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

Science.gov (United States)

Tiwary, Pratyush

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

Atomistic simulations of dislocation processes in copper

DEFF Research Database (Denmark)

Vegge, T.; Jacobsen, K.W.

2002-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-03-24

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Quantum Corrections to the 'Atomistic' MOSFET Simulations

Science.gov (United States)

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

2000-01-01

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

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

International Nuclear Information System (INIS)

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

2005-01-01

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

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Science.gov (United States)

Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

2018-05-01

Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Directory of Open Access Journals (Sweden)

Zhiwei Zhang

2018-05-01

Full Text Available Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young’s modulus, ultimate tensile strength (UTS, and strain at fracture is observed.

Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

Science.gov (United States)

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

1999-01-01

We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

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

Science.gov (United States)

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

2010-04-15

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

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

KAUST Repository

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2013-01-01

We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide

Passing waves from atomistic to continuum

Science.gov (United States)

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

2018-02-01

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

Communication: Multiple atomistic force fields in a single enhanced sampling simulation

Energy Technology Data Exchange (ETDEWEB)

Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

2015-07-14

The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

Dynamic aspects of dislocation motion: atomistic simulations

International Nuclear Information System (INIS)

Bitzek, Erik; Gumbsch, Peter

2005-01-01

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

Atomistic simulations of graphite etching at realistic time scales.

Science.gov (United States)

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

2017-10-01

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

Computer code for the atomistic simulation of lattice defects and dynamics

International Nuclear Information System (INIS)

Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

1980-04-01

This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability

Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension

Science.gov (United States)

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.

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...

Adaptive resolution simulation of an atomistic protein in MARTINI water

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Soppa, E.A., E-mail: ewa.soppa@mpa.uni-stuttgart.de; Kohler, C., E-mail: christopher.kohler@mpa.uni-stuttgart.de; Roos, E., E-mail: eberhard.roos@mpa.uni-stuttgart.de

2014-03-01

Experimental investigations on the austenitic stainless steel X6CrNiNb18-10 (AISI – 347) and concomitant atomistic simulations of a FeNi nanocrystalline model system have been performed in order to understand the basic mechanisms of fatigue damage under cyclic loading. Using electron backscatter diffraction (EBSD) the influence of deformation induced martensitic transformation and NbC size distribution on the fatigue crack formation has been demonstrated. The martensite nucleates prevalently at grain boundaries, triple points and at the specimen free surface and forms small (∼1 µm sized) differently oriented grains. The atomistic simulations show the role of regions of a high density of stacking faults for the martensitic transformation.

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

Science.gov (United States)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

DEFF Research Database (Denmark)

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

2011-01-01

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

Atomistic simulation and continuum modeling of graphene nanoribbons under uniaxial tension

International Nuclear Information System (INIS)

Lu, Qiang; Gao, Wei; Huang, Rui

2011-01-01

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

Linking Well-Tempered Metadynamics Simulations with Experiments

Science.gov (United States)

Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele

2010-01-01

Abstract Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data. PMID:20441734

Atomistic spin dynamics simulations on Mn-doped GaAs and CuMn

Energy Technology Data Exchange (ETDEWEB)

Hellsvik, Johan, E-mail: johan.hellsvik@fysik.uu.s [Department of Physics and Materials Science, Uppsala University, Box 530, SE-751 21 Uppsala (Sweden)

2010-01-01

The magnetic dynamical behavior of two random alloys have been investigated in atomistic spin dynamics (ASD) simulations. For both materials, magnetic exchange parameters calculated with first principles electronic structure methods were used. From experiments it is well known that CuMn is a highly frustrated magnetic system and a good manifestation of a Heisenberg spin glass. In our ASD simulations the behavior of the autocorrelation function indicate spin glass behavior. The diluted magnetic semiconductor (DMS) Mn-doped GaAs is engineered with hopes of high enough Curie temperatures to operate in spintronic devices. Impurities such as As antisites and Mn interstitials change the exhange couplings from being mainly ferromagnetic to also have antiferromagnetic components. We explore how the resulting frustration affects the magnetization dynamics for a varying rate of As antisites.

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

Science.gov (United States)

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

2017-10-01

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

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

Science.gov (United States)

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

2000-01-01

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

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

Science.gov (United States)

Rapaport, D C

2009-04-01

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

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.

Long-time atomistic simulations with the Parallel Replica Dynamics method

Science.gov (United States)

Perez, Danny

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

Atomistic simulation of graphene-based polymer nanocomposites

International Nuclear Information System (INIS)

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

2016-01-01

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

Dynamic characteristics of nanoindentation using atomistic simulation

International Nuclear Information System (INIS)

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

2009-01-01

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

Dynamic characteristics of nanoindentation using atomistic simulation

Energy Technology Data Exchange (ETDEWEB)

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

2009-06-15

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

Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

2013-10-01

In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.

3d visualization of atomistic simulations on every desktop

Science.gov (United States)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-08-01

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

3d visualization of atomistic simulations on every desktop

International Nuclear Information System (INIS)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-01-01

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

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

Science.gov (United States)

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

2018-01-01

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

Atomistic Simulation of Initiation in Hexanitrostilbene

Science.gov (United States)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

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

DEFF Research Database (Denmark)

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

2007-01-01

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

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

International Nuclear Information System (INIS)

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

2005-01-01

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

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

DEFF Research Database (Denmark)

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

2017-01-01

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

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

International Nuclear Information System (INIS)

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

2007-01-01

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

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

Science.gov (United States)

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

2016-12-13

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

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...

Universality and Realistic Extensions to the Semi-Analytic Simulation Principle in GNSS Signal Processing

Directory of Open Access Journals (Sweden)

O. Jakubov

2012-06-01

Full Text Available Semi-analytic simulation principle in GNSS signal processing bypasses the bit-true operations at high sampling frequency. Instead, signals at the output branches of the integrate&dump blocks are successfully modeled, thus making extensive Monte Carlo simulations feasible. Methods for simulations of code and carrier tracking loops with BPSK, BOC signals have been introduced in the literature. Matlab toolboxes were designed and published. In this paper, we further extend the applicability of the approach. Firstly, we describe any GNSS signal as a special instance of linear multi-dimensional modulation. Thereby, we state universal framework for classification of differently modulated signals. Using such description, we derive the semi-analytic models generally. Secondly, we extend the model for realistic scenarios including delay in the feed back, slowly fading multipath effects, finite bandwidth, phase noise, and a combination of these. Finally, a discussion on connection of this semi-analytic model and position-velocity-time estimator is delivered, as well as comparison of theoretical and simulated characteristics, produced by a prototype simulator developed at CTU in Prague.

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

International Nuclear Information System (INIS)

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

2011-01-01

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

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

Science.gov (United States)

Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

2009-01-01

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Quantum-based Atomistic Simulation of Transition Metals

International Nuclear Information System (INIS)

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

2005-01-01

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

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

International Nuclear Information System (INIS)

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

2004-01-01

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

Atomistic simulations of contact area and conductance at nanoscale interfaces.

Science.gov (United States)

Hu, Xiaoli; Martini, Ashlie

2017-11-09

Atomistic simulations were used to study conductance across the interface between a nanoscale gold probe and a graphite surface with a step edge. Conductance on the graphite terrace was observed to increase with load and be approximately proportional to contact area calculated from the positions of atoms in the interface. The relationship between area and conductance was further explored by varying the position of the contact relative to the location of the graphite step edge. These simulations reproduced a previously-reported current dip at step edges measured experimentally and the trend was explained by changes in both contact area and the distribution of distances between atoms in the interface. The novel approach reported here provides a foundation for future studies of the fundamental relationships between conductance, load and surface topography at the atomic scale.

Near-ideal strength in metal nanotubes revealed by atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

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

2013-12-02

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

De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers

Energy Technology Data Exchange (ETDEWEB)

Nakano, A; Kalia, R K; Nomura, K; Sharma, A; Vashishta, P; Shimojo, F; van Duin, A; Goddard, III, W A; Biswas, R; Srivastava, D; Yang, L H

2006-09-04

We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) simulations explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) simulations are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling simulation algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto Petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/computation structures, as well as its implementation using hybrid Grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations--1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids--in addition to 134 billion-atom non-reactive space-time multiresolution MD, with the parallel efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM

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

NARCIS (Netherlands)

Starikov, Sergey V.; Stegailov, Vladimir V.

2009-01-01

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

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

International Nuclear Information System (INIS)

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

2010-01-01

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

Structural and functional analysis of glycoprotein butyrylcholinesterase using atomistic molecular dynamics

Science.gov (United States)

Bernardi, Austen; Faller, Roland

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

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

Science.gov (United States)

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

2018-03-01

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

Atomistic simulation of MgO nanowires subject to electromagnetic wave

International Nuclear Information System (INIS)

Wang, Xianqiao; Lee, James D

2010-01-01

This work is concerned with the application of atomistic field theory (AFT) in modeling and simulation of polarizable materials under an electromagnetic (EM) field. AFT enables us to express an atomic scale local property of a multi-element crystalline (which has more than one kind of atom in the unit cell) system in terms of the distortions of lattice cells and the rearrangement of atoms within the lattice cell, thereby making AFT suitable to fully reproduce both acoustic and optical branches in phonon dispersion relations. Due to the applied EM field, the inhomogeneous motions of discrete atoms in the polarizable crystal give rise to the rearrangement of microstructure and polarization. The AFT and its corresponding finite element implementation are briefly introduced. Single-crystal MgO nanowires under an EM field is modeled and simulated. The numerical results have demonstrated that AFT can serve as a tool to analyze the electromagnetic phenomena of multi-element crystal materials at micro/nano-level within a field framework

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

International Nuclear Information System (INIS)

Stukowski, Alexander

2010-01-01

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

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

Science.gov (United States)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

International Nuclear Information System (INIS)

Ogawa, Hiroshi

2015-01-01

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

Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

Science.gov (United States)

Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.

2011-01-01

Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

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

International Nuclear Information System (INIS)

Patinet, S.

2009-12-01

The glide of edge and screw dislocation in solid solution is modeled through atomistic simulations in two model alloys of Ni(Al) and Al(Mg) described within the embedded atom method. Our approach is based on the study of the elementary interaction between dislocations and solutes to derive solid solution hardening of face centered cubic binary alloys. We identify the physical origins of the intensity and range of the interaction between a dislocation and a solute atom. The thermally activated crossing of a solute atom by a dislocation is studied at the atomistic scale. We show that hardening of edge and screw segments are similar. We develop a line tension model that reproduces quantitatively the atomistic calculations of the flow stress. We identify the universality class to which the dislocation depinning transition in solid solution belongs. (author)

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

KAUST Repository

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

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 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.)

Atomistic Simulations of Small-scale Materials Tests of Nuclear Materials

International Nuclear Information System (INIS)

Shin, Chan Sun; Jin, Hyung Ha; Kwon, Jun Hyun

2012-01-01

Degradation of materials properties under neutron irradiation is one of the key issues affecting the lifetime of nuclear reactors. Evaluating the property changes of materials due to irradiations and understanding the role of microstructural changes on mechanical properties are required for ensuring reliable and safe operation of a nuclear reactor. However, high dose of neuron irradiation capabilities are rather limited and it is difficult to discriminate various factors affecting the property changes of materials. Ion beam irradiation can be used to investigate radiation damage to materials in a controlled way, but has the main limitation of small penetration depth in the length scale of micro meters. Over the past decade, the interest in the investigations of size-dependent mechanical properties has promoted the development of various small-scale materials tests, e.g. nanoindentation and micro/nano-pillar compression tests. Small-scale materials tests can address the issue of the limitation of small penetration depth of ion irradiation. In this paper, we present small-scale materials tests (experiments and simulation) which are applied to study the size and irradiation effects on mechanical properties. We have performed molecular dynamics simulations of nanoindentation and nanopillar compression tests. These atomistic simulations are expected to significantly contribute to the investigation of the fundamental deformation mechanism of small scale irradiated materials

Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins.

Science.gov (United States)

Lee, Kuo Hao; Chen, Jianhan

2017-11-15

Recasting temperature replica exchange (T-RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, J. Chem. Phys., 2011, 135, 194110). To critically examine if T-RE with independence sampling (T-REis) improves conformational sampling, we performed T-RE and T-REis simulations of ordered and disordered proteins using coarse-grained and atomistic models. The results demonstrate that T-REis effectively increase the replica mobility in temperatures space with minimal computational overhead, especially for folded proteins. However, enhanced mixing does not translate well into improved conformational sampling. The convergences of thermodynamic properties interested are similar, with slight improvements for T-REis of ordered systems. The study re-affirms the efficiency of T-RE does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational re-arrangements. Due to its simplicity and efficacy of enhanced mixing, T-REis is expected to be more effective when incorporated with various Hamiltonian-RE protocols. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

Directory of Open Access Journals (Sweden)

Qian Wang

2017-01-01

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

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.

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

Science.gov (United States)

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

2018-01-01

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

Atomistic simulations of screw dislocations in bcc tungsten: From core structures and static properties to interaction with vacancies

Energy Technology Data Exchange (ETDEWEB)

Xu, Ke [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Niu, Liang-Liang [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Department of Nuclear Engineering and Radiological Science, University of Michigan, Ann Arbor, MI 48109 (United States); Jin, Shuo, E-mail: jinshuo@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Shu, Xiaolin [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Xie, Hongxian [School of Mechanical Engineering, Hebei University of Technology, Tianjin 300132 (China); Wang, Lifang; Lu, Guang-Hong [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China)

2017-02-15

Atomistic simulations have been used to investigate the core structures, static properties of isolated 1/2 <1 1 1> screw dislocations, and their interaction with vacancies in bcc tungsten (W) based on three empirical interatomic potentials. Differential displacement maps show that only one embedded atom method potential is able to reproduce the compact non-degenerate core as evidenced by ab initio calculations. The obtained strain energy and stress distribution from atomistic simulations are, in general, consistent with elasticity theory predictions. In particular, one component of the calculated shear stress, which is not present according to elasticity theory, is non-negligible in the core region of our dislocation model. The differences between the results calculated from three interatomic potentials are in details, such as the specific value and the symmetry, but the trend of spatial distributions of static properties in the long range are close to each other. By calculating the binding energies between the dislocations and vacancies, we demonstrate that the dislocations act as vacancy sinks, which may be important for the nucleation and growth of hydrogen bubbles in W under irradiation.

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

Science.gov (United States)

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

2018-02-14

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

Redox reactions with empirical potentials: atomistic battery discharge simulations.

Science.gov (United States)

Dapp, Wolf B; Müser, Martin H

2013-08-14

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

Thermodynamics of low-temperature phyllosilicates: from a macroscopic perspective towards achieving atomistic simulation

International Nuclear Information System (INIS)

Dubacq, B.

