the FCC lattice towards the BCC structure is more apparent at particle velocity of 2.4 km/s, and at this particle velocity, the atomic percentage of BCC
Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca
2017-06-01
ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural and chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.
Energy Technology Data Exchange (ETDEWEB)
Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca
2017-03-20
ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural and chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.
Atomistic Conversion Reaction Mechanism of WO _{3} in Secondary Ion Batteries of Li, Na, and Ca
Energy Technology Data Exchange (ETDEWEB)
He, Yang [Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh PA 15261 USA; Gu, Meng [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Xiao, Haiyan [School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu 610054 China; Luo, Langli [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Shao, Yuyan [Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland WA 99352 USA; Gao, Fei [Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor MI 48109 USA; Du, Yingge [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Mao, Scott X. [Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh PA 15261 USA; Wang, Chongmin [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA
2016-04-13
Reversible insertion and extraction of ionic species into a host lattice governs the basic operating principle for both rechargeable battery (such as lithium batteries) and electrochromic devices (such as ANA Boeing 787-8 Dreamliner electrochromic window). Intercalation and/or conversion are two fundamental chemical processes for some materials in response to the ion insertion. The interplay between these two chemical processes has never been established. It is speculated that the conversion reaction is initiated by ion intercalation. However, experimental evidence of intercalation and subsequent conversion remains unexplored. Here, using in situ HRTEM and spectroscopy, we captured the atomistic conversion reaction processes during lithium, sodium and calcium ion insertion into tungsten trioxide (WO3) single crystal model electrodes. An intercalation step right prior to conversion is explicitly revealed at atomic scale for the first time for these three ion species. Combining nanoscale diffraction and ab initio molecular dynamics simulations, it is found that, beyond intercalation, the inserted ion-oxygen bonding formation destabilized the transition-metal framework which gradually shrunk, distorted and finally collapsed to a pseudo-amorphous structure. This study provides a full atomistic picture on the transition from intercalation to conversion, which is of essential for material applications in both secondary ion batteries and electrochromic devices.
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.
The atomistic mechanism for Sb segregation and As displacement of Sb in InSb(001) surfaces
Anderson, Evan M.; Millunchick, Joanna M.
2018-01-01
Interfacial broadening occurs in mixed-anion alloy heterostructures such as InAs/InAsSb due to both Sb-segregation and As-for-Sb exchange. In order to determine the atomistic mechanisms for these processes, we conduct ab initio calculations coupled with a cluster expansion formalism to determine the surface reconstructions of the pure and As-exposed InSb(001) surfaces. This approach provides a predicted phase diagram for pure InSb that is in better agreement with experiments. Namely, the α2(2 × 4) and α3c(4 × 4) structures are ultimately stable at 0K, but the α(4 × 3) and α2c(2 × 6) are within 1 meV/Å2. Exposure of the InSb(001) surface to As results in the As atoms infiltrating into the crystal and displacing subsurface Sb, thus providing the atomistic mechanisms for experimental observations of the As-for-Sb exchange reaction and Sb segregation. Experiments show that the widely reported A-(1 × 3) reconstruction is actually comprised of multiple reconstructions, which is consistent with the prediction of several nearly stable possible reconstructions.
Yuan, Xuebo; Wang, Youshan
2017-10-01
The radial deformation of carbon nanotubes (CNTs) adhering to a substrate may prominently affect their mechanical and physical properties. In this study, both classical atomistic simulations and continuum analysis are carried out, to investigate the lateral adhesion of single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) to a silicon substrate. A linear elastic model for analyzing the adhesion of 2D shells to a rigid semi-infinite substrate is constructed in the framework of continuum mechanics. Good agreement is achieved between the cross-section profiles of adhesive CNTs obtained by the continuum model and by the atomistic simulation approach. It is found that the adhesion of a CNT to the silicon substrate is significantly influenced by its initial diameter and the number of walls. CNTs with radius larger than a certain critical radius are deformed radially on the silicon substrate with flat contact regions. With increasing number of walls, the extent of radial deformation of a MWCNT on the substrate decreases dramatically, and the flat contact area reduces—and eventually vanishes—due to increasing equivalent bending stiffness. It is analytically predicted that large-diameter MWCNTs with a large number of walls are likely to ‘stand’ on the silicon substrate. The present work can be useful for understanding the radial deformation of CNTs adhering to a solid planar substrate.
Directory of Open Access Journals (Sweden)
M. S. M. Al-Kharusi
2016-01-01
Full Text Available The mechanical behavior of SWCNTs is characterized using an atomistic-based continuum method. At nanoscale, interatomic energy among carbon atoms and the corresponding force constants are defined. Subsequently, we used an atomistic finite element analysis to calculate the energy stored in the SWCNT model, which forms a basis for calculating effective elastic moduli. In the finite element model, the force interaction among carbon atoms in a SWCNT is modeled using load-carrying structural beams. At macroscale, the SWCNT is taken as cylindrical continuum solid with transversely isotropic mechanical properties. Equivalence of energies of both models establishes a framework to calculate effective elastic moduli of armchair and zigzag nanotubes. This is achieved by solving five boundary value problems under distinct essential-controlled boundary conditions, which generates a prescribed uniform strain field in both models. Elastic constants are extracted from the calculated elastic moduli. While results of Young’s modulus obtained in this study generally concur with the published theoretical and numerical predictions, values of Poisson’s ratio are on the high side.
Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.
2017-10-01
We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.
DEFF Research Database (Denmark)
Wang, Yong
, for example, accurately quantifying the free energy differences and transition times of protein conformational exchanges and their dependence on sequence modications, we are still at the early stages. In this dissertation, I present a number of new methodological improvements and applications for protein...... folding, conformational exchange and binding with ligands at long time scales. In Chapter 2, we benchmarked how well the current force elds and molecular dynamics (MD) simulations could model changes in structure, dynamics, free energy and kinetics for an extensively studied protein called T4 lysozyme (T4......", and subsequently used to estimate the free energy dierences based on a twostate assumption. To show its practical utility, we applied this approach by taking T4L-benzene system as the model system in which binding free energies from kinetics, free energy perturbation and experiments are all in good agreement...
Indian Academy of Sciences (India)
Abstract. This paper presents the detailed turbulent kinetic energy budget and higher order statistics of flow behind a surface-mounted rib with and without superimposed acoustic excitation. Pattern recognition technique is used to determine the large-scale structure magnitude. It is observed that most of the turbulence ...
Modeling chemical kinetics graphically
Heck, A.
2012-01-01
In literature on chemistry education it has often been suggested that students, at high school level and beyond, can benefit in their studies of chemical kinetics from computer supported activities. Use of system dynamics modeling software is one of the suggested quantitative approaches that could
SHORT COMMUNICATION KINETIC SPECTROPHOTOMETRIC ...
African Journals Online (AJOL)
Preferred Customer
ABSTRACT. ABSTRACT. A novel catalytic kinetic spectrophotometric method for the determination of iron is developed based on the catalytic effect of Fe(III) on the oxidation reaction of p-acetylarsenazo(ASApA) by potassium periodate. Maximum absorbance of the Fe(III)-ASApA-KIO4 system in 8.0 × 10-3 M sulfuric acid ...
CATALYTIC KINETIC SPECTROPHOTOMETRIC DETERMINATION ...
African Journals Online (AJOL)
Based on the property that in 0.12 M sulfuric acid medium titanium(IV) catalyzes the discoloring reaction of DBS-arsenazo oxidized by potassium bromate, a new catalytic kinetic spectrophotometric method for the determination of trace titanium (IV) was developed. The linear range of the determination of titanium is
CATALYTIC KINETIC SPECTROPHOTOMETRIC DETERMINATION ...
African Journals Online (AJOL)
Preferred Customer
Research Center for Nanotechnology, Changchun University of Science and Technology,. Changchun 130022 ... Although catalytic kinetic spectrophotometry has been used in the determination of copper, the selectivity ... In this paper CPApA was used as the chromogenic agent, H2O2 as the oxidant, Cu(II) as the catalyst.
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
Status of Monte-Carlo Event Generators
Energy Technology Data Exchange (ETDEWEB)
Hoeche, Stefan; /SLAC
2011-08-11
Recent progress on general-purpose Monte-Carlo event generators is reviewed with emphasis on the simulation of hard QCD processes and subsequent parton cascades. Describing full final states of high-energy particle collisions in contemporary experiments is an intricate task. Hundreds of particles are typically produced, and the reactions involve both large and small momentum transfer. The high-dimensional phase space makes an exact solution of the problem impossible. Instead, one typically resorts to regarding events as factorized into different steps, ordered descending in the mass scales or invariant momentum transfers which are involved. In this picture, a hard interaction, described through fixed-order perturbation theory, is followed by multiple Bremsstrahlung emissions off initial- and final-state and, finally, by the hadronization process, which binds QCD partons into color-neutral hadrons. Each of these steps can be treated independently, which is the basic concept inherent to general-purpose event generators. Their development is nowadays often focused on an improved description of radiative corrections to hard processes through perturbative QCD. In this context, the concept of jets is introduced, which allows to relate sprays of hadronic particles in detectors to the partons in perturbation theory. In this talk, we briefly review recent progress on perturbative QCD in event generation. The main focus lies on the general-purpose Monte-Carlo programs HERWIG, PYTHIA and SHERPA, which will be the workhorses for LHC phenomenology. A detailed description of the physics models included in these generators can be found in [8]. We also discuss matrix-element generators, which provide the parton-level input for general-purpose Monte Carlo.
Monte Carlo Simulation of an American Option
Directory of Open Access Journals (Sweden)
Gikiri Thuo
2007-04-01
Full Text Available We implement gradient estimation techniques for sensitivity analysis of option pricing which can be efficiently employed in Monte Carlo simulation. Using these techniques we can simultaneously obtain an estimate of the option value together with the estimates of sensitivities of the option value to various parameters of the model. After deriving the gradient estimates we incorporate them in an iterative stochastic approximation algorithm for pricing an option with early exercise features. We illustrate the procedure using an example of an American call option with a single dividend that is analytically tractable. In particular we incorporate estimates for the gradient with respect to the early exercise threshold level.