2008-12-01

Phyllosilicates are important minerals in metamorphic petrology as well as in waste storage sites where clays are extensively used. Despite this fact, there is no thermodynamic model allowing to describe and to predict properly the behaviour of clay minerals (for example variation of volume with dehydration) and their phase relations with other minerals in metamorphic conditions. Inversely, the thermodynamic models of phengites are well constrained at high pressure and temperature but do not allow accurate thermo-barometric estimations at temperatures less than about 350 C. In this study, we propose two new thermodynamic models for smectites, illites, mixed-layers illites / smectites and phengites. With these models, it is possible to predict the composition of stable clays at low temperature and to estimate the pressure and temperature of crystallisation of di-octahedral aluminous phyllosilicates. These models take into consideration the hydration state of clay minerals as a function of pressure, temperature and water activity. The thermodynamic properties of solid solutions and hydrated mica-like end-members have been estimated in order to reproduce experimental results of i) clay dehydration, ii) nature of stable phases, iii) calorimetric measurements, as well as known (or estimated with independent methods) pressure-temperature conditions of crystallization of phyllosilicates analyses, from diagenesis conditions to ultra - high - pressure / temperature conditions. Phase diagrams have been computed with these models in simple systems. Conditions of crystallization of phyllosilicates have been estimated on many samples, including electron microprobe compositional maps. We investigated several approaches to estimate thermodynamic properties of minerals. All these methods revealed to be insufficiently accurate to estimate standard enthalpy of formation; calculated enthalpies of formation can not be directly used for thermo-barometric estimations. However, we

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

KAUST Repository

Shao, Jing

2015-10-27

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

Relaxation Mechanisms, Structure and Properties of Semi-Coherent Interfaces

Directory of Open Access Journals (Sweden)

Shuai Shao

2015-10-01

Full Text Available In this work, using the Cu–Ni (111 semi-coherent interface as a model system, we combine atomistic simulations and defect theory to reveal the relaxation mechanisms, structure, and properties of semi-coherent interfaces. By calculating the generalized stacking fault energy (GSFE profile of the interface, two stable structures and a high-energy structure are located. During the relaxation, the regions that possess the stable structures expand and develop into coherent regions; the regions with high-energy structure shrink into the intersection of misfit dislocations (nodes. This process reduces the interface excess potential energy but increases the core energy of the misfit dislocations and nodes. The core width is dependent on the GSFE of the interface. The high-energy structure relaxes by relative rotation and dilatation between the crystals. The relative rotation is responsible for the spiral pattern at nodes. The relative dilatation is responsible for the creation of free volume at nodes, which facilitates the nodes’ structural transformation. Several node structures have been observed and analyzed. The various structures have significant impact on the plastic deformation in terms of lattice dislocation nucleation, as well as the point defect formation energies.

Molecular modeling and simulation of atactic polystyrene/amorphous silica nanocomposites

International Nuclear Information System (INIS)

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

2016-01-01

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

From HADES to PARADISE-atomistic simulation of defects in minerals

Energy Technology Data Exchange (ETDEWEB)

Parker, Stephen C; Cooke, David J; Kerisit, Sebastien; Marmier, Arnaud S; Taylor, Sarah L; Taylor, Stuart N [Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom)

2004-07-14

The development of the HADES code by Michael Norgett in the 1970s enabled, for the first time, the routine simulation of point defects in inorganic solids at the atomic scale. Using examples from current research we illustrate how the scope and applications of atomistic simulations have widened with time and yet still follow an approach readily identifiable with this early work. Firstly we discuss the use of the Mott-Littleton methodology to study the segregation of various isovalent cations to the (00.1) and (01.2) surfaces of haematite ({alpha}-Fe{sub 2}O{sub 3}). The results show that the size of the impurities has a considerable effect on the magnitude of the segregation energy. We then extend these simulations to investigate the effect of the concentration of the impurities at the surface on the segregation process using a supercell approach. We consider next the effect of segregation to stepped surfaces illustrating this with recent work on segregation of La{sup 3+} to CaF{sub 2} surfaces, which show enhanced segregation to step edges. We discuss next the application of lattice dynamics to modelling point defects in complex oxide materials by applying this to the study of hydrogen incorporation into {beta}-Mg{sub 2}SiO{sub 4}. Finally our attention is turned to a method for considering the surface energy of physically defective surfaces and we illustrate its approach by considering the low index surfaces of {alpha}-Al{sub 2}O{sub 3}.

Atomistic mechanism of graphene growth on a SiC substrate: Large-scale molecular dynamics simulations based on a new charge-transfer bond-order type potential

Science.gov (United States)

Takamoto, So; Yamasaki, Takahiro; Nara, Jun; Ohno, Takahisa; Kaneta, Chioko; Hatano, Asuka; Izumi, Satoshi

2018-03-01

Thermal decomposition of silicon carbide is a promising approach for the fabrication of graphene. However, the atomistic growth mechanism of graphene remains unclear. This paper describes the development of a new charge-transfer interatomic potential. Carbon bonds with a wide variety of characteristics can be reproduced by the proposed vectorized bond-order term. A large-scale thermal decomposition simulation enables us to observe the continuous growth process of the multiring carbon structure. The annealing simulation reveals the atomistic process by which the multiring carbon structure is transformed to flat graphene involving only six-membered rings. Also, it is found that the surface atoms of the silicon carbide substrate enhance the homogeneous graphene formation.

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

Science.gov (United States)

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

Multiscale modeling of dislocation processes in BCC tantalum: bridging atomistic and mesoscale simulations

International Nuclear Information System (INIS)

Yang, L H; Tang, M; Moriarty, J A

2001-01-01

Plastic deformation in bcc metals at low temperatures and high-strain rates is controlled by the motion of a/2 screw dislocations, and understanding the fundamental atomistic processes of this motion is essential to develop predictive multiscale models of crystal plasticity. The multiscale modeling approach presented here for bcc Ta is based on information passing, where results of simulations at the atomic scale are used in simulations of plastic deformation at mesoscopic length scales via dislocation dynamics (DD). The relevant core properties of a/2 screw dislocations in Ta have been obtained using quantum-based interatomic potentials derived from model generalized pseudopotential theory and an ab-initio data base together with an accurate Green's-function simulation method that implements flexible boundary conditions. In particular, the stress-dependent activation enthalpy for the lowest-energy kink-pair mechanism has been calculated and fitted to a revealing analytic form. This is the critical quantity determining dislocation mobility in the DD simulations, and the present activation enthalpy is found to be in good agreement with the previous empirical form used to explain the temperature dependence of the yield stress

Simulation and visualization of ion-implantation in diamond

International Nuclear Information System (INIS)

Adler, Joan; Silverman, Amihai; Ierushalmi, Niv; Sorkin, Anastassia; Kalish, Rafi

2014-01-01

We have explored aspects of ion implantation in diamonds with molecular dynamics and tightbinding atomistic simulations. Relevant experiments and their potential applications as well as our computer models and computational approaches are described. Our simulations have been designed to answer questions proposed by experimental researchers concerning optimal laboratory schedules for the preparation of samples with potential applications to diamond membranes and NV centers for quantum computers. Simulation and visualization of results enable us to peek inside samples where experimental techniques cannot tread. In order to provide the requisite Brazilian component a new connection between these models and bootstrap percolation is made

Addressing uncertainty in atomistic machine learning

DEFF Research Database (Denmark)

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

2017-01-01

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

Semi-physical Simulation Platform of a Parafoil Nonlinear Dynamic System

International Nuclear Information System (INIS)

Gao Hai-Tao; Yang Sheng-Bo; Zhu Er-Lin; Sun Qing-Lin; Chen Zeng-Qiang; Kang Xiao-Feng

2013-01-01

Focusing on the problems in the process of simulation and experiment on a parafoil nonlinear dynamic system, such as limited methods, high cost and low efficiency we present a semi-physical simulation platform. It is designed by connecting parts of physical objects to a computer, and remedies the defect that a computer simulation is divorced from a real environment absolutely. The main components of the platform and its functions, as well as simulation flows, are introduced. The feasibility and validity are verified through a simulation experiment. The experimental results show that the platform has significance for improving the quality of the parafoil fixed-point airdrop system, shortening the development cycle and saving cost

GYSELA, a full-f global gyrokinetic Semi-Lagrangian code for ITG turbulence simulations

International Nuclear Information System (INIS)

Grandgirard, V.; Sarazin, Y.; Garbet, X.; Dif-Pradalier, G.; Ghendrih, Ph.; Crouseilles, N.; Latu, G.; Sonnendruecker, E.; Besse, N.; Bertrand, P.

2006-01-01

This work addresses non-linear global gyrokinetic simulations of ion temperature gradient (ITG) driven turbulence with the GYSELA code. The particularity of GYSELA code is to use a fixed grid with a Semi-Lagrangian (SL) scheme and this for the entire distribution function. The 4D non-linear drift-kinetic version of the code already showns the interest of such a SL method which exhibits good properties of energy conservation in non-linear regime as well as an accurate description of fine spatial scales. The code has been upgrated to run 5D simulations of toroidal ITG turbulence. Linear benchmarks and non-linear first results prove that semi-lagrangian codes can be a credible alternative for gyrokinetic simulations

Atomistic minimal model for estimating profile of electrodeposited nanopatterns

Science.gov (United States)

Asgharpour Hassankiadeh, Somayeh; Sadeghi, Ali

2018-06-01

We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip.

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

Directory of Open Access Journals (Sweden)

Elena ePapaleo

2015-05-01

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

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

Directory of Open Access Journals (Sweden)

Pavel V. Komarov

2013-09-01

Full Text Available Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic and minority (hydrophilic subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping mechanism as a significant contributor to the proton conductivity.

Physically representative atomistic modeling of atomic-scale friction

Science.gov (United States)

Dong, Yalin

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

Atomistic simulation of fatigue in face centred cubic metals

International Nuclear Information System (INIS)

Fan, Zhengxuan

2016-01-01

Fatigue is one of the major damage mechanisms of metals. It is characterized by strong environmental effects and wide lifetime dispersions which must be better understood. Different face centred cubic metals, al, Cu, Ni, and Ag are analyzed. The mechanical behaviour of surface steps naturally created by the glide of dislocations subjected to cyclic loading is examined using molecular dynamics simulations in vacuum and in air for Cu and Ni. an atomistic reconstruction phenomenon is observed at these surface steps which can induce strong irreversibility. Three different mechanisms of reconstruction are defined. Surface slip irreversibility under cyclic loading is analyzed. all surface steps are intrinsically irreversible under usual fatigue laboratory loading amplitude without the arrival of opposite sign dislocations on direct neighbor plane.With opposite sign dislocations on non direct neighbour planes, irreversibility cumulates cycle by cycle and a micro-notch is produced whose depth gradually increases.Oxygen environment affects the surface (first stage of oxidation) but does not lead to higher irreversibility as it has no major influence on the different mechanisms linked to surface relief evolution.a rough estimation of surface irreversibility is carried out for pure edge dislocations in persistent slip bands in so-called wavy materials. It gives an irreversibility fraction between 0.5 and 0.75 in copper in vacuum and in air, in agreement with recent atomic force microscopy measurements.Crack propagation mechanisms are simulated in inert environment. Cracks can propagate owing to the irreversibility of generated dislocations because of their mutual interactions up to the formation of dislocation junctions. (author) [fr

Axisymmetric Tornado Simulations with a Semi-Slip Boundary

Directory of Open Access Journals (Sweden)

Brian H. Fiedler

2017-12-01

Full Text Available The structure of natural tornadoes and simulated analogs are sensitive to the lower boundary condition for friction. Three-dimensional numerical simulations of storms require a choice for turbulence parameterizations and resolution of wind near the lower boundary. This article explores some of the consequences of choices of a surface drag coefficient on the structure of a mature simulated tornado, using a conventional axisymmetric model. The surface drag parameterization is explored over the range of the semi-slip condition, including the extremes of no-slip and free-slip. A moderate semi-slip condition allows for an extreme pressure deficit, but without the unrealistic vortex breakdown of the no-slip condition.

Atomistically-informed dislocation dynamics in FCC crystals

International Nuclear Information System (INIS)

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

2008-01-01

Full text of publication follows. We will present a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions, and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our fundings to the plastic behaviour of' monocrystalline fcc metals. (authors)

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

Science.gov (United States)

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations

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...... that was not included in our model. In numerous independent simulations we observed the formation of a salt bridge between ARC 27 and GLU40. The salt bridge closed the flexible loop that formed in the linker and kept it in the vicinity of the membrane-water interface. All simulations supported this conclusion...... that the linker has a clear affinity for the interface and preferentially arranges its residues to reside next to the membrane, without a tendency to relocate into the water phase. Furthermore, an extensive analysis of databases for sequences of membrane proteins that have a single transmembrane helical segment...

Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

Science.gov (United States)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

A semi-empirical approach to calculate gamma activities in environmental samples

International Nuclear Information System (INIS)

Palacios, D.; Barros, H.; Alfonso, J.; Perez, K.; Trujillo, M.; Losada, M.

2006-01-01

We propose a semi-empirical method to calculate radionuclide concentrations in environmental samples without the use of reference material and avoiding the typical complexity of Monte-Carlo codes. The calculation of total efficiencies was carried out from a relative efficiency curve (obtained from the gamma spectra data), and the geometric (simulated by Monte-Carlo), absorption, sample and intrinsic efficiencies at energies between 130 and 3000 keV. The absorption and sample efficiencies were determined from the mass absorption coefficients, obtained by the web program XCOM. Deviations between computed results and measured efficiencies for the RGTh-1 reference material are mostly within 10%. Radionuclide activities in marine sediment samples calculated by the proposed method and by the experimental relative method were in satisfactory agreement. The developed method can be used for routine environmental monitoring when efficiency uncertainties of 10% can be sufficient.(Author)

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.

Redox reactions with empirical potentials: Atomistic battery discharge simulations

OpenAIRE

Dapp, Wolf B.; Müser, Martin H.

2013-01-01

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Atomistic simulations of thermal transport in Si and SiGe based materials: From bulk to nanostructures

Science.gov (United States)

Savic, Ivana; Mingo, Natalio; Donadio, Davide; Galli, Giulia

2010-03-01

It has been recently proposed that Si and SiGe based nanostructured materials may exhibit low thermal conductivity and overall promising properties for thermoelectric applications. Hence there is a considerable interest in developing accurate theoretical and computational methods which can help interpret recent measurements, identify the physical origin of the reduced thermal conductivity, as well as shed light on the interplay between disorder and nanostructuring in determining a high figure of merit. In this work, we investigate the capability of an atomistic Green's function method [1] to describe phonon transport in several types of Si and SiGe based systems: amorphous Si, SiGe alloys, planar and nanodot Si/SiGe multilayers. We compare our results with experimental data [2,3], and with the findings of molecular dynamics simulations and calculations based on the Boltzmann transport equation. [1] I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008). [2] S.-M. Lee, D. G. Cahill, and R. Venkatasubramanian, Appl. Phys. Lett. 70, 2957 (1997). [3] G. Pernot et al., submitted.

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

Science.gov (United States)

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

2016-01-01

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

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

KAUST Repository

Hong, Bingbing

2013-10-02

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

Atomistic modeling of carbon Cottrell atmospheres in bcc iron

Science.gov (United States)

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

2013-01-01

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

Semi-Automated Processing of Trajectory Simulator Output Files for Model Evaluation

Science.gov (United States)

2018-01-01

ARL-TR-8284 ● JAN 2018 US Army Research Laboratory Semi-Automated Processing of Trajectory Simulator Output Files for Model...Semi-Automated Processing of Trajectory Simulator Output Files for Model Evaluation 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...although some minor changes may be needed. The program processes a GTRAJ output text file that contains results from 2 or more simulations , where each

On the use of atomistic simulations to aid bulk metallic glasses structural elucidation with solid-state NMR.

Science.gov (United States)

Ferreira, Ary R; Rino, José P

2017-08-24

Solid-state nuclear magnetic resonance (ssNMR) experimental 27 Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

Energy Technology Data Exchange (ETDEWEB)

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

2014-02-21

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

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

International Nuclear Information System (INIS)

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

2014-01-01

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

Atomistic simulations of the yielding of gold nanowires

International Nuclear Information System (INIS)

Diao Jiankuai; Gall, Ken; Dunn, Martin L.; Zimmerman, Jonathan A.

2006-01-01

We performed atomistic simulations to study the effect of free surfaces on the yielding of gold nanowires. Tensile surface stresses on the surfaces of the nanowires cause them to contract along the length with respect to the bulk face-centered cubic lattice and induce compressive stress in the interior. When the cross-sectional area of a nanowire is less than 2.45 nm x 2.45 nm, the wire yields under its surface stresses. Under external forces and surface stresses, nanowires yield via the nucleation and propagation of the {1 1 1} partial dislocations. The magnitudes of the tensile and compressive yield stress of nanowires increase and decrease, respectively, with a decrease of the wire width. The magnitude of the tensile yield stress is much larger than that of the compressive yield stress for small nanowires, while for small nanowires, tensile and compressive yield stresses have similar magnitudes. The critical resolved shear stress (RSS) by external forces depends on wire width, orientation and loading condition (tension vs. compression). However, the critical RSS in the interior of the nanowires, which is exerted by both the external force and the surface-stress-induced compressive stress, does not change significantly with wire width for same orientation and same loading condition, and can thus serve as a 'local' criterion. This local criterion is invoked to explain the observed size dependence of yield behavior and tensile/compressive yield stress asymmetry, considering surface stress effects and different slip systems active in tensile and compressive yielding

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

International Nuclear Information System (INIS)

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

2013-01-01

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

Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations

DEFF Research Database (Denmark)

Franova, M. D.; Vattulainen, I.; Ollila, O. H. S.

2014-01-01

The lateral pressure profile of lipid bilayers has gained a lot of attention, since changes in the pressure profile have been suggested to shift the membrane protein conformational equilibrium. This relation has been mostly studied with theoretical methods, especially with molecular dynamics....../monomer fluorescence ratio has been assumed to represent the lateral pressure in the location of the pyrene moieties. Here, we consider the validity of this assumption through atomistic molecular dynamics simulations in a DOPC (dioleoylphosphatidylcholine) membrane, which hosts di-pyr-PC probes with different acyl...... simulations, since established methods to measure the lateral pressure profile experimentally have not been available. The only experiments that have attempted to gauge the lateral pressure profile have been done by using di-pyrenyl-phosphatidylcholine (di-pyr-PC) probes. In these experiments, the excimer...

A semi-physical simulation platform of attitude determination and control system for satellite

Directory of Open Access Journals (Sweden)

Yuanjin Yu

2016-05-01

Full Text Available A semi-physical simulation platform for attitude determination and control system is proposed to verify the attitude estimator and controller on ground. A simulation target, a host PC, many attitude sensors, and actuators compose the simulation platform. The simulation target is composed of a central processing unit board with VxWorks operating system and many input/output boards connected via Compact Peripheral Component Interconnect bus. The executable programs in target are automatically generated from the simulation models in Simulink based on Real-Time Workshop of MATLAB. A three-axes gyroscope, a three-axes magnetometer, a sun sensor, a star tracer, three flywheels, and a Global Positioning System receiver are connected to the simulation target, which formulates the attitude control cycle of a satellite. The simulation models of the attitude determination and control system are described in detail. Finally, the semi-physical simulation platform is used to demonstrate the availability and rationality of the control scheme of a micro-satellite. Comparing the results between the numerical simulation in Simulink and the semi-physical simulation, the semi-physical simulation platform is available and the control scheme successfully achieves three-axes stabilization.

Self-evolving atomistic kinetic Monte Carlo: fundamentals and applications

International Nuclear Information System (INIS)

Xu Haixuan; Osetsky, Yuri N; Stoller, Roger E

2012-01-01

The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed and applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.

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.

Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

Science.gov (United States)

Lépinoux, J.; Sigli, C.

2018-01-01

In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.

AACSD: An atomistic analyzer for crystal structure and defects

Science.gov (United States)

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

2018-01-01

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

Magneto-optical properties of semi-parabolic plus semi-inverse squared quantum wells

Science.gov (United States)

Tung, Luong V.; Vinh, Pham T.; Phuc, Huynh V.

2018-06-01

We theoretically study the optical absorption in a quantum well with the semi-parabolic potential plus the semi-inverse squared potential (SPSIS) in the presence of a static magnetic field in which both one- and two-photon absorption processes have been taken into account. The expression of the magneto-optical absorption coefficient (MOAC) is expressed by the second-order golden rule approximation including the electron-LO phonon interaction. We also use the profile method to obtain the full width at half maximum (FWHM) of the absorption peaks. Our numerical results show that either MOAC or FWHM strongly depends on the confinement frequency, temperature, and magnetic field but their dependence on the parameter β is very weak. The temperature dependence of FWHM is consistent with the previous theoretical and experimental works.

The Design and Semi-Physical Simulation Test of Fault-Tolerant Controller for Aero Engine

Science.gov (United States)

Liu, Yuan; Zhang, Xin; Zhang, Tianhong

2017-11-01

A new fault-tolerant control method for aero engine is proposed, which can accurately diagnose the sensor fault by Kalman filter banks and reconstruct the signal by real-time on-board adaptive model combing with a simplified real-time model and an improved Kalman filter. In order to verify the feasibility of the method proposed, a semi-physical simulation experiment has been carried out. Besides the real I/O interfaces, controller hardware and the virtual plant model, semi-physical simulation system also contains real fuel system. Compared with the hardware-in-the-loop (HIL) simulation, semi-physical simulation system has a higher degree of confidence. In order to meet the needs of semi-physical simulation, a rapid prototyping controller with fault-tolerant control ability based on NI CompactRIO platform is designed and verified on the semi-physical simulation test platform. The result shows that the controller can realize the aero engine control safely and reliably with little influence on controller performance in the event of fault on sensor.

Numerical simulation of a semi-indirect evaporative cooler

Energy Technology Data Exchange (ETDEWEB)

Martin, R. Herrero [Departamento de Ingenieria Termica y de Fluidos, Universidad Politecnica de Cartagena, C/Dr. Fleming, s/n (Campus Muralla), 30202 Cartagena, Murcia (Spain)

2009-11-15

This paper presents the experimental study and numerical simulation of a semi-indirect evaporative cooler (SIEC), which acts as an energy recovery device in air conditioning systems. The numerical simulation was conducted by applying the CFD software FLUENT implementing a UDF to model evaporation/condensation. The numerical model was validated by comparing the simulation results with experimental data. Experimental data and numerical results agree for the lower relative humidity series but not for higher relative humidity values. (author)

From empirical to ab initio: transferable potentials in the atomistic simulation of amorphous carbons

International Nuclear Information System (INIS)

Marks, N.A.; Goringe, C.M.; McKenzie, D.R.; McCulloch, D.G.; Royal Melbourne Institute of Technology University, Melbourne, VIC

2000-01-01

Full text: Silicon is often described as the prototype covalent material, and when it comes to developing atomistic models this situation is well described by the sentiment that 'everything works for silicon'. The same cannot be said for carbon though, where the interaction potential has always proved problematical, be it with empirical, tight-binding or ab initio methods. Thus far the most decisive contributions to understanding amorphous carbon networks have come from ab initio simulations using the Car-Parrinello method, where the fully quantum treatment of the valence electrons has provided unexpected insight into the local structure. However such first principles calculations are restricted spatially and temporally to systems with approximately 100 atoms and times of order one picosecond. There is therefore demand for less expensive techniques capable of resolving important questions whose solution can only to found with larger simulations running for longer times. In the case of tetrahedral amorphous carbon, such issues include the release of compressive stress through annealing, the origin of graphitic surface layers and the nature of the film growth process and thermal spike. Against this background tight-binding molecular dynamics has emerged as a popular alternative to first principles methods, and our group has an ongoing program to understand film growth using one of the efficient variants of tight-binding. Another direction of research is a new empirical potential based on the Environment Dependent Interaction Potential (EDIP) recently developed for silicon. The EDIP approach represents a promising direction for empirical potentials through its use of ab initio data to motivate the functional form as well as the more conventional parametrisation. By inverting ab initio cohesive energy curves the authors of EDIP arrived at a pair potential expression which reduces to the well-known Stillinger-Weber form at integer coordination, while providing

How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations

DEFF Research Database (Denmark)

Aijanen, T.; Koivuniemi, A.; Javanainen, M.

2014-01-01

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...

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

NARCIS (Netherlands)

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

2016-01-01

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

Simulating the Physical World

Science.gov (United States)

Berendsen, Herman J. C.

2004-06-01

The simulation of physical systems requires a simplified, hierarchical approach which models each level from the atomistic to the macroscopic scale. From quantum mechanics to fluid dynamics, this book systematically treats the broad scope of computer modeling and simulations, describing the fundamental theory behind each level of approximation. Berendsen evaluates each stage in relation to its applications giving the reader insight into the possibilities and limitations of the models. Practical guidance for applications and sample programs in Python are provided. With a strong emphasis on molecular models in chemistry and biochemistry, this book will be suitable for advanced undergraduate and graduate courses on molecular modeling and simulation within physics, biophysics, physical chemistry and materials science. It will also be a useful reference to all those working in the field. Additional resources for this title including solutions for instructors and programs are available online at www.cambridge.org/9780521835275. The first book to cover the wide range of modeling and simulations, from atomistic to the macroscopic scale, in a systematic fashion Providing a wealth of background material, it does not assume advanced knowledge and is eminently suitable for course use Contains practical examples and sample programs in Python

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

Science.gov (United States)

Zhai, Ming-Xing; Wang, Xue-Feng

2016-01-01

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

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

Atomistic k ⋅ p theory

Energy Technology Data Exchange (ETDEWEB)

Pryor, Craig E., E-mail: craig-pryor@uiowa.edu [Department of Physics and Astronomy, University of Iowa, Iowa City, Iowa 52242 (United States); Pistol, M.-E., E-mail: mats-erik.pistol@ftf.lth.se [NanoLund and Solid State Physics, Lund University, P.O. Box 118, 221 00 Lund (Sweden)

2015-12-14

Pseudopotentials, tight-binding models, and k ⋅ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ⋅ p theory. In its usual formulation, k ⋅ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ⋅ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp{sup 3} tight-binding model. We can thus directly derive the parameters in the sp{sup 3} tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III–V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ⋅ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ⋅ p models to be combined in the same system.

Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations

DEFF Research Database (Denmark)

Koivuniemi, A.; Vuorela, T.; Kovanen, P. T.

2012-01-01

molecular dynamics simulations to unravel the mechanisms associated with the CETP-mediated lipid exchange. To this end we used both atomistic and coarse-grained models whose results were consistent with each other. We found CETP to bind to the surface of high density lipoprotein (HDL) -like lipid droplets......Cholesteryl ester transfer protein (CETP) transports cholesteryl esters, triglycerides, and phospholipids between different lipoprotein fractions in blood plasma. The inhibition of CETP has been shown to be a sound strategy to prevent and treat the development of coronary heart disease. We employed...... evidence that helix X acts as a lid which conducts lipid exchange by alternating the open and closed states. The findings have potential for the design of novel molecular agents to inhibit the activity of CETP....

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

International Nuclear Information System (INIS)

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

2011-01-01

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

Evaluating variability with atomistic simulations: the effect of potential and calculation methodology on the modeling of lattice and elastic constants

Science.gov (United States)

Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.

2018-07-01

Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

Science.gov (United States)

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-01

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

Simulation of a SAGD well blowout using a reservoir-wellbore coupled simulator

Energy Technology Data Exchange (ETDEWEB)

Walter, J.; Vanegas, P.; Cunha, L.B. [Alberta Univ., Edmonton, AB (Canada); Worth, D.J. [C-FER Technologies, Edmonton, AB (Canada); Crepin, S. [Petrocedeno, Caracas (Venezuela)

2008-10-15

Single barrier completion systems are typically used in SAGD projects due to the lack of equipment suitable for high temperature SAGD downhole environments. This study used a wellbore and reservoir coupled thermal simulator tool to investigate the blowout behaviour of a steam assisted gravity drainage (SAGD) well pair when the safety barrier has failed. Fluid flow pressure drop through the wellbore and heat losses between the wellbore and the reservoir were modelled using a discretized wellbore option and a semi-analytical model. The fully coupled mechanistic model accounted for the simultaneous transient pressure and temperature variations along the wellbore and the reservoir. The simulations were used to predict flowing potential and fluid compositions of both wells in a SAGD well pair under various flowing conditions. Blowout scenarios were created for 3 different points in the well pair's life. Three flow paths during the blowout were evaluated for both the production and injection wells. Results of the study were used to conduct a comparative risk assessment between a double barrier and a single barrier completion. The modelling study confirmed that both the injection and production wells had the potential for blowouts lasting significant periods of time, with liquid rates over 50 times the normal production liquid rates. The model successfully predicted the blowout flow potential of the SAGD well pairs. 8 refs., 3 tabs., 18 figs.

Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

International Nuclear Information System (INIS)

Djurabekova, F.G.; Domingos, R.; Cerchiara, G.; Castin, N.; Vincent, E.; Malerba, L.

2007-01-01

Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed

Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

Energy Technology Data Exchange (ETDEWEB)

Djurabekova, F.G. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Domingos, R. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Cerchiara, G. [Department of Nuclear and Production Engineering, University of Pisa (Italy); Castin, N. [Catholic University of Louvain-la-Neuve (Belgium); Vincent, E. [LMPGM UMR-8517, University of Lille I, Villeneuve d' Ascq (France); Malerba, L. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium)]. E-mail: lmalerba@sckcen.be

2007-02-15

Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed.

Cationic Dimyristoylphosphatidylcholine and Dioleoyloxytrimethylammonium Propane Lipid Bilayers: Atomistic Insight for Structure and Dynamics

DEFF Research Database (Denmark)

Zhao, W.; Gurtovenko, A. A.; Vattulainen, I.

2012-01-01

We performed atomistic molecular dynamics simulations of lipid bilayers consisting of a mixture of cationic dioleoyloxytrimethylammonium propane (DOTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) lipids at different DOTAP fractions. Our primary focus was the specific effects...... of unsaturated lipid chains on structural and dynamic properties of mixed cationic bilayers. The bilayer area, as well as the ordering of lipid tails, shows a pronounced nonmonotonic behavior when TAP lipid fraction increases. The minimum in area (maximum in ordering) was observed for a bilayer with TAP fraction...... lipids, which were found to form PC-PC and PC-TAP pairs, and the formation of lipid clusters....

Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc(1) complex

DEFF Research Database (Denmark)

Poyry, S.; Cramariuc, O.; Postila, P. A.

2013-01-01

by both ensuring the structural integrity of the protein complex and also by taking part in the proton uptake. Yet, the atom-scale understanding of these highly charged four-tail lipids in the cyt bc(1) function has remained quite unclear. We consider this issue through atomistic molecular dynamics...... the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics...... simulations that are applied to the entire cyt bc(1) dimer of the purple photosynthetic bacterium Rhodobacter capsulatus embedded in a lipid bilayer. We find CLs to spontaneously diffuse to the dimer interface to the immediate vicinity of the higher potential heme b groups of the complex's catalytic Q...

Constraint methods that accelerate free-energy simulations of biomolecules.

Science.gov (United States)

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

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

Science.gov (United States)

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

2018-03-27

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

Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry

DEFF Research Database (Denmark)

Petersen, Michael; Madsen, Jeppe B; Jørgensen, Thomas J D

2017-01-01

activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations...... are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1......Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen...

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......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...... 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....

Crack growth and fracture toughness of amorphous Li-Si anodes: Mechanisms and role of charging/discharging studied by atomistic simulations

Science.gov (United States)

Khosrownejad, S. M.; Curtin, W. A.

2017-10-01

Fracture is the main cause of degradation and capacity fading in lithiated silicon during cycling. Experiments on the fracture of lithiated silicon show conflicting results, and so mechanistic models can help interpret experiments and guide component design. Here, large-scale K-controlled atomistic simulations of crack propagation (R-curve KI vs. Δa) are performed at LixSi compositions x = 0.5 , 1.0 , 1.5 for as-quenched/relaxed samples and at x = 0.5 , 1.0 for samples created by discharging from higher Li compositions. In all cases, the fracture mechanism is void nucleation, growth, and coalescence. In as-quenched materials, with increasing Li content the plastic flow stress and elastic moduli decrease but void nucleation and growth happen at smaller stress, so that the initial fracture toughness KIc ≈ 1.0 MPa√{ m} decreases slightly but the initial fracture energy JIc ≈ 10.5J/m2 is similar. After 10 nm of crack growth, the fracture toughnesses increase and become similar at KIc ≈ 1.9 MPa√{ m} across all compositions. Plane-strain equi-biaxial expansion simulations of uncracked samples provide complementary information on void nucleation and growth. The simulations are interpreted within the framework of Gurson model for ductile fracture, which predicts JIc = ασy D where α ≃ 1 and D is the void spacing, and good agreement is found. In spite of flowing plastically, the fracture toughness of LixSi is low because voids nucleate within nano-sized distances ahead of the crack (D ≈ 1nm). Scaling simulation results to experimental conditions, reasonable agreement with experimentally-estimated fracture toughnesses is obtained. The discharging process facilitates void nucleation but decreases the flow stress (as shown previously), leading to enhanced fracture toughness at all levels of crack growth. Therefore, the fracture behavior of lithiated silicon at a given composition is not a material property but instead depends on the history of charging

Key role of water in proton transfer at the Q(o)-site of the cytochrome bc(1) complex predicted by atomistic molecular dynamics simulations

DEFF Research Database (Denmark)

Postila, P. A.; Kaszuba, K.; Sarewicz, M.

2013-01-01

of the cyt bc(1) function have remained unclear especially regarding the substrate binding at the Q(o)-site. In this work we address this issue by performing extensive atomistic molecular dynamics simulations with the cyt bc(1) complex of Rhodobacter capsulatus embedded in a lipid bilayer. Based...... on the simulations we are able to show the atom-level binding modes of two substrate forms: quinol (QH(2)) and quinone (Q). The QH(2) binding at the Q(o)-site involves a coordinated water arrangement that produces an exceptionally close and stable interaction between the cyt b and iron sulfur protein subunits...

Molecular dynamics simulation of self-driven solid state amorphization at Ni/Zr interfaces

Energy Technology Data Exchange (ETDEWEB)

Fernandes, M.G. [Ecole Polytechnique, 91 - Palaiseau (France). Lab. des Solides Irradies]|[Massachusetts Inst. of Tech., Cambridge (United States). Dept. of Materials Science and Engineering; Pontikis, V. [Ecole Polytechnique, 91 - Palaiseau (France). Lab. des Solides Irradies

1996-08-01

We present results of an atomistic simulation study of a Ni/Zr heterophase interface. Our model is consistent with experiments and shows that the semi-coherent boundary is stable at finite temperatures and mixing does not occur. The introduction of free surfaces intercepting the hetero-interface allows for composition fluctuations to take place and trigger the mixing process. Interdiffusion proceeds and produces a disordered structure which propagates into the volume at the expense of the ordered phase. (orig.)

Atomistic approach for modeling metal-semiconductor interfaces

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Atomistically informed solute drag in Al–Mg

International Nuclear Information System (INIS)

Zhang, F; Curtin, W A

2008-01-01

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

Cathodoluminescence studies of chevron features in semi-polar (11 2 ¯ 2 ) InGaN/GaN multiple quantum well structures

Science.gov (United States)

Brasser, C.; Bruckbauer, J.; Gong, Y.; Jiu, L.; Bai, J.; Warzecha, M.; Edwards, P. R.; Wang, T.; Martin, R. W.

2018-05-01

Epitaxial overgrowth of semi-polar III-nitride layers and devices often leads to arrowhead-shaped surface features, referred to as chevrons. We report on a study into the optical, structural, and electrical properties of these features occurring in two very different semi-polar structures, a blue-emitting multiple quantum well structure, and an amber-emitting light-emitting diode. Cathodoluminescence (CL) hyperspectral imaging has highlighted shifts in their emission energy, occurring in the region of the chevron. These variations are due to different semi-polar planes introduced in the chevron arms resulting in a lack of uniformity in the InN incorporation across samples, and the disruption of the structure which could cause a narrowing of the quantum wells (QWs) in this region. Atomic force microscopy has revealed that chevrons can penetrate over 150 nm into the sample and quench light emission from the active layers. The dominance of non-radiative recombination in the chevron region was exposed by simultaneous measurement of CL and the electron beam-induced current. Overall, these results provide an overview of the nature and impact of chevrons on the luminescence of semi-polar devices.

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

Energy Technology Data Exchange (ETDEWEB)

Gray, Alan [The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Harlen, Oliver G. [University of Leeds, Leeds LS2 9JT (United Kingdom); Harris, Sarah A., E-mail: s.a.harris@leeds.ac.uk [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Leeds, Leeds LS2 9JT (United Kingdom); Khalid, Syma; Leung, Yuk Ming [University of Southampton, Southampton SO17 1BJ (United Kingdom); Lonsdale, Richard [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg (Germany); Mulholland, Adrian J. [University of Bristol, Bristol BS8 1TS (United Kingdom); Pearson, Arwen R. [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Hamburg, Hamburg (Germany); Read, Daniel J.; Richardson, Robin A. [University of Leeds, Leeds LS2 9JT (United Kingdom); The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom)

2015-01-01

The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

From beta-relaxation to alpha-decay: Atomistic picture from molecular dynamics simulations for glass-forming Ni0.5Zr0.5 melt

Energy Technology Data Exchange (ETDEWEB)

Teichler, Helmar [Inst. Materialphysik, Univ Goettingen (Germany)

2013-07-01

In glass-forming melts the decay of structural fluctuation shows the well known transition from beta-relaxation (von-Schweidler law with exponent b) to alpha-decay (KWW law with exponent beta). Here we present results from molecular dynamics simulations for a metallic glass forming Ni0.5Zr0.5 model aimed at giving an understanding of this transition on the atomistic scale. At the considered temperature below mode coupling Tc, the dynamics of the system can be interpreted by residence of the particles in their neighbour cages and escape from the cages as rare processes. Our analysis yields that the fraction of residing particles is characterized by a hierarchical law in time, with von-Schweidler b explicitly related to the exponent of this law. In the alpha-decay regime the stretching exponent reflects, in addition, floating of the cages due to strain effects of escaped particles. Accordingly, the change from beta-relaxation to alpha-decay indicates the transition from low to large fraction of escaped particles.

Reducing the cost of semi-automated in-gel tryptic digestion and GeLC sample preparation for high-throughput proteomics.

Science.gov (United States)

Ruelcke, Jayde E; Loo, Dorothy; Hill, Michelle M

2016-10-21

Peptide generation by trypsin digestion is typically the first step in mass spectrometry-based proteomics experiments, including 'bottom-up' discovery and targeted proteomics using multiple reaction monitoring. Manual tryptic digest and the subsequent clean-up steps can add variability even before the sample reaches the analytical platform. While specialized filter plates and tips have been designed for automated sample processing, the specialty reagents required may not be accessible or feasible due to their high cost. Here, we report a lower-cost semi-automated protocol for in-gel digestion and GeLC using standard 96-well microplates. Further cost savings were realized by re-using reagent tips with optimized sample ordering. To evaluate the methodology, we compared a simple mixture of 7 proteins and a complex cell-lysate sample. The results across three replicates showed that our semi-automated protocol had performance equal to or better than a manual in-gel digestion with respect to replicate variability and level of contamination. In this paper, we also provide the Agilent Bravo method file, which can be adapted to other liquid handlers. The simplicity, reproducibility, and cost-effectiveness of our semi-automated protocol make it ideal for routine in-gel and GeLC sample preparations, as well as high throughput processing of large clinical sample cohorts. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigating dislocation motion through a field of solutes with atomistic simulations and reaction rate theory

International Nuclear Information System (INIS)

Saroukhani, S.; Warner, D.H.

2017-01-01

The rate of thermally activated dislocation motion across a field of solutes is studied using traditional and modern atomistically informed rate theories. First, the accuracy of popular variants of the Harmonic Transition State Theory, as the most common approach, is examined by comparing predictions to direct MD simulations. It is shown that HTST predictions are grossly inaccurate due to the anharmonic effect of thermal softening. Next, the utility of the Transition Interface Sampling was examined as the method was recently shown to be effective for predicting the rate of dislocation-precipitate interactions. For dislocation-solute interactions studied here, TIS is found to be accurate only when the dislocation overcomes multiple obstacles at a time, i.e. jerky motion, and it is inaccurate in the unpinning regime where the energy barrier is of diffusive nature. It is then shown that the Partial Path TIS method - designed for diffusive barriers - provides accurate predictions in the unpinning regime. The two methods are then used to study the temperature and load dependence of the rate. It is shown that Meyer-Neldel (MN) rule prediction of the entropy barrier is not as accurate as it is in the case of dislocation-precipitate interactions. In response, an alternative model is proposed that provides an accurate prediction of the entropy barrier. This model can be combined with TST to offer an attractively simple rate prediction approach. Lastly, (PP)TIS is used to predict the Strain Rate Sensitivity (SRS) factor at experimental strain rates and the predictions are compared to experimental values.

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

Science.gov (United States)

Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

2015-01-01

Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores

Science.gov (United States)

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

Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations

DEFF Research Database (Denmark)

Heikkila, E.; Martinez-Seara, H.; Gurtovenko, A. A.

2014-01-01

Despite being chemically inert as a bulk material, nanoscale gold can pose harmful side effects to living organisms. In particular, cationic Au nanoparticles (AuNP+) of 2 nm diameter or less permeate readily through plasma membranes and induce cell death. We report atomistic simulations of cationic...... to be governed by cooperative effects where AuNP+, counterions, water, and the two membrane leaflets all contribute. On the extracellular side, we find that the nanoparticle has to cross a free energy barrier of about 5 k(B)T prior forming a stable contact with the membrane. This results in a rearrangement...

Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations

Science.gov (United States)

Piaggi, Pablo M.; Valsson, Omar; Parrinello, Michele

2017-07-01

Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. As in all first order first transitions, there is an interplay between enthalpy and entropy. Based on this idea, in order to drive crystallization in molecular simulations, we introduce two collective variables, one enthalpic and the other entropic. Defined in this way, these collective variables do not prejudge the structure into which the system is going to crystallize. We show the usefulness of this approach by studying the cases of sodium and aluminum that crystallize in the bcc and fcc crystalline structures, respectively. Using these two generic collective variables, we perform variationally enhanced sampling and well tempered metadynamics simulations and find that the systems transform spontaneously and reversibly between the liquid and the solid phases.

Adhesive contact: from atomistic model to continuum model

International Nuclear Information System (INIS)

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

2011-01-01

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

IrPd nanoalloys: simulations, from surface segregation to local electronic properties

Energy Technology Data Exchange (ETDEWEB)

Andriamiharintsoa, T. H. [Institut de Physique et Chimie des Matériaux de Strasbourg CNRS-UDS UMR 7504 (France); Rakotomahevitra, A. [Institut pour la Maîtrise de l’Énergie, Faculté des sciences d’Antananarivo (Madagascar); Piccolo, L. [Institut de Recherches sur la Catalyse et l’Environnement de Lyon IRCELYON, UMR 5256 CNRS and Université Lyon 1 (France); Goyhenex, C., E-mail: christine.goyhenex@ipcms.unistra.fr [Institut de Physique et Chimie des Matériaux de Strasbourg CNRS-UDS UMR 7504 (France)

2015-05-15

Using semi-empirical modeling, namely tight-binding at different levels of accuracy, the chemical, crystallographic, and electronic structures of bimetallic IrPd nanoparticles are characterized. For the purpose, model cuboctahedral particles containing 561 atoms are considered. Atomistic simulations show that core–shell nanoparticles are highly stable, with a strong surface segregation of Pd, at least for one atomic shell thickness. Within self-consistent tight-binding calculations founded on the density functional theory, an accurate insight is given into the electronic structure of these materials which have a high potential as catalysts.

Numerical simulation of 2D ablation profile in CCI-2 experiment by moving particle semi-implicit method

Energy Technology Data Exchange (ETDEWEB)

Chai, Penghui, E-mail: phchai@vis.t.u-tokyo.ac.jp; Kondo, Masahiro; Erkan, Nejdet; Okamoto, Koji

2016-05-15

Highlights: • Multiphysics models were developed based on Moving Particle Semi-implicit method. • Mixing process, chemical reaction can be simulated in MCCI calculation. • CCI-2 experiment was simulated to validate the models. • Simulation and experimental results for sidewall ablation agree well. • Simulation results confirm the rapid erosion phenomenon observed in the experiment. - Abstract: Numerous experiments have been performed to explore the mechanisms of molten core-concrete interaction (MCCI) phenomena since the 1980s. However, previous experimental results show that uncertainties pertaining to several aspects such as the mixing process and crust behavior remain. To explore the mechanism governing such aspects, as well as to predict MCCI behavior in real severe accident events, a number of simulation codes have been developed for process calculations. However, uncertainties exist among the codes because of the use of different empirical models. In this study, a new computational code is developed using multiphysics models to simulate MCCI phenomena based on the moving particle semi-implicit (MPS) method. Momentum and energy equations are used to solve the velocity and temperature fields, and multiphysics models are developed on the basis of the basic MPS method. The CCI-2 experiment is simulated by applying the developed code. With respect to sidewall ablation, good agreement is observed between the simulation and experimental results. However, axial ablation is slower in the simulation, which is probably due to the underestimation of the enhancement effect of heat transfer provided by the moving bubbles at the bottom. In addition, the simulation results confirm the rapid erosion phenomenon observed in the experiment, which in the numerical simulation is explained by solutal convection provided by the liquid concrete at the corium/concrete interface. The results of the comparison of different model combinations show the effect of each

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Science.gov (United States)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations.