A Monte Carlo algorithm for degenerate plasmas
Energy Technology Data Exchange (ETDEWEB)
Turrell, A.E., E-mail: a.turrell09@imperial.ac.uk; Sherlock, M.; Rose, S.J.
2013-09-15
A procedure for performing Monte Carlo calculations of plasmas with an arbitrary level of degeneracy is outlined. It has possible applications in inertial confinement fusion and astrophysics. Degenerate particles are initialised according to the Fermi–Dirac distribution function, and scattering is via a Pauli blocked binary collision approximation. The algorithm is tested against degenerate electron–ion equilibration, and the degenerate resistivity transport coefficient from unmagnetised first order transport theory. The code is applied to the cold fuel shell and alpha particle equilibration problem of inertial confinement fusion.
Markov chains analytic and Monte Carlo computations
Graham, Carl
2014-01-01
Markov Chains: Analytic and Monte Carlo Computations introduces the main notions related to Markov chains and provides explanations on how to characterize, simulate, and recognize them. Starting with basic notions, this book leads progressively to advanced and recent topics in the field, allowing the reader to master the main aspects of the classical theory. This book also features: Numerous exercises with solutions as well as extended case studies.A detailed and rigorous presentation of Markov chains with discrete time and state space.An appendix presenting probabilistic notions that are nec
Energy Technology Data Exchange (ETDEWEB)
Marcus, Ryan C. [Los Alamos National Laboratory
2012-07-24
Overview of this presentation is (1) Exascale computing - different technologies, getting there; (2) high-performance proof-of-concept MCMini - features and results; and (3) OpenCL toolkit - Oatmeal (OpenCL Automatic Memory Allocation Library) - purpose and features. Despite driver issues, OpenCL seems like a good, hardware agnostic tool. MCMini demonstrates the possibility for GPGPU-based Monte Carlo methods - it shows great scaling for HPC application and algorithmic equivalence. Oatmeal provides a flexible framework to aid in the development of scientific OpenCL codes.
Efficient Monte Carlo sampling by parallel marginalization.
Weare, Jonathan
2007-07-31
Markov chain Monte Carlo sampling methods often suffer from long correlation times. Consequently, these methods must be run for many steps to generate an independent sample. In this paper, a method is proposed to overcome this difficulty. The method utilizes information from rapidly equilibrating coarse Markov chains that sample marginal distributions of the full system. This is accomplished through exchanges between the full chain and the auxiliary coarse chains. Results of numerical tests on the bridge sampling and filtering/smoothing problems for a stochastic differential equation are presented.
Mosaic crystal algorithm for Monte Carlo simulations
Seeger, P A
2002-01-01
An algorithm is presented for calculating reflectivity, absorption, and scattering of mosaic crystals in Monte Carlo simulations of neutron instruments. The algorithm uses multi-step transport through the crystal with an exact solution of the Darwin equations at each step. It relies on the kinematical model for Bragg reflection (with parameters adjusted to reproduce experimental data). For computation of thermal effects (the Debye-Waller factor and coherent inelastic scattering), an expansion of the Debye integral as a rapidly converging series of exponential terms is also presented. Any crystal geometry and plane orientation may be treated. The algorithm has been incorporated into the neutron instrument simulation package NISP. (orig.)
Canonical demon Monte Carlo renormalization group
Hasenbusch, M; Wieczerkowski, C
1994-01-01
We describe a new method to compute renormalized coupling constants in a Monte Carlo renormalization group calculation. The method can be used for a general class of models, e.g., lattice spin or gauge models. The basic idea is to simulate a joint system of block spins and canonical demons. In contrast to the Microcanonical Renormalization Group invented by Creutz et al. our method does not suffer from systematical errors stemming from a simultaneous use of two different ensembles. We present numerical results for the O(3) nonlinear \\sigma-model.
Score Bounded Monte-Carlo Tree Search
Cazenave, Tristan; Saffidine, Abdallah
Monte-Carlo Tree Search (MCTS) is a successful algorithm used in many state of the art game engines. We propose to improve a MCTS solver when a game has more than two outcomes. It is for example the case in games that can end in draw positions. In this case it improves significantly a MCTS solver to take into account bounds on the possible scores of a node in order to select the nodes to explore. We apply our algorithm to solving Seki in the game of Go and to Connect Four.
by means of FLUKA Monte Carlo method
Directory of Open Access Journals (Sweden)
Ermis Elif Ebru
2015-01-01
Full Text Available Calculations of gamma-ray mass attenuation coefficients of various detector materials (crystals were carried out by means of FLUKA Monte Carlo (MC method at different gamma-ray energies. NaI, PVT, GSO, GaAs and CdWO4 detector materials were chosen in the calculations. Calculated coefficients were also compared with the National Institute of Standards and Technology (NIST values. Obtained results through this method were highly in accordance with those of the NIST values. It was concluded from the study that FLUKA MC method can be an alternative way to calculate the gamma-ray mass attenuation coefficients of the detector materials.
Archimedes, the Free Monte Carlo simulator
Sellier, Jean Michel D
2012-01-01
Archimedes is the GNU package for Monte Carlo simulations of electron transport in semiconductor devices. The first release appeared in 2004 and since then it has been improved with many new features like quantum corrections, magnetic fields, new materials, GUI, etc. This document represents the first attempt to have a complete manual. Many of the Physics models implemented are described and a detailed description is presented to make the user able to write his/her own input deck. Please, feel free to contact the author if you want to contribute to the project.
Scalar QED, NLO and PHOTOS Monte Carlo
Nanava, G.; Was, Z.
2006-01-01
Recently, QED bremsstrahlung in $B$-meson decays into pair of scalars (\\pi's and/or K's) is of interest. If experimental acceptance must be taken into account, PHOTOS Monte Carlo is often used in experimental simulations. We will use scalar QED to benchmark PHOTOS, even though this theory is of limited use for complex objects. We present the analytical form of the kernel used in the older versions of PHOTOS, and the new, exact (scalar QED) one. Matrix element and phase-space Jacobians are sep...
Monte Carlo simulations of dense quantum plasmas
Energy Technology Data Exchange (ETDEWEB)
Filinov, V S [Institute for High Energy Density, Izhorskay 13/19, Moscow 125412 (Russian Federation); Bonitz, M [Universitaet Kiel, Leibnizstrasse 15, 24098 Kiel (Germany); Fortov, V E [Institute for High Energy Density, Izhorskay 13/19, Moscow 125412 (Russian Federation); Ebeling, W [Humbold Universitaet Berlin, Invalidenstrasse 110, D-10115 Berlin (Germany); Fehske, H [Universitaet Greifswald, Domstrasse 10a, D-17487, Greifswald (Germany); Kremp, D [Universitaet Rostock, Universitaetsplatz 3, D-18051 Rostock (Germany); Kraeft, W D [Universitaet Greifswald, Domstrasse 10a, D-17487, Greifswald (Germany); Bezkrovniy, V [Universitaet Rostock, Universitaetsplatz 3, D-18051 Rostock (Germany); Levashov, P [Institute for High Energy Density, Izhorskay 13/19, Moscow 125412 (Russian Federation)
2006-04-28
Thermodynamic properties of the equilibrium strongly coupled quantum plasmas investigated by direct path integral Monte Carlo (DPIMC) simulations within a wide region of density, temperature and positive to negative particle mass ratio. Pair distribution functions (PDF), equation of state (EOS), internal energy and Hugoniot are compared with available theoretical and experimental results. Possibilities of the phase transition in hydrogen and electron-hole plasma from neutral particle system to metallic-like state and crystal-like structures, including antiferromagnetic hole structure in semiconductors at low temperatures, are discussed.
Learning Chemical Kinetics with Spreadsheets.
Blickensderfer, Roger
1990-01-01
Presented are several simple kinetic systems together with the spreadsheets used to solve them. A set of exercises in chemical kinetics appropriate for an introductory course in physical chemistry is given. Error propagation calculations with experimental data are illustrated. (CW)
Kinetics of Melanin Polymerization during Enzymatic and Nonenzymatic Oxidation.
Mondal, Sayan; Thampi, Arya; Puranik, Mrinalini
2018-02-22
Melanin is an abundant biopigment in the animal kingdom, but its structure remains poorly understood. This is a substantial impediment to understanding the mechanistic origin of its observed functions. Proposed models of melanin structure include aggregates of both linear and macrocyclic units and noncovalently held monomers. Both models are broadly in agreement with current experimental data. To constrain the structural and kinetic models of melanin, experimental data of high resolution with chemical specificity accompanied by atomistic modeling are required. We have addressed this by obtaining electronic absorption, infrared, and ultraviolet resonance Raman (RR) spectra of melanin at several wavelengths of excitation that are sensitive to small changes in structure. From these experiments, we observed kinetics of the formation of different species en route to melanin polymerization. Exclusive chemical signatures of monomer 3,4-dihydroxyphenylalanine (dopa), intermediate dopachrome (DC), and early-time polymer are established through their vibrational bands at 1292, 1670, and 1616 cm -1 respectively. Direct evidence of reduced heterogeneity of melanin oligomers in tyrosinase-induced formation is provided from experimental measurements of vibrational bandwidths. Models made with density functional theory show that the linear homopolymeric structures of 5,6-dihydroxyindole can account for experimentally observed wavenumbers and broad bandwidth in Raman spectra of dopa-melanin. We capture resonance Raman (RR) signature of DC, the intermediate stabilized by the enzyme tyrosinase, for the first time in an enzyme-assisted melanization reaction using 488 nm excitation wavelength and propose that this wavelength can be used to probe reaction intermediates of melanin formation in solution.
Adams, William T., Ed.