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.

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-10-15

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

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

African Journals Online (AJOL)

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

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

Science.gov (United States)

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

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

Investigation of the removing process of cathode material in micro-EDM using an atomistic-continuum model

International Nuclear Information System (INIS)

Guo, Jianwen; Zhang, Guojun; Huang, Yu; Ming, Wuyi; Liu, Min; Huang, Hao

2014-01-01

Highlights: • An atomistic-continuum computational simulation model for single-discharge micro-EDM process of Cu cathode is constructed. • Cathode material is removed mainly in the form of single atoms or small clusters in micro-EDM. • Electric action leads to the formation of peaks on the surface of crater. • Removing process of cathode material under the hybrid action combining the thermal action and the electric action is studied, and the strength of either action needed for material to remove is much reduced. - Abstract: In micro-electrical discharge machining (micro-EDM), the discharge duration is ultra-short, and both the electric action and the thermal action by the discharge channel play important roles in the removing process of cathode material. However, in most researches on the machining mechanism of micro-EDM, only the thermal action is concerned. In this article, a combined atomistic-continuum modeling method in which the two-temperature model and the molecular dynamics simulation model are integrated is used to construct the simulation model for cathode in single-discharge micro-EDM process. With this simulation model, removing processes of Cu cathode material in micro-EDM under pure thermal action, pure electric action and the combination of them are investigated in a simulative way. By analyzing evolutions of temperature, stress and micro-structure of material as well as the dynamical behaviors of material in the removing process, mechanisms of the cathode material removal and crater formation are revealed. In addition, the removing process of cathode material under the combination of pure thermal action and pure electric action is compared with those under the two pure actions respectively to analyze the interactive effect between the thermal action and the electric action

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

Science.gov (United States)

Kumar, Rajesh; Parashar, Avinash

2016-01-07

Due to their exceptional mechanical properties, thermal conductivity and a wide band gap (5-6 eV), boron nitride nanotubes and nanosheets have promising applications in the field of engineering and biomedical science. Accurate modeling of failure or fracture in a nanomaterial inherently involves coupling of atomic domains of cracks and voids as well as a deformation mechanism originating from grain boundaries. This review highlights the recent progress made in the atomistic modeling of boron nitride nanofillers. Continuous improvements in computational power have made it possible to study the structural properties of these nanofillers at the atomistic scale.

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

International Nuclear Information System (INIS)

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

2008-01-01

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

Characteristic Performance Evaluation of a new SAGe Well Detector for Small and Large Sample Geometries

International Nuclear Information System (INIS)

Adekola, A.S.; Colaresi, J.; Douwen, J.; Jaederstroem, H.; Mueller, W.F.; Yocum, K.M.; Carmichael, K.

2015-01-01

Environmental scientific research requires a detector that has sensitivity low enough to reveal the presence of any contaminant in the sample at a reasonable counting time. Canberra developed the germanium detector geometry called Small Anode Germanium (SAGe) Well detector, which is now available commercially. The SAGe Well detector is a new type of low capacitance germanium well detector manufactured using small anode technology capable of advancing many environmental scientific research applications. The performance of this detector has been evaluated for a range of sample sizes and geometries counted inside the well, and on the end cap of the detector. The detector has energy resolution performance similar to semi-planar detectors, and offers significant improvement over the existing coaxial and Well detectors. Energy resolution performance of 750 eV Full Width at Half Maximum (FWHM) at 122 keV γ-ray energy and resolution of 2.0 - 2.3 keV FWHM at 1332 keV γ-ray energy are guaranteed for detector volumes up to 425 cm 3 . The SAGe Well detector offers an optional 28 mm well diameter with the same energy resolution as the standard 16 mm well. Such outstanding resolution performance will benefit environmental applications in revealing the detailed radionuclide content of samples, particularly at low energy, and will enhance the detection sensitivity resulting in reduced counting time. The detector is compatible with electric coolers without any sacrifice in performance and supports the Canberra Mathematical efficiency calibration method (In situ Object Calibration Software or ISOCS, and Laboratory Source-less Calibration Software or LABSOCS). In addition, the SAGe Well detector supports true coincidence summing available in the ISOCS/LABSOCS framework. The improved resolution performance greatly enhances detection sensitivity of this new detector for a range of sample sizes and geometries counted inside the well. This results in lower minimum detectable

Characteristic Performance Evaluation of a new SAGe Well Detector for Small and Large Sample Geometries

Energy Technology Data Exchange (ETDEWEB)

Adekola, A.S.; Colaresi, J.; Douwen, J.; Jaederstroem, H.; Mueller, W.F.; Yocum, K.M.; Carmichael, K. [Canberra Industries Inc., 800 Research Parkway, Meriden, CT 06450 (United States)

2015-07-01

Environmental scientific research requires a detector that has sensitivity low enough to reveal the presence of any contaminant in the sample at a reasonable counting time. Canberra developed the germanium detector geometry called Small Anode Germanium (SAGe) Well detector, which is now available commercially. The SAGe Well detector is a new type of low capacitance germanium well detector manufactured using small anode technology capable of advancing many environmental scientific research applications. The performance of this detector has been evaluated for a range of sample sizes and geometries counted inside the well, and on the end cap of the detector. The detector has energy resolution performance similar to semi-planar detectors, and offers significant improvement over the existing coaxial and Well detectors. Energy resolution performance of 750 eV Full Width at Half Maximum (FWHM) at 122 keV γ-ray energy and resolution of 2.0 - 2.3 keV FWHM at 1332 keV γ-ray energy are guaranteed for detector volumes up to 425 cm{sup 3}. The SAGe Well detector offers an optional 28 mm well diameter with the same energy resolution as the standard 16 mm well. Such outstanding resolution performance will benefit environmental applications in revealing the detailed radionuclide content of samples, particularly at low energy, and will enhance the detection sensitivity resulting in reduced counting time. The detector is compatible with electric coolers without any sacrifice in performance and supports the Canberra Mathematical efficiency calibration method (In situ Object Calibration Software or ISOCS, and Laboratory Source-less Calibration Software or LABSOCS). In addition, the SAGe Well detector supports true coincidence summing available in the ISOCS/LABSOCS framework. The improved resolution performance greatly enhances detection sensitivity of this new detector for a range of sample sizes and geometries counted inside the well. This results in lower minimum detectable

Analyzing and Driving Cluster Formation in Atomistic Simulations.

Science.gov (United States)

Tribello, Gareth A; Giberti, Federico; Sosso, Gabriele C; Salvalaglio, Matteo; Parrinello, Michele

2017-03-14

In this paper a set of computational tools for identifying the phases contained in a system composed of atoms or molecules is introduced. The method is rooted in graph theory and combines atom centered symmetry functions, adjacency matrices, and clustering algorithms to identify regions of space where the properties of the system constituents can be considered uniform. We show how this method can be used to define collective variables and how these collective variables can be used to enhance the sampling of nucleation events. We then show how this method can be used to analyze simulations of crystal nucleation and growth by using it to analyze simulations of the nucleation of the molecular crystal urea and simulations of nucleation in a semiconducting alloy. The semiconducting alloy example we discuss is particular challenging as multiple nucleation centers are formed. We show, however, that our algorithm is able to detect the grain boundaries in the resulting polycrystal.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

Science.gov (United States)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

CHARACTERISTIC OF AIRBORNE PARTICULATE MATTER SAMPLES COLLECTED FROM TWO SEMI INDUSTRIAL SITES IN BANDUNG, INDONESIA

Directory of Open Access Journals (Sweden)

Diah Dwiana Lestiani

2013-12-01

Full Text Available Air particulate matter concentrations, black carbon as well as elemental concentrations in two semi industrial sites were investigated as a preliminary study for evaluation of air quality in these areas. Sampling of airborne particulate matter was conducted in July 2009 using a Gent stacked filter unit sampler and a total of 18 pairs of samples were collected. Black carbon was determined by reflectance measurement and elemental analysis was performed using particle induced X-ray emission (PIXE. Elements Na, Mg, Al, Si, P, S, Cl, K, Ca, Ti, Cr, Mn, Fe, Cu, Zn and As were detected. Twenty four hour PM2.5 concentration at semi industrial sites Kiaracondong and Holis ranged from 4.0 to 22.2 µg m-3, while the PM10 concentration ranged from 24.5 to 77.1 µg m-3. High concentration of crustal elements, sulphur and zinc were identified in fine and coarse fractions for both sites. The fine fraction data from both sites were analyzed using a multivariate principal component analysis and for Kiaracondong site, identified factors are attributed to sea-salt with soil dust, vehicular emissions and biomass burning, non ferrous smelter, and iron/steel work industry, while for Holis site identified factors are attributed to soil dust, industrial emissions, vehicular emissions with biomass burning, and sea-salt. Although particulate samples were collected from semi industrial sites, vehicular emissions constituted with S, Zn and BC were identified in both sites.

Atomistic characterization of pseudoelasticity and shape memory in NiTi nanopillars

International Nuclear Information System (INIS)

Zhong Yuan; Gall, Ken; Zhu Ting

2012-01-01

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

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

Science.gov (United States)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Porosity estimation by semi-supervised learning with sparsely available labeled samples

Science.gov (United States)

Lima, Luiz Alberto; Görnitz, Nico; Varella, Luiz Eduardo; Vellasco, Marley; Müller, Klaus-Robert; Nakajima, Shinichi

2017-09-01

This paper addresses the porosity estimation problem from seismic impedance volumes and porosity samples located in a small group of exploratory wells. Regression methods, trained on the impedance as inputs and the porosity as output labels, generally suffer from extremely expensive (and hence sparsely available) porosity samples. To optimally make use of the valuable porosity data, a semi-supervised machine learning method was proposed, Transductive Conditional Random Field Regression (TCRFR), showing good performance (Görnitz et al., 2017). TCRFR, however, still requires more labeled data than those usually available, which creates a gap when applying the method to the porosity estimation problem in realistic situations. In this paper, we aim to fill this gap by introducing two graph-based preprocessing techniques, which adapt the original TCRFR for extremely weakly supervised scenarios. Our new method outperforms the previous automatic estimation methods on synthetic data and provides a comparable result to the manual labored, time-consuming geostatistics approach on real data, proving its potential as a practical industrial tool.

Deductive multiscale simulation using order parameters

Science.gov (United States)

Ortoleva, Peter J.

2017-05-16

Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

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

International Nuclear Information System (INIS)

Molina, J.J.

2011-01-01

Ions in solution play a fundamental role in many physical, chemical, and biological processes. The PUREX process used in the nuclear industry to the treatment of spent nuclear fuels is considered as an example. For industrial applications these systems are usually described using simple analytical models which are fitted to reproduce the available experimental data. In this work, we propose a multi-scale coarse graining procedure to derive such models from atomistic descriptions. First, parameters for classical force-fields of ions in solution are extracted from ab-initio calculations. Effective (McMillan-Mayer) ion-ion potentials are then derived from radial distribution functions measured in classical molecular dynamics simulations, allowing us to define an implicit solvent model of electrolytes. Finally, perturbation calculations are performed to define the best possible representation for these systems, in terms of charged hard-sphere models. Our final model is analytical and contains no free 'fitting' parameters. It shows good agreement with the exact results obtained from Monte-Carlo simulations for the thermodynamic and structural properties. Development of a similar model for the electrolyte viscosity, from information derived from atomistic descriptions, is also introduced. (author)

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

Semi-blind identification of wideband MIMO channels via stochastic sampling

OpenAIRE

Andrieu, Christophe; Piechocki, Robert J.; McGeehan, Joe P.; Armour, Simon M.

2003-01-01

In this paper we address the problem of wide-band multiple-input multiple-output (MIMO) channel (multidimensional time invariant FIR filter) identification using Markov chains Monte Carlo methods. Towards this end we develop a novel stochastic sampling technique that produces a sequence of multidimensional channel samples. The method is semi-blind in the sense that it uses a very short training sequence. In such a framework the problem is no longer analytically tractable; hence we resort to s...

An atomistic methodology of energy release rate for graphene at nanoscale

International Nuclear Information System (INIS)

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

2014-01-01

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

Critical assessment of Pt surface energy - An atomistic study

Science.gov (United States)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

Science.gov (United States)

Hofman, G. L.; Bozzolo, G.; Mosca, H. O.; Yacout, A. M.

2011-07-01

Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

Energy Technology Data Exchange (ETDEWEB)

Hofman, G.L. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Bozzolo, G., E-mail: guille_bozzolo@yahoo.com [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Mosca, H.O. [Gerencia de Investigaciones y Aplicaciones, CNEA, Av. Gral Paz 1499, B165KNA, San Martin, Buenos Aires (Argentina); Yacout, A.M. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States)

2011-07-15

Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

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

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

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

A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

Science.gov (United States)

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.

Gender Wage Gap : A Semi-Parametric Approach With Sample Selection Correction

NARCIS (Netherlands)

Picchio, M.; Mussida, C.

2010-01-01

Sizeable gender differences in employment rates are observed in many countries. Sample selection into the workforce might therefore be a relevant issue when estimating gender wage gaps. This paper proposes a new semi-parametric estimator of densities in the presence of covariates which incorporates

Numerical simulation of the induction heating of hybrid semi-finished materials into the semi-solid state

Science.gov (United States)

Seyboldt, Christoph; Liewald, Mathias

2017-10-01

Current research activities at the Institute for Metal Forming Technology (IFU) of the University of Stuttgart are focusing on the manufacturing of hybrid components using semi-solid forming strategies. As part of the research project "Hybrid interaction during and after thixoforging of multi-material systems", which is founded by the German Research Foundation (DFG), a thixoforging process for producing hybrid components with cohesive metal-to-metal connections is developed. In this context, this paper deals with the numerical simulation of the inductive heating process of hybrid semi-finished materials, consisting of two different aluminium alloys. By reason of the skin effect that leads to inhomogeneous temperature distributions during inductive heating processes, the aluminium alloy with the higher melting point is thereby assembled in the outer side and the alloy with the lower melting point is assembled in the core of the semi-finished material. In this way, the graded heat distribution can be adapted to the used materialś flow properties that are heavily heat dependent. Without this graded heat distribution a proper forming process in the semi-solid state will not be possible. For numerically modelling the inductive heating system of the institute, a coupling of the magnetostatic and the thermal solver was realized by using Ansys Workbench. While the electromagnetic field and its associated heat production rate were solved in a frequency domain, the temperature development was solved in the time based domain. The numerical analysis showed that because of the high thermal conductivity of the aluminium, which leads to a rapid temperature equalization in the semi-finished material, the heating process has to be fast and with a high frequency for produce most heat in the outer region of the material. Finally, the obtained numerical results were validated with experimental heating tests.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

Science.gov (United States)

Drenscko, Mihaela

small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Deformation behaviors of three-dimensional graphene honeycombs under out-of-plane compression: Atomistic simulations and predictive modeling

Science.gov (United States)

Meng, Fanchao; Chen, Cheng; Hu, Dianyin; Song, Jun

2017-12-01

Combining atomistic simulations and continuum modeling, a comprehensive study of the out-of-plane compressive deformation behaviors of equilateral three-dimensional (3D) graphene honeycombs was performed. It was demonstrated that under out-of-plane compression, the honeycomb exhibits two critical deformation events, i.e., elastic mechanical instability (including elastic buckling and structural transformation) and inelastic structural collapse. The above events were shown to be strongly dependent on the honeycomb cell size and affected by the local atomic bonding at the cell junction. By treating the 3D graphene honeycomb as a continuum cellular solid, and accounting for the structural heterogeneity and constraint at the junction, a set of analytical models were developed to accurately predict the threshold stresses corresponding to the onset of those deformation events. The present study elucidates key structure-property relationships of 3D graphene honeycombs under out-of-plane compression, and provides a comprehensive theoretical framework to predictively analyze their deformation responses, and more generally, offers critical new knowledge for the rational bottom-up design of 3D networks of two-dimensional nanomaterials.