To be used as teaching aids, these interviews were developed in a training program for VISTA volunteers in Monte Vista, Colorado, during the summer of 1965. The instructors, whose comments constitute a major scope of the document were mothers, ex-delinquents, school dropouts, and young unwed mothers from the poverty area. It is felt that this…
Monte Carlo Based Framework to Support HAZOP Study
DEFF Research Database (Denmark)
Danko, Matej; Frutiger, Jerome; Jelemenský, Ľudovít
2017-01-01
This study combines Monte Carlo based process simulation features with classical hazard identification techniques for consequences of deviations from normal operating conditions investigation and process safety examination. A Monte Carlo based method has been used to sample and evaluate different...... deviations in process parameters simultaneously, thereby bringing an improvement to the Hazard and Operability study (HAZOP), which normally considers only one at a time deviation in process parameters. Furthermore, Monte Carlo filtering was then used to identify operability and hazard issues including...
The computation of Greeks with multilevel Monte Carlo
Sylvestre Burgos; M. B. Giles
2011-01-01
In mathematical finance, the sensitivities of option prices to various market parameters, also known as the “Greeks”, reflect the exposure to different sources of risk. Computing these is essential to predict the impact of market moves on portfolios and to hedge them adequately. This is commonly done using Monte Carlo simulations. However, obtaining accurate estimates of the Greeks can be computationally costly. Multilevel Monte Carlo offers complexity improvements over standard Monte Carl...
Kinetics of enzymatic reactions in lipid membranes containing domains.
Zhdanov, Vladimir P; Höök, Fredrik
2015-03-06
An appreciable part of enzymes operating in vivo is associated with lipid membranes. The function of such enzymes can be influenced by the presence of domains containing proteins and/or composed of different lipids. The corresponding experimental model-system studies can be performed under well controlled conditions, e.g., on a planar supported lipid bilayer or surface-immobilized vesicles. To clarify what may happen in such systems, we propose general kinetic equations describing the enzyme-catalyzed substrate conversion occurring via the Michaelis-Menten (MM) mechanism on a membrane with domains which do not directly participate in reaction. For two generic situations when a relatively slow reaction takes place primarily in or outside domains, we take substrate saturation and lateral substrate-substrate interactions at domains into account and scrutinize the dependence of the reaction rate on the average substrate coverage. With increasing coverage, depending on the details, the reaction rate reaches saturation via an inflection point or monotonously as in the conventional MM case. In addition, we show analytically the types of reaction kinetics occurring primarily at domain boundaries. In the physically interesting situation when the domain growth is fast on the reaction time scale, the latter kinetics are far from conventional. The opposite situation when the reaction is fast and controlled by diffusion has been studied by using the Monte Carlo technique. The corresponding results indicate that the dependence of the reaction kinetics on the domain size may be weak.
Evaluating Wave Random Path Using Multilevel Monte Carlo
Directory of Open Access Journals (Sweden)
Behrouz Fathi-Vajargah
2017-06-01
Full Text Available Wind waves are important due to their high energy and impact on marine activities. This phenomenon is affects directly or indirectly the construction of coastal infrastructure, shipping and recreational activities. Due to the issues presented, marine parameters are very important. In this study, we try to pay attention to wave as one of the most important marine parameters. As the movements of waves have high uncertainty, financial models can be used to simulate the wave's paths. We use the Monte Carlo method for this purpose. The Monte Carlo simulation is a flexible and simple tool that is widely used in the evaluation of random paths. To compute a random path, we require an integral discretization. In this paper, we study the valuation of European options using Monte Carlo simulation and then compare this result with multi-level Monte Carlo approach and other antithetic variables. Then, we use the multi-level Monte Carlo approach proposed by (M. B. Giles, 2008 for pricing under the two-factor stochastic volatility model. We show that the multi-level Monte Carlo method reduces the computational complexity and also cost of the two-factor stochastic volatility model when compared with the standard Monte Carlo method. Also, we compare the multi-level Monte Carlo method and standard Monte Carlo method using an Euler discretization scheme and then, analyze the numerical results.
Monte Carlo modeling of spatial coherence: free-space diffraction.
Fischer, David G; Prahl, Scott A; Duncan, Donald D
2008-10-01
We present a Monte Carlo method for propagating partially coherent fields through complex deterministic optical systems. A Gaussian copula is used to synthesize a random source with an arbitrary spatial coherence function. Physical optics and Monte Carlo predictions of the first- and second-order statistics of the field are shown for coherent and partially coherent sources for free-space propagation, imaging using a binary Fresnel zone plate, and propagation through a limiting aperture. Excellent agreement between the physical optics and Monte Carlo predictions is demonstrated in all cases. Convergence criteria are presented for judging the quality of the Monte Carlo predictions.
Composite biasing in Monte Carlo radiative transfer
Baes, Maarten; Gordon, Karl D.; Lunttila, Tuomas; Bianchi, Simone; Camps, Peter; Juvela, Mika; Kuiper, Rolf
2016-05-01
Biasing or importance sampling is a powerful technique in Monte Carlo radiative transfer, and can be applied in different forms to increase the accuracy and efficiency of simulations. One of the drawbacks of the use of biasing is the potential introduction of large weight factors. We discuss a general strategy, composite biasing, to suppress the appearance of large weight factors. We use this composite biasing approach for two different problems faced by current state-of-the-art Monte Carlo radiative transfer codes: the generation of photon packages from multiple components, and the penetration of radiation through high optical depth barriers. In both cases, the implementation of the relevant algorithms is trivial and does not interfere with any other optimisation techniques. Through simple test models, we demonstrate the general applicability, accuracy and efficiency of the composite biasing approach. In particular, for the penetration of high optical depths, the gain in efficiency is spectacular for the specific problems that we consider: in simulations with composite path length stretching, high accuracy results are obtained even for simulations with modest numbers of photon packages, while simulations without biasing cannot reach convergence, even with a huge number of photon packages.
Parallel Monte Carlo Search for Hough Transform
Lopes, Raul H. C.; Franqueira, Virginia N. L.; Reid, Ivan D.; Hobson, Peter R.
2017-10-01
We investigate the problem of line detection in digital image processing and in special how state of the art algorithms behave in the presence of noise and whether CPU efficiency can be improved by the combination of a Monte Carlo Tree Search, hierarchical space decomposition, and parallel computing. The starting point of the investigation is the method introduced in 1962 by Paul Hough for detecting lines in binary images. Extended in the 1970s to the detection of space forms, what came to be known as Hough Transform (HT) has been proposed, for example, in the context of track fitting in the LHC ATLAS and CMS projects. The Hough Transform transfers the problem of line detection, for example, into one of optimization of the peak in a vote counting process for cells which contain the possible points of candidate lines. The detection algorithm can be computationally expensive both in the demands made upon the processor and on memory. Additionally, it can have a reduced effectiveness in detection in the presence of noise. Our first contribution consists in an evaluation of the use of a variation of the Radon Transform as a form of improving theeffectiveness of line detection in the presence of noise. Then, parallel algorithms for variations of the Hough Transform and the Radon Transform for line detection are introduced. An algorithm for Parallel Monte Carlo Search applied to line detection is also introduced. Their algorithmic complexities are discussed. Finally, implementations on multi-GPU and multicore architectures are discussed.
Engineered barrier experiment Mont Terri underground laboratory
Energy Technology Data Exchange (ETDEWEB)
Mayor, J.C. [Empresa Nacional de Residuos Radiactivos, SA (ENRESA), Madrid (Spain); Alonso, E. [Universitat Polytechnica de Catalunya (UPC-CIMNE), Madrid (Spain); Garcia-Sineriz, J.L. [AITEMIN, Madrid (Spain)
2005-07-01
The Engineered Barrier (EB) experiment is being carried out at the Mont Terri underground laboratory (Switzerland). The aim of the EB experiment is the demonstration of a new concept for the buffer construction of HLW repositories in horizontal drifts, in competent clay formations. The principle of this new buffer construction method is based on the combined use of a lower bed made of compacted bentonite blocks, and an upper backfill made with a bentonite pellets based material. The emplacement layout proposed in this project represents an important innovation for repositories in horizontal drifts. The fact of filling the upper part of the gap between the canister and the rock with a pellets-based type of material makes the emplacement operation much simpler, eliminating some of the most critical aspects of such operation. The experiment is carried out in a gallery excavated in the shaly facies of the Opalinus clay of Mont Terri. The geometry of the test site is a horseshoe section, 2,55 m high, 3 m wide and 15 m long. A dummy canister of the same dimensions and weight than the reference one was installed on the top of a compacted bentonite blocks bed, and the gap canister-rock was backfilled with compacted bentonite pellets. The experimental area was isolated by a concrete plug. An artificial hydration system was installed to accelerate the hydration process. In order to monitor the evolution of the system and record the values of different parameters, a data acquisition system was installed. (authors)
Multi-Index Monte Carlo (MIMC)
Haji Ali, Abdul Lateef
2016-01-06
We propose and analyze a novel Multi-Index Monte Carlo (MIMC) method for weak approximation of stochastic models that are described in terms of differential equations either driven by random measures or with random coefficients. The MIMC method is both a stochastic version of the combination technique introduced by Zenger, Griebel and collaborators and an extension of the Multilevel Monte Carlo (MLMC) method first described by Heinrich and Giles. Inspired by Giles s seminal work, instead of using first-order differences as in MLMC, we use in MIMC high-order mixed differences to reduce the variance of the hierarchical differences dramatically. Under standard assumptions on the convergence rates of the weak error, variance and work per sample, the optimal index set turns out to be of Total Degree (TD) type. When using such sets, MIMC yields new and improved complexity results, which are natural generalizations of Giles s MLMC analysis, and which increase the domain of problem parameters for which we achieve the optimal convergence, O(TOL-2).
Multi-Index Monte Carlo (MIMC)
Haji Ali, Abdul Lateef
2015-01-07
We propose and analyze a novel Multi-Index Monte Carlo (MIMC) method for weak approximation of stochastic models that are described in terms of differential equations either driven by random measures or with random coefficients. The MIMC method is both a stochastic version of the combination technique introduced by Zenger, Griebel and collaborators and an extension of the Multilevel Monte Carlo (MLMC) method first described by Heinrich and Giles. Inspired by Giles’s seminal work, instead of using first-order differences as in MLMC, we use in MIMC high-order mixed differences to reduce the variance of the hierarchical differences dramatically. Under standard assumptions on the convergence rates of the weak error, variance and work per sample, the optimal index set turns out to be of Total Degree (TD) type. When using such sets, MIMC yields new and improved complexity results, which are natural generalizations of Giles’s MLMC analysis, and which increase the domain of problem parameters for which we achieve the optimal convergence.