Thermally activated magnetization reversal in monatomic magnetic chains on surfaces studied by classical atomistic spin-dynamics simulations

International Nuclear Information System (INIS)

Bauer, David S G; Mavropoulos, Phivos; Bluegel, Stefan; Lounis, Samir

2011-01-01

We analyse the spontaneous magnetization reversal of supported monatomic chains of finite length due to thermal fluctuations via atomistic spin-dynamics simulations. Our approach is based on the integration of the Landau-Lifshitz equation of motion of a classical spin Hamiltonian in the presence of stochastic forces. The associated magnetization lifetime is found to obey an Arrhenius law with an activation barrier equal to the domain wall energy in the chain. For chains longer than one domain wall width, the reversal is initiated by nucleation of a reversed magnetization domain primarily at the chain edge followed by a subsequent propagation of the domain wall to the other edge in a random-walk fashion. This results in a linear dependence of the lifetime on the chain length, if the magnetization correlation length is not exceeded. We studied chains of uniaxial and triaxial anisotropy and found that a triaxial anisotropy leads to a reduction of the magnetization lifetime due to a higher reversal attempt rate, even though the activation barrier is not changed.

Irradiation-induced void evolution in iron: A phase-field approach with atomistic derived parameters

International Nuclear Information System (INIS)

Wang Yuan-Yuan; Ding Jian-Hua; Huang Shao-Song; Zhao Ji-Jun; Liu Wen-Bo; Ke Xiao-Qin; Wang Yun-Zhi; Zhang Chi

2017-01-01

A series of material parameters are derived from atomistic simulations and implemented into a phase field (PF) model to simulate void evolution in body-centered cubic (bcc) iron subjected to different irradiation doses at different temperatures. The simulation results show good agreement with experimental observations — the porosity as a function of temperature varies in a bell-shaped manner and the void density monotonically decreases with increasing temperatures; both porosity and void density increase with increasing irradiation dose at the same temperature. Analysis reveals that the evolution of void number and size is determined by the interplay among the production, diffusion and recombination of vacancy and interstitial. (paper)

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

Energy Technology Data Exchange (ETDEWEB)

Roentzsch, L.

2007-07-01

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

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

International Nuclear Information System (INIS)

Roentzsch, L.

2007-01-01

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

On the atomistic mechanisms of alkane (methane-pentane) separation by distillation: a molecular dynamics study.

Science.gov (United States)

Zahn, Dirk

2007-11-01

Insights into the liquid-vapor transformation of methane-pentane mixtures were obtained from transition path sampling molecular dynamics simulations. This case study of the boiling of non-azeotropic mixtures demonstrates an unprejudiced identification of the atomistic mechanisms of phase separation in the course of vaporization which form the basis of distillation processes. From our simulations we observe spontaneous segregation events in the liquid mixture to trigger vapor nucleation. The formation of vapor domains stabilizes and further promotes the separation process by preferential evaporation of methane molecules. While this discrimination holds for all mixtures of different composition studied, a full account of the boiling process requires a more complex picture. At low methane concentration the nucleation of the vapor domains includes both methane and pentane molecules. The pentane molecules, however, tend to form small aggregates and undergo rapid re-condensation within picoseconds to nanoseconds scales. Accordingly, two aspects of selectivity accounting for methane-pentane separation in the course of liquid-vapor transformations were made accessible to molecular dynamics simulations: spontaneous segregation in the liquid phase leading to selective vapor nucleation and growth favoring methane vaporization and selective re-condensation of pentane molecules.

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

Science.gov (United States)

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

2016-12-01

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

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

Directory of Open Access Journals (Sweden)

Jianfeng Wang

2009-01-01

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

Control algorithm for multiscale flow simulations of water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Walther, Jens Honore; Kaxiras, E.

2009-01-01

We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions...

Continuum simulations of water flow past fullerene molecules

DEFF Research Database (Denmark)

Popadic, A.; Praprotnik, M.; Koumoutsakos, P.

2015-01-01

We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow...

A method of integration of atomistic simulations and continuum mechanics by collecting of dynamical systems with dimensional reduction

International Nuclear Information System (INIS)

Kaczmarek, J.

2002-01-01

Elementary processes responsible for phenomena in material are frequently related to scale close to atomic one. Therefore atomistic simulations are important for material sciences. On the other hand continuum mechanics is widely applied in mechanics of materials. It seems inevitable that both methods will gradually integrate. A multiscale method of integration of these approaches called collection of dynamical systems with dimensional reduction is introduced in this work. The dimensional reduction procedure realizes transition between various scale models from an elementary dynamical system (EDS) to a reduced dynamical system (RDS). Mappings which transform variables and forces, skeletal dynamical system (SDS) and a set of approximation and identification methods are main components of this procedure. The skeletal dynamical system is a set of dynamical systems parameterized by some constants and has variables related to the dimensionally reduced model. These constants are identified with the aid of solutions of the elementary dynamical system. As a result we obtain a dimensionally reduced dynamical system which describes phenomena in an averaged way in comparison with the EDS. Concept of integration of atomistic simulations with continuum mechanics consists in using a dynamical system describing evolution of atoms as an elementary dynamical system. Then, we introduce a continuum skeletal dynamical system within the dimensional reduction procedure. In order to construct such a system we have to modify a continuum mechanics formulation to some degree. Namely, we formalize scale of averaging for continuum theory and as a result we consider continuum with finite-dimensional fields only. Then, realization of dimensional reduction is possible. A numerical example of realization of the dimensional reduction procedure is shown. We consider a one dimensional chain of atoms interacting by Lennard-Jones potential. Evolution of this system is described by an elementary

Development of a simulation model of semi-active suspension for monorail

Science.gov (United States)

Hasnan, K.; Didane, D. H.; Kamarudin, M. A.; Bakhsh, Qadir; Abdulmalik, R. E.

2016-11-01

The new Kuala Lumpur Monorail Fleet Expansion Project (KLMFEP) uses semiactive technology in its suspension system. It is recognized that the suspension system influences the ride quality. Thus, among the way to further improve the ride quality is by fine- tuning the semi-active suspension system on the new KL Monorail. The semi-active suspension for the monorail specifically in terms of improving ride quality could be exploited further. Hence a simulation model which will act as a platform to test the design of a complete suspension system particularly to investigate the ride comfort performance is required. MSC Adams software was considered as the tool to develop the simulation platform, where all parameters and data are represented by mathematical equations; whereas the new KL Monorail being the reference model. In the simulation, the model went through step disturbance on the guideway for stability and ride comfort analysis. The model has shown positive results where the monorail is in stable condition as an outcome from stability analysis. The model also scores a Rating 1 classification in ISO 2631 Ride Comfort performance which is very comfortable as an overall outcome from ride comfort analysis. The model is also adjustable, flexibile and understandable by the engineers within the field for the purpose of further development.

NEAMS FPL M2 Milestone Report: Development of a UO₂ Grain Size Model using Multicale Modeling and Simulation

Energy Technology Data Exchange (ETDEWEB)

Tonks, Michael R [Idaho National Lab. (INL), Idaho Falls, ID (United States); Zhang, Yongfeng [Idaho National Lab. (INL), Idaho Falls, ID (United States); Bai, Xianming [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2014-06-01

This report summarizes development work funded by the Nuclear Energy Advanced Modeling Simulation program's Fuels Product Line (FPL) to develop a mechanistic model for the average grain size in UO₂ fuel. The model is developed using a multiscale modeling and simulation approach involving atomistic simulations, as well as mesoscale simulations using INL's MARMOT code.

A Semi-Analytical Methodology for Multiwell Productivity Index of Well-Industry-Production-Scheme in Tight Oil Reservoirs

Directory of Open Access Journals (Sweden)

Guangfeng Liu

2018-04-01

Full Text Available Recently, the well-industry-production-scheme (WIPS has attracted more and more attention to improve tight oil recovery. However, multi-well pressure interference (MWPI induced by well-industry-production-scheme (WIPS strongly challenges the traditional transient pressure analysis methods, which focus on single multi-fractured horizontal wells (SMFHWs without MWPI. Therefore, a semi-analytical methodology for multiwell productivity index (MPI was proposed to study well performance of WIPS scheme in tight reservoir. To facilitate methodology development, the conceptual models of tight formation and WIPS scheme were firstly described. Secondly, seepage models of tight reservoir and hydraulic fractures (HFs were sequentially established and then dynamically coupled. Numerical simulation was utilized to validate our model. Finally, identification of flow regimes and sensitivity analysis were conducted. Our results showed that there was good agreement between our proposed model and numerical simulation; moreover, our approach also gave promising calculation speed over numerical simulation. Some expected flow regimes were significantly distorted due to WIPS. The slope of type curves which characterize the linear or bi-linear flow regime is bigger than 0.5 or 0.25. The horizontal line which characterize radial flow regime is also bigger 0.5. The smaller the oil rate, the more severely flow regimes were distorted. Well rate mainly determines the distortion of MPI curves, while fracture length, well spacing, fracture spacing mainly determine when the distortion of the MPI curves occurs. The bigger the well rate, the more severely the MPI curves are distorted. While as the well spacing decreases, fracture length increases, fracture spacing increases, occurrence of MWPI become earlier. Stress sensitivity coefficient mainly affects the MPI at the formation pseudo-radial flow stage, almost has no influence on the occurrence of MWPI. This work gains some

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

KAUST Repository

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

2015-01-01

experimental and simulation studies, we showed the capability of our Monte Carlo scheme on representing polymerization kinetics in batch and semi-batch processes. Various kinetics information, such as instant monomer conversion, molecular weight

Well-posedness for Semi-relativistic Hartree Equations of Critical Type

International Nuclear Information System (INIS)

Lenzmann, Enno

2007-01-01

We prove local and global well-posedness for semi-relativistic, nonlinear Schroedinger equations with initial data in H s (R 3 ). Here F(u) is a critical Hartree nonlinearity that corresponds to Coulomb or Yukawa type self-interactions. For focusing F(u), which arise in the quantum theory of boson stars, we derive global-in-time existence for small initial data, where the smallness condition is expressed in terms of the L 2 -norm of solitary wave ground states. Our proof of well-posedness does not rely on Strichartz type estimates. As a major benefit from this, our method enables us to consider external potentials of a quite general class

Atomistic simulations of cross-slip of jogged screw dislocations in copper

DEFF Research Database (Denmark)

Vegge, T.; Rasmussen, T.; Leffers, T.

2001-01-01

We have performed atomic-scare simulations of cross-slip processes of screw dislocations in copper, simulating jog-free dislocations as well as different types of jogged screw dislocations. Minimum-energy paths and corresponding transition state energies are obtained using the nudged-elastic...

Predicting the constitutive behavior of semi-solids via a direct finite element simulation: application to AA5182

Science.gov (United States)

Phillion, A. B.; Cockcroft, S. L.; Lee, P. D.

2009-07-01

The methodology of direct finite element (FE) simulation was used to predict the semi-solid constitutive behavior of an industrially important aluminum-magnesium alloy, AA5182. Model microstructures were generated that detail key features of the as-cast semi-solid: equiaxed-globular grains of random size and shape, interconnected liquid films, and pores at the triple-junctions. Based on the results of over fifty different simulations, a model-based constitutive relationship which includes the effects of the key microstructure features—fraction solid, grain size and fraction porosity—was derived using regression analysis. This novel constitutive equation was then validated via comparison with both the FE simulations and experimental stress/strain data. Such an equation can now be used to incorporate the effects of microstructure on the bulk semi-solid flow stress within a macro- scale process model.

Predicting the constitutive behavior of semi-solids via a direct finite element simulation: application to AA5182

International Nuclear Information System (INIS)

Phillion, A B; Cockcroft, S L; Lee, P D

2009-01-01

The methodology of direct finite element (FE) simulation was used to predict the semi-solid constitutive behavior of an industrially important aluminum-magnesium alloy, AA5182. Model microstructures were generated that detail key features of the as-cast semi-solid: equiaxed-globular grains of random size and shape, interconnected liquid films, and pores at the triple-junctions. Based on the results of over fifty different simulations, a model-based constitutive relationship which includes the effects of the key microstructure features—fraction solid, grain size and fraction porosity—was derived using regression analysis. This novel constitutive equation was then validated via comparison with both the FE simulations and experimental stress/strain data. Such an equation can now be used to incorporate the effects of microstructure on the bulk semi-solid flow stress within a macro- scale process model

Atomistic and holistic understanding in physics

International Nuclear Information System (INIS)

Bohm, A.

1992-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-04-05

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

Optimal kernel shape and bandwidth for atomistic support of continuum stress

International Nuclear Information System (INIS)

Ulz, Manfred H; Moran, Sean J

2013-01-01

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

The challenges of understanding glycolipid functions: An open outlook based on molecular simulations

DEFF Research Database (Denmark)

Manna, M.; Rog, T.; Vattulainen, I.

2014-01-01

and molecular simulations can be used to shed light on the role of glycolipids in membrane structure and dynamics, receptor function, and other phenomena related to emergence of diseases such as Parkinson's. The cases we discuss highlight the challenge to understand how glycolipids function in cell membranes......, and the significant added value that one would gain by bridging molecular simulations with experiments. This article is part of a Special Issue entitled Tools to study lipid functions. (C) 2014 Elsevier B.V. All rights reserved.......Glycolipids are the most complex lipid type in cell membranes, characterized by a great diversity of different structures and functions. The underlying atomistic/molecular interactions and mechanisms associated with these functions are not well understood. Here we discuss how atomistic...