Quantum Monte Carlo Endstation for Petascale Computing
Energy Technology Data Exchange (ETDEWEB)
Lubos Mitas
2011-01-26
NCSU research group has been focused on accomplising the key goals of this initiative: establishing new generation of quantum Monte Carlo (QMC) computational tools as a part of Endstation petaflop initiative for use at the DOE ORNL computational facilities and for use by computational electronic structure community at large; carrying out high accuracy quantum Monte Carlo demonstration projects in application of these tools to the forefront electronic structure problems in molecular and solid systems; expanding the impact of QMC methods and approaches; explaining and enhancing the impact of these advanced computational approaches. In particular, we have developed quantum Monte Carlo code (QWalk, www.qwalk.org) which was significantly expanded and optimized using funds from this support and at present became an actively used tool in the petascale regime by ORNL researchers and beyond. These developments have been built upon efforts undertaken by the PI's group and collaborators over the period of the last decade. The code was optimized and tested extensively on a number of parallel architectures including petaflop ORNL Jaguar machine. We have developed and redesigned a number of code modules such as evaluation of wave functions and orbitals, calculations of pfaffians and introduction of backflow coordinates together with overall organization of the code and random walker distribution over multicore architectures. We have addressed several bottlenecks such as load balancing and verified efficiency and accuracy of the calculations with the other groups of the Endstation team. The QWalk package contains about 50,000 lines of high quality object-oriented C++ and includes also interfaces to data files from other conventional electronic structure codes such as Gamess, Gaussian, Crystal and others. This grant supported PI for one month during summers, a full-time postdoc and partially three graduate students over the period of the grant duration, it has resulted in 13
An atomistic study on configuration, mechanics and growth of nanoscale filaments
Shahabi, Alireza
conformations in these electronically active filaments open up the possibility of non-linear stretchable interconnects, and we study their reliability by extracting the elastic stiffness of the various conformations. We extract force-displacement curves of scrolls and plectonemes in the various systems. Our analysis sheds light on the relation between the shape of the nanostructures and the elastic stiffness of the nanofilaments. In overall, our study provides us with a novel route to engineer the nanofilaments and tune their mechanical properties using a combination of physical constraints and mechanical loading. In the next part of the dissertation, we perform a comprehensive atomistic study of the nanoscale crystal growth mechanisms of Au-catalyzed silicon nanowires grown via the vapor liquid solid method (VLS) during early stages of the droplet to nanowire transition. The transition sets the size of the nanowire, and the principles of diameter selection remain poorly understood. Our analysis reveals the role of the initial configuration of the nanodroplet and the effect of surface tension on the success of the VLS growth process. We observe lateral extension of liquid feet from the sides of nanodroplet during the VLS process. In addition to the nanodroplet diameter, the liquid feet plays a crucial role on determining the final geometry of the nanowire. We also observe an important correlation between the rate of deposition of Si atoms and presence of the twining in the nanowire structure, which significantly affects its properties. Higher deposition rates result in incorporation of metallic impurities in the nanowire structure, which consequently results in the formation of twining deformation. Our MD studies uncover a previously ignored interplay between solute trapping of catalyst particles in the nanowire, and twin formation, and we discuss this effect in the context of past experimental reports on twin formation in semiconducting nanowires, and the ability to
The Soft Mode Driven Dynamics in Ferroelectric Perovskites at the Nanoscale: An Atomistic Study
McCash, Kevin
The discovery of ferroelectricity at the nanoscale has incited a lot of interest in perovskite ferroelectrics not only for their potential in device application but also for their potential to expand fundamental understanding of complex phenomena at very small size scales. Unfortunately, not much is known about the dynamics of ferroelectrics at this scale. Many of the widely held theories for ferroelectric materials are based on bulk dynamics which break down when applied to smaller scales. In an effort to increase understanding of nanoscale ferroelectric materials we use atomistic resolution computational simulations to investigate the dynamics of polar perovskites. Within the framework of a well validated effective Hamiltonian model we are able to accurately predict many of the properties of ferroelectric materials at the nanoscale including the response of the soft mode to mechanical boundary conditions and the polarization reversal dynamics of ferroelectric nanowires. Given that the focus of our study is the dynamics of ferroelectric perovskites we begin by developing an effective Hamiltonian based model that could simultaneously describe both static and dynamic properties of such materials. Our study reveals that for ferroelectric perovskites that undergo a sequence of phase transitions, such as BaTiO3. for example, the minimal parameter effective Hamiltonian model is unable to reproduce both static and dynamical properties simultaneously. Nevertheless we developed two sets of parameters that accurately describes the static properties and dynamic properties of BaTiO3 independently. By creating a tool that accurately models the dynamical properties of perovskite ferroelectrics we are able to investigate the frequencies of the soft modes in the perovskite crystal. The lowest energy transverse optical soft modes in perovskite ferroelectrics are known to be cause of the ferroelectric phase transition in these materials and affect a number of electrical properties
Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores
Yang, Guomin; Neretnieks, Ivars; Holmboe, Michael
2017-08-01
During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and
Directory of Open Access Journals (Sweden)
V.G. Morozov
2009-01-01
Full Text Available We present a kinetic theory of radiative processes in many-component plasmas with relativistic electrons and nonrelativistic heavy particles. Using the non-equilibrium Green's function technique in many-particle QED, we show that the transverse field correlation functions can be naturally decomposed into sharply peaked (non-Lorentzian parts that describe resonant (propagating photons and off-shell parts corresponding to virtual photons in the medium. Analogous decompositions are obtained for the longitudinal field correlation functions and the correlation functions of relativistic electrons. We derive a kinetic equation for the resonant photons with a finite spectral width and show that the off-shell parts of the particle and field correlation functions are essential to calculate the local radiating power in plasmas and recover the results of vacuum QED. The plasma effects on radiative processes are discussed.
Directory of Open Access Journals (Sweden)
A.C. Faleiros
2000-07-01
Full Text Available The kinetic model for change of phases developed by M. Avrami at the end of the thirties has been used to describe the temporal behavior of phase changes. Until today this model is studied and adapted to include broader hypotheses. However, the mathematical format presented by M. Avrami is difficult to be understood by beginners. The purpose of this work is to clarify the mathematical treatment of Avrami's work, going straightforward to the arguments that led to his main results.
Rapid mixing kinetic techniques.
Martin, Stephen R; Schilstra, Maria J
2013-01-01
Almost all of the elementary steps in a biochemical reaction scheme are either unimolecular or bimolecular processes that frequently occur on sub-second, often sub-millisecond, time scales. The traditional approach in kinetic studies is to mix two or more reagents and monitor the changes in concentrations with time. Conventional spectrophotometers cannot generally be used to study reactions that are complete within less than about 20 s, as it takes that amount of time to manually mix the reagents and activate the instrument. Rapid mixing techniques, which generally achieve mixing in less than 2 ms, overcome this limitation. This chapter is concerned with the use of these techniques in the study of reactions which reach equilibrium; the application of these methods to the study of enzyme kinetics is described in several excellent texts (Cornish-Bowden, Fundamentals of enzyme kinetics. Portland Press, 1995; Gutfreund, Kinetics for the life sciences. Receptors, transmitters and catalysis. Cambridge University Press, 1995).There are various ways to monitor changes in concentration of reactants, intermediates and products after mixing, but the most common way is to use changes in optical signals (absorbance or fluorescence) which often accompany reactions. Although absorbance can sometimes be used, fluorescence is often preferred because of its greater sensitivity, particularly in monitoring conformational changes. Such methods are continuous with good time resolution but they seldom permit the direct determination of the concentrations of individual species. Alternatively, samples may be taken from the reaction volume, mixed with a chemical quenching agent to stop the reaction, and their contents assessed by techniques such as HPLC. These methods can directly determine the concentrations of different species, but are discontinuous and have a limited time resolution.
Marklof, Jens
2009-01-01
One of the central challenges in kinetic theory is the derivation of macroscopic evolution equations--describing, for example, the dynamics of an electron gas--from the underlying fundamental microscopic laws of classical or quantum mechanics. An iconic mathematical model in this research area is the Lorentz gas, which describes an ensemble of non-interacting point particles in an infinite array of spherical scatterers. In the case of a disordered scatterer configuration, the classical result...
Trochet, Mickaël; Mousseau, Normand
2017-10-01
With large specific and volumetric capacity, lithiated silicon is an excellent anode for lithium-ion batteries. Its application is challenged today, however, by the formation of an amorphous a -LixSi phase associated with a large volume change that occurs at relatively low Li concentration and remains only very partly understood at the microscopic level. In this paper, we characterize the full energy landscape associated with the onset of Li insertion in crystalline Si as a first step for understanding the lithiation process. We identify the diffusion mechanisms and migration energies for one to ten Li atoms in a Si crystal as well as the average lifetime of small lithium aggregates, using the kinetic activation-relaxation technique (kART), an off-lattice kinetic Monte-Carlo method with on-the-fly catalog building capabilities coupled to a newly developed force field (ReaxFF) used as potential based on ab initio results. We show that the short lifetimes of the bound states (from meV to ten meV) mean that Li atoms move in the interstitial sublattice with little interactions, explaining how high Li concentration in Si can be reached.
Energy Technology Data Exchange (ETDEWEB)
Indenhuck, A. [Wissenschaftlich-Technische Ingenieurberatung GmbH (WTI), Juelich (Germany)
2011-07-01
The author studied under which conditions the reactivity of a fuel element loaded transport and storage cask can be determined. From all available measuring methods only the source-jerk method (SJM), which is based on point kinetic reactor equations, is adequate for Monte-Carlo based simulations. The necessary measuring time of several 10 minutes seems to be acceptable in order to reach a sufficient statistical accuracy. For SRJ method validation measurements on known sources should be performed in order to compare the results with the calculated multiplication factor.