Impact of model structure on flow simulation and hydrological realism: from a lumped to a semi-distributed approach

Science.gov (United States)

Garavaglia, Federico; Le Lay, Matthieu; Gottardi, Fréderic; Garçon, Rémy; Gailhard, Joël; Paquet, Emmanuel; Mathevet, Thibault

2017-08-01

Model intercomparison experiments are widely used to investigate and improve hydrological model performance. However, a study based only on runoff simulation is not sufficient to discriminate between different model structures. Hence, there is a need to improve hydrological models for specific streamflow signatures (e.g., low and high flow) and multi-variable predictions (e.g., soil moisture, snow and groundwater). This study assesses the impact of model structure on flow simulation and hydrological realism using three versions of a hydrological model called MORDOR: the historical lumped structure and a revisited formulation available in both lumped and semi-distributed structures. In particular, the main goal of this paper is to investigate the relative impact of model equations and spatial discretization on flow simulation, snowpack representation and evapotranspiration estimation. Comparison of the models is based on an extensive dataset composed of 50 catchments located in French mountainous regions. The evaluation framework is founded on a multi-criterion split-sample strategy. All models were calibrated using an automatic optimization method based on an efficient genetic algorithm. The evaluation framework is enriched by the assessment of snow and evapotranspiration modeling against in situ and satellite data. The results showed that the new model formulations perform significantly better than the initial one in terms of the various streamflow signatures, snow and evapotranspiration predictions. The semi-distributed approach provides better calibration-validation performance for the snow cover area, snow water equivalent and runoff simulation, especially for nival catchments.

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

Science.gov (United States)

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

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

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

Science.gov (United States)

Quevillon, Michael J; Whitmer, Jonathan K

2018-01-02

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure-constant temperature ensemble. These materials exhibit a distinct "smectic" liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

Multiscale Simulations Using Particles

DEFF Research Database (Denmark)

Walther, Jens Honore

vortex methods for problems in continuum fluid dynamics, dissipative particle dynamics for flow at the meso scale, and atomistic molecular dynamics simulations of nanofluidic systems. We employ multiscale techniques to breach the atomistic and continuum scales to study fundamental problems in fluid...... dynamics. Recent work on the thermophoretic motion of water nanodroplets confined inside carbon nanotubes, and multiscale techniques for polar liquids will be discussed in detail at the symposium....

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

Science.gov (United States)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

2017-01-01

We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

International Nuclear Information System (INIS)

Stimson, Lorna M.

2003-01-01

Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a single dendrimer molecule in the gas phase at the atomistic level, semi-atomistic molecular dynamics of a single molecule in liquid crystalline solvents and a coarse-grained molecular dynamics study of the dendrimer in the bulk. The coarse-grained model has been developed and parameterized using the results of the atomistic and semi-atomistic work. The single molecule studies showed that the liquid crystalline dendrimer was able to change its structure by conformational changes in the flexible chains that link the mesogenic groups to the core. Structural change was seen under the application of a mean field ordering potential in the gas phase, and in the presence of liquid crystalline solvents. No liquid crystalline phases were observed for the bulk phase studies of the coarse-grained model. However, when the length of the mesogenic units was increased there was some evidence for microphase separation in these systems. (author)

Self-absorption corrections of various sample-detector geometries in gamma-ray spectrometry using sample Monte Carlo Simulations

International Nuclear Information System (INIS)

Ahmad Saat; Appleby, P.G.; Nolan, P.J.

1997-01-01

Corrections for self-absorption in gamma-ray spectrometry have been developed using a simple Monte Carlo simulation technique. The simulation enables the calculation of gamma-ray path lengths in the sample which, using available data, can be used to calculate self-absorption correction factors. The simulation was carried out on three sample geometries: disk, Marinelli beaker, and cylinder (for well-type detectors). Mathematical models and experimental measurements are used to evaluate the simulations. A good agreement of within a few percents was observed. The simulation results are also in good agreement with those reported in the literature. The simulation code was carried out in FORTRAN 90,

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

International Nuclear Information System (INIS)

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

2004-01-01

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

Simulating chemical systems : MPI and GPU parallelization of novel SD algorithms

NARCIS (Netherlands)

Goga, N.

Molecular dynamics is used for simulating chemical systems with the goal of studying a large range of phenomena starting from cell structures to the design of new materials, drugs, etc. A very important component of molecular dynamics is the use of well-suited atomistic and molecular modelling of

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-07-01

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

The simulation of naturally ventilated residential buildings in semi-arid regions

Energy Technology Data Exchange (ETDEWEB)

Ghiabaklou, Z.; Ballinger, J.A.; Prasad, D.K. [New South Wales Univ., Kensington, NSW (Australia). Solar Architecture Research Unit

1995-12-31

The most important consideration in hot arid and semi-arid zones is to reduce the internal day temperature and to maintain the interior spaces of buildings in a comfortable condition. An important contributor to errors in the thermal analysis of naturally ventilated buildings is inaccurate airflow predictions. These predictions are important for designers in regions where most buildings are naturally ventilated. Passive cooling by day and night natural ventilation in a single story residential building in Wagga Wagga, a semi-arid location in New South Wales has been compared and analyzed theoretically. A modified version of the computer simulation program CHEETAH, has been used to consider a building with continuous natural ventilation to simulate indoor air temperature. The aim of the study was to investigate the thermal behaviour of the building with continuous ventilation (24 hour/day) and the same building with only night time ventilation. Using night time ventilation in high mass buildings in such a climate, leads to a considerable decrease in room air temperature. Simulation results showed that increasing the effective area of windows is effective only when the wind blows. Using a steady averaged air change per hour can also cause a reduction in room air temperatures which results in different temperatures than the actual air changes per hour. (author). 3 figs., 4 refs.

A spatio-temporal evaluation of the WRF physical parameterisations for numerical rainfall simulation in semi-humid and semi-arid catchments of Northern China

Science.gov (United States)

Tian, Jiyang; Liu, Jia; Wang, Jianhua; Li, Chuanzhe; Yu, Fuliang; Chu, Zhigang

2017-07-01

Mesoscale Numerical Weather Prediction systems can provide rainfall products at high resolutions in space and time, playing an increasingly more important role in water management and flood forecasting. The Weather Research and Forecasting (WRF) model is one of the most popular mesoscale systems and has been extensively used in research and practice. However, for hydrologists, an unsolved question must be addressed before each model application in a different target area. That is, how are the most appropriate combinations of physical parameterisations from the vast WRF library selected to provide the best downscaled rainfall? In this study, the WRF model was applied with 12 designed parameterisation schemes with different combinations of physical parameterisations, including microphysics, radiation, planetary boundary layer (PBL), land-surface model (LSM) and cumulus parameterisations. The selected study areas are two semi-humid and semi-arid catchments located in the Daqinghe River basin, Northern China. The performance of WRF with different parameterisation schemes is tested for simulating eight typical 24-h storm events with different evenness in space and time. In addition to the cumulative rainfall amount, the spatial and temporal patterns of the simulated rainfall are evaluated based on a two-dimensional composed verification statistic. Among the 12 parameterisation schemes, Scheme 4 outperforms the other schemes with the best average performance in simulating rainfall totals and temporal patterns; in contrast, Scheme 6 is generally a good choice for simulations of spatial rainfall distributions. Regarding the individual parameterisations, Single-Moment 6 (WSM6), Yonsei University (YSU), Kain-Fritsch (KF) and Grell-Devenyi (GD) are better choices for microphysics, planetary boundary layers (PBL) and cumulus parameterisations, respectively, in the study area. These findings provide helpful information for WRF rainfall downscaling in semi-humid and semi

IslandFAST: A Semi-numerical Tool for Simulating the Late Epoch of Reionization

Energy Technology Data Exchange (ETDEWEB)

Xu, Yidong; Chen, Xuelei [Key Laboratory for Computational Astrophysics, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Yue, Bin [National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

2017-08-01

We present the algorithm and main results of our semi-numerical simulation, islandFAST, which was developed from 21cmFAST and designed for the late stage of reionization. The islandFAST simulation predicts the evolution and size distribution of the large-scale underdense neutral regions (neutral islands), and we find that the late Epoch of Reionization proceeds very fast, showing a characteristic scale of the neutral islands at each redshift. Using islandFAST, we compare the impact of two types of absorption systems, i.e., the large-scale underdense neutral islands versus small-scale overdense absorbers, in regulating the reionization process. The neutral islands dominate the morphology of the ionization field, while the small-scale absorbers dominate the mean-free path of ionizing photons, and also delay and prolong the reionization process. With our semi-numerical simulation, the evolution of the ionizing background can be derived self-consistently given a model for the small absorbers. The hydrogen ionization rate of the ionizing background is reduced by an order of magnitude in the presence of dense absorbers.

Bacteriological analysis of well water samples in Sagamu | Idowu ...

African Journals Online (AJOL)

Majority of the population in semi-urban and urban areas of Nigeria depend on wells as their source of water supply. Due to increasing cases of water-borne diseases in recent times, this study was carried out to examine the microbial quality of well water in Sagamu, Nigeria as a way of safeguarding public health against ...

Spatial Sampling of Weather Data for Regional Crop Yield Simulations

Science.gov (United States)

Van Bussel, Lenny G. J.; Ewert, Frank; Zhao, Gang; Hoffmann, Holger; Enders, Andreas; Wallach, Daniel; Asseng, Senthold; Baigorria, Guillermo A.; Basso, Bruno; Biernath, Christian;

Simulation and experimental verification of the filling process of semi-solid die forging for cup shell

OpenAIRE

Jianbo TAN; Zichao WANG; Dongxu WANG

2015-01-01

The filling mold process of semi-solid alloy blank influences severely the forming and properties of finished piece. In this paper, DEFORM is applied to simulate the process of cup-type 6061 alloy die forging casting. The influences of the temperature of semi-solid alloy blank, preheating temperature, and downward press speed of pressure head on process of mold filling and velocity field are investigated. The results show that the mold filling of semi-solid alloy paste smoothly fills along th...

Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures

Science.gov (United States)

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

2017-10-01

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

Molecular cooperativity and compatibility via full atomistic simulation

Science.gov (United States)

Kwan Yang, Kenny

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

Semi-automated operation of Mars Climate Simulation chamber - MCSC modelled for biological experiments

Science.gov (United States)

Tarasashvili, M. V.; Sabashvili, Sh. A.; Tsereteli, S. L.; Aleksidze, N. D.; Dalakishvili, O.

2017-10-01

The Mars Climate Simulation Chamber (MCSC) (GEO PAT 12 522/01) is designed for the investigation of the possible past and present habitability of Mars, as well as for the solution of practical tasks necessary for the colonization and Terraformation of the Planet. There are specific tasks such as the experimental investigation of the biological parameters that allow many terrestrial organisms to adapt to the imitated Martian conditions: chemistry of the ground, atmosphere, temperature, radiation, etc. MCSC is set for the simulation of the conduction of various biological experiments, as well as the selection of extremophile microorganisms for the possible Settlement, Ecopoesis and/or Terraformation purposes and investigation of their physiological functions. For long-term purposes, it is possible to cultivate genetically modified organisms (e.g., plants) adapted to the Martian conditions for future Martian agriculture to sustain human Mars missions and permanent settlements. The size of the chamber allows preliminary testing of the functionality of space-station mini-models and personal protection devices such as space-suits, covering and building materials and other structures. The reliability of the experimental biotechnological materials can also be tested over a period of years. Complex and thorough research has been performed to acquire the most appropriate technical tools for the accurate engineering of the MCSC and precious programmed simulation of Martian environmental conditions. This paper describes the construction and technical details of the equipment of the MCSC, which allows its semi-automated, long-term operation.

Multiscale modeling of polyisoprene on graphite

International Nuclear Information System (INIS)

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

2014-01-01

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

Insights into the charge carrier terahertz mobility in polyfluorenes from large-scale atomistic simulations and time-resolved terahertz spectroscopy

Czech Academy of Sciences Publication Activity Database

Vukmirović, N.; Ponseca, C.S.; Němec, Hynek; Yartsev, A.; Sundström, V.

2012-01-01

Roč. 116, č. 37 (2012), s. 19665-1972 ISSN 1932-7447 Institutional research plan: CEZ:AV0Z10100520 Keywords : charge carrier mobility * time-resolved terahertz spectroscopy * multiscale atomistic calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.814, year: 2012

Linking Bayesian and agent-based models to simulate complex social-ecological systems in semi-arid regions

Directory of Open Access Journals (Sweden)

Aloah J Pope

2015-08-01

Full Text Available Interdependencies of ecologic, hydrologic, and social systems challenge traditional approaches to natural resource management in semi-arid regions. As a complex social-ecological system, water demands in the Sonoran Desert from agricultural and urban users often conflicts with water needs for its ecologically-significant riparian corridors. To explore this system, we developed an agent-based model to simulate complex feedbacks between human decisions and environmental conditions in the Rio Sonora Watershed. Cognitive mapping in conjunction with stakeholder participation produced a Bayesian model of conditional probabilities of local human decision-making processes resulting to changes in water demand. Probabilities created in the Bayesian model were incorporated into the agent-based model, so that each agent had a unique probability to make a positive decision based on its perceived environment at each point in time and space. By using a Bayesian approach, uncertainty in the human decision-making process could be incorporated. The spatially-explicit agent-based model simulated changes in depth-to-groundwater by well pumping based on an agent’s water demand. Changes in depth-to-groundwater feedback to influence agent behavior, as well as determine unique vegetation classes within the riparian corridor. Each vegetation class then provides varying stakeholder-defined quality values of ecosystem services. Using this modeling approach allowed us to examine effects on both the ecological and social system of semi-arid riparian corridors under various scenarios. The insight provided by the model contributes to understanding how specific interventions may alter the complex social-ecological system in the future.

Calibration of semi-stochastic procedure for simulating high-frequency ground motions

Science.gov (United States)

Seyhan, Emel; Stewart, Jonathan P.; Graves, Robert

2013-01-01

Broadband ground motion simulation procedures typically utilize physics-based modeling at low frequencies, coupled with semi-stochastic procedures at high frequencies. The high-frequency procedure considered here combines deterministic Fourier amplitude spectra (dependent on source, path, and site models) with random phase. Previous work showed that high-frequency intensity measures from this simulation methodology attenuate faster with distance and have lower intra-event dispersion than in empirical equations. We address these issues by increasing crustal damping (Q) to reduce distance attenuation bias and by introducing random site-to-site variations to Fourier amplitudes using a lognormal standard deviation ranging from 0.45 for Mw  100 km).

Activated states for cross-slip at screw dislocation intersections in face-centered cubic nickel and copper via atomistic simulation

International Nuclear Information System (INIS)

Rao, S.I.; Dimiduk, D.M.; El-Awady, J.A.; Parthasarathy, T.A.; Uchic, M.D.; Woodward, C.

2010-01-01

We extend our recent simulation studies where a screw dislocation in face-centered cubic (fcc) Ni was found to spontaneously attain a low energy partially cross-slipped configuration upon intersecting a forest dislocation. Using atomistic (molecular statics) simulations with embedded atom potentials, we evaluated the activation barrier for a dislocation to transform from fully residing on the glide plane to fully residing on a cross-slip plane intersecting a forest dislocation in both Ni and Cu. The activation energies were obtained by determining equilibrium configurations (energies) when variable pure tensile or compressive stresses were applied along the [1 1 1] direction on the partially cross-slipped state. We show that the activation energy is a factor of 2-5 lower than that for cross-slip in isolation via the Escaig process. The cross-slip activation energies obtained at the intersection in Cu were in reasonable accord with the experimentally determined cross-slip activation energy for Cu. Further, the activation barrier for cross-slip at these intersections was shown to be linearly proportional to (d/b)[ln(√(3)d/b)] 1/2 , as in the Escaig process, where d is the Shockley partial dislocation spacing and b is the Burgers vector of the screw dislocation. These results suggest that cross-slip should be preferentially observed at selected screw dislocation intersections in fcc materials.

Multiscale modeling for ferroelectric materials: identification of the phase-field model’s free energy for PZT from atomistic simulations

International Nuclear Information System (INIS)

Völker, Benjamin; Landis, Chad M; Kamlah, Marc

2012-01-01

Within a knowledge-based multiscale simulation approach for ferroelectric materials, the atomic level can be linked to the mesoscale by transferring results from first-principles calculations into a phase-field model. A recently presented routine (Völker et al 2011 Contin. Mech. Thermodyn. 23 435–51) for adjusting the Helmholtz free energy coefficients to intrinsic and extrinsic ferroelectric material properties obtained by DFT calculations and atomistic simulations was subject to certain limitations: caused by too small available degrees of freedom, an independent adjustment of the spontaneous strains and piezoelectric coefficients was not possible, and the elastic properties could only be considered in cubic instead of tetragonal symmetry. In this work we overcome such restrictions by expanding the formulation of the free energy function, i.e. by motivating and introducing new higher-order terms that have not appeared in the literature before. Subsequently we present an improved version of the adjustment procedure for the free energy coefficients that is solely based on input parameters from first-principles calculations performed by Marton and Elsässer, as documented in Völker et al (2011 Contin. Mech. Thermodyn. 23 435–51). Full sets of adjusted free energy coefficients for PbTiO 3 and tetragonal Pb(Zr,Ti)O 3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed. (paper)

Spatial distribution sampling and Monte Carlo simulation of radioactive isotopes

CERN Document Server

Krainer, Alexander Michael

2015-01-01

This work focuses on the implementation of a program for random sampling of uniformly spatially distributed isotopes for Monte Carlo particle simulations and in specific FLUKA. With FLUKA it is possible to calculate the radio nuclide production in high energy fields. The decay of these nuclide, and therefore the resulting radiation field, however can only be simulated in the same geometry. This works gives the tool to simulate the decay of the produced nuclide in other geometries. With that the radiation field from an irradiated object can be simulated in arbitrary environments. The sampling of isotope mixtures was tested by simulating a 50/50 mixture of $Cs^{137}$ and $Co^{60}$. These isotopes are both well known and provide therefore a first reliable benchmark in that respect. The sampling of uniformly distributed coordinates was tested using the histogram test for various spatial distributions. The advantages and disadvantages of the program compared to standard methods are demonstrated in the real life ca...

Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model

Science.gov (United States)

Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

2017-03-01

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.

Parallel multiscale simulations of a brain aneurysm

Energy Technology Data Exchange (ETDEWEB)

Grinberg, Leopold [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States); Fedosov, Dmitry A. [Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich 52425 (Germany); Karniadakis, George Em, E-mail: george_karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States)

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in

Parallel multiscale simulations of a brain aneurysm

International Nuclear Information System (INIS)

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2013-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in

Single asperity nanocontacts: Comparison between molecular dynamics simulations and continuum mechanics models

NARCIS (Netherlands)

Solhjoo, Soheil; Vakis, Antonis I.

Abstract Using classical molecular dynamics, atomic scale simulations of normal contact between a nominally flat substrate and different atomistic and non-atomistic spherical particles were performed to investigate the applicability of classical contact theories at the nanoscale, and further

Systematic and efficient navigating potential energy surface: Data for silver doped gold clusters.

Science.gov (United States)

Chaban, Vitaly V

2016-06-01

Locating global minimum of certain atomistic ensemble is known to be a highly challenging and resource consuming task. This dataset represents joint usage of the semi-empirical PM7 Hamiltonian, Broyden-Fletcher-Goldfarb-Shanno algorithm and basin hopping scheme to navigate a potential energy surface. The Au20 nanocluster was used for calibration as its global minimum structure is well-known. Furthermore, Au18Ag2 and Au15Ag5 were simulated for illustration of the algorithm performance. The work shows encouraging results and, particularly, underlines proper accuracy of PM7 as applied to this type of heavy metal systems. The reported dataset motivates to use the benchmarked method for studying potential energy surfaces of manifold systems and locate their global-minimum atomistic configurations.

Free-energy landscape of protein oligomerization from atomistic simulations

Science.gov (United States)

Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K.; Parrinello, Michele

2013-01-01

In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. PMID:24248370

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Science.gov (United States)

2018-01-01

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

Deformation behavior of Cu bicrystals with the Σ9(110)(221) symmetric tilt grain boundary under pure shear studied by atomistic simulation method

International Nuclear Information System (INIS)

Wan Liang; Wang Shaoqing

2010-01-01

The deformation behavior of Cu bicrystals with the symmetric tilt grain boundary (STGB) under pure shear has been studied by atomistic simulation method with the embedded atom method (EAM) interatomic potentials. By using an energy minimization method, it shows that there are two optimized structures of this grain boundary (GB) which correspond to two local energy minima on the potential energy surface of the GB. The structure with lower energy is the stable one while the other is a metastable structure. The pure shear process of the bicrystals at ambient temperature has been studied by molecular dynamics (MD) simulation method. The simulated results indicate that there are three structure transformation modes of this GB depending on the shear direction: (1) pure GB sliding; (2) GB atomic shuffling accompanied by dislocation emission from GB; (3) GB migration coupled GB sliding, namely, GB coupling motion. In addition, an analysis of the structure evolution of the GB shows that, there are two mechanisms for GB coupling motion depending on the shear direction. One is the collective motion of GB atoms and the other is structure transformation realized by uncorrelated atomic shuffling processes. The former mechanism can induce structure transition of GB between the stable one and the metastable one, while the latter introduces faceting of the GB. (authors)

On the Fidelity of Semi-distributed Hydrologic Model Simulations for Large Scale Catchment Applications

Science.gov (United States)

Ajami, H.; Sharma, A.; Lakshmi, V.

2017-12-01

Application of semi-distributed hydrologic modeling frameworks is a viable alternative to fully distributed hyper-resolution hydrologic models due to computational efficiency and resolving fine-scale spatial structure of hydrologic fluxes and states. However, fidelity of semi-distributed model simulations is impacted by (1) formulation of hydrologic response units (HRUs), and (2) aggregation of catchment properties for formulating simulation elements. Here, we evaluate the performance of a recently developed Soil Moisture and Runoff simulation Toolkit (SMART) for large catchment scale simulations. In SMART, topologically connected HRUs are delineated using thresholds obtained from topographic and geomorphic analysis of a catchment, and simulation elements are equivalent cross sections (ECS) representative of a hillslope in first order sub-basins. Earlier investigations have shown that formulation of ECSs at the scale of a first order sub-basin reduces computational time significantly without compromising simulation accuracy. However, the implementation of this approach has not been fully explored for catchment scale simulations. To assess SMART performance, we set-up the model over the Little Washita watershed in Oklahoma. Model evaluations using in-situ soil moisture observations show satisfactory model performance. In addition, we evaluated the performance of a number of soil moisture disaggregation schemes recently developed to provide spatially explicit soil moisture outputs at fine scale resolution. Our results illustrate that the statistical disaggregation scheme performs significantly better than the methods based on topographic data. Future work is focused on assessing the performance of SMART using remotely sensed soil moisture observations using spatially based model evaluation metrics.

Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers

Science.gov (United States)

Badalkhani-Khamseh, Farideh; Ebrahim-Habibi, Azadeh; Hadipour, Nasser L.

2017-12-01

Poly(amidoamine) (PAMAM) dendrimers have been extensively studied as delivery vectors in biomedical applications. A limited number of molecular dynamics (MD) simulation studies have investigated the effect of surface chemistry on therapeutic molecules loading, with the aim of providing insights for biocompatibility improvement and increase in drug loading capacity of PAMAM dendrimers. In this work, fully atomistic MD simulations were employed to study the association of 5-Fluorouracil (5-FU) with amine (NH2)- and hydroxyl (OH)-terminated PAMAM dendrimers of generations 3 and 4 (G3 and G4). MD results show a 1:12, 1:1, 1:27, and 1:4 stoichiometry, respectively, for G3NH2-FU, G3OH-FU, G4NH2-FU, and G4OH-FU complexes, which is in good agreement with the isothermal titration calorimetry results. The results obtained showed that NH2-terminated dendrimers assume segmented open structures with large cavities and more drug molecules can encapsulate inside the dendritic cavities of amine terminated dendrimers. However, OH-terminated have a densely packed structure and therefore, 5-FU drug molecules are more stable to locate close to the surface of the dendrimers. Intermolecular hydrogen bonding analysis showed that 5-FU drug molecules have more tendency to form hydrogen bonds with terminal monomers of OH-terminated dendrimers, while in NH2-terminated these occur both in the inner region and the surface. Furthermore, MM-PBSA analysis revealed that van der Waals and electrostatic energies are both important to stabilize the complexes. We found that drug molecules are distributed uniformly inside the amine and hydroxyl terminated dendrimers and therefore, both dendrimers are promising candidates as drug delivery systems for 5-FU drug molecules.

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

Directory of Open Access Journals (Sweden)

Ramon Reigada

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

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

Science.gov (United States)

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

2015-03-01

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

Automated sampling and control of gaseous simulations

KAUST Repository

Huang, Ruoguan

2013-05-04

In this work, we describe a method that automates the sampling and control of gaseous fluid simulations. Several recent approaches have provided techniques for artists to generate high-resolution simulations based on a low-resolution simulation. However, often in applications the overall flow in the low-resolution simulation that an animator observes and intends to preserve is composed of even lower frequencies than the low resolution itself. In such cases, attempting to match the low-resolution simulation precisely is unnecessarily restrictive. We propose a new sampling technique to efficiently capture the overall flow of a fluid simulation, at the scale of user\\'s choice, in such a way that the sampled information is sufficient to represent what is virtually perceived and no more. Thus, by applying control based on the sampled data, we ensure that in the resulting high-resolution simulation, the overall flow is matched to the low-resolution simulation and the fine details on the high resolution are preserved. The samples we obtain have both spatial and temporal continuity that allows smooth keyframe matching and direct manipulation of visible elements such as smoke density through temporal blending of samples. We demonstrate that a user can easily configure a simulation with our system to achieve desired results. © 2013 Springer-Verlag Berlin Heidelberg.

Inter-ribbon tunneling in graphene: An atomistic Bardeen approach

Energy Technology Data Exchange (ETDEWEB)

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

2016-06-07

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

Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

Science.gov (United States)

Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

2017-01-01

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890

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

DEFF Research Database (Denmark)

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

2017-01-01

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

Simulated biomass, environmental impacts and best management practices for long-term switchgrass systems in a semi-arid region

International Nuclear Information System (INIS)

Wang, Limei; Qian, Yaling; Brummer, Joe E.; Zheng, Jiyong; Wilhelm, Sarah; Parton, William J.

2015-01-01

Long-term information on switchgrass (Panicum virgatum L.) as a biomass energy crop grown on marginally saline soil and the associated impacts on soil carbon (C) and nitrogen (N) dynamics, greenhouse gas (GHG) emissions, and best management practices (BMPs) are limited. In this study, we employed the DAYCENT model, based on a 4-year switchgrass field experiment, to evaluate the long-term biomass yield potential and environmental impacts, and further to develop BMPs for switchgrass in a semi-arid region. The model showed that long-term (14-year) annual mean biomass yields were 9.6 and 5.2 Mg ha −1 for irrigated and rainfed switchgrass systems, respectively. The simulated biomass yields correlated well with field-measured biomass with r 2 values of 0.99 and 0.89 for irrigated and rainfed systems, respectively. Soil organic carbon (SOC) and soil total nitrogen (STN) accumulated rapidly after switchgrass establishment, with mean accrual rates of 0.99–1.13 Mg C ha −1  yr −1 and 0.04–0.08 Mg N ha −1  yr −1 , respectively. Based on the outputs of numerous long-term model simulations with variable irrigation water supplies and N rates, the irrigation regime and N rate with the highest yield to input ratio were chosen as BMPs. The DAYCENT model predicted-BMP was irrigating every 14 days at 70% potential evapotranspiration combined with an N rate of 67 kg ha −1  yr −1 . Switchgrass established and produced biomass reasonably well in this semi-arid region; however, appropriate irrigation and N fertilization were needed for optimal biomass yield. Switchgrass had a great potential to sequester C into soils with low N 2 O emissions while supplying significant quantities of biomass for biofuel synthesis. - Highlights: • The DAYCENT model reliably simulated the growth of switchgrass on marginal land. • Long-term biomass and environmental impacts were simulated using the DAYCENT model. • Switchgrass produced biomass well on marginal land, but

Boundary crossover in semi-infinite non-equilibrium growth processes

International Nuclear Information System (INIS)

Allegra, Nicolas; Fortin, Jean-Yves; Henkel, Malte

2014-01-01

The growth of stochastic interfaces in the vicinity of a boundary and the non-trivial crossover towards the behaviour deep in the bulk are analysed. The causal interactions of the interface with the boundary lead to a roughness larger near to the boundary than deep in the bulk. This is exemplified in the semi-infinite Edwards–Wilkinson model in one dimension, from both its exact solution and numerical simulations, as well as from simulations on the semi-infinite one-dimensional Kardar–Parisi–Zhang model. The non-stationary scaling of interface heights and widths is analysed and a universal scaling form for the local height profile is proposed. (paper)

Atomistic modelling of diffusional phase transformations with elastic strain

International Nuclear Information System (INIS)

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

2004-01-01

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

Atomistic simulation on charge mobility of amorphous tris(8-hydroxyquinoline) aluminum (Alq3): origin of Poole-Frenkel-type behavior.

Science.gov (United States)

Nagata, Yuki; Lennartz, Christian

2008-07-21

The atomistic simulation of charge transfer process for an amorphous Alq(3) system is reported. By employing electrostatic potential charges, we calculate site energies and find that the standard deviation of site energy distribution is about twice as large as predicted in previous research. The charge mobility is calculated via the Miller-Abrahams formalism and the master equation approach. We find that the wide site energy distribution governs Poole-Frenkel-type behavior of charge mobility against electric field, while the spatially correlated site energy is not a dominant mechanism of Poole-Frenkel behavior in the range from 2x10(5) to 1.4x10(6) V/cm. Also we reveal that randomly meshed connectivities are, in principle, required to account for the Poole-Frenkel mechanism. Charge carriers find a zigzag pathway at low electric field, while they find a straight pathway along electric field when a high electric field is applied. In the space-charge-limited current scheme, the charge-carrier density increases with electric field strength so that the nonlinear behavior of charge mobility is enhanced through the strong charge-carrier density dependence of charge mobility.

An adhesive contact mechanics formulation based on atomistically induced surface traction

Energy Technology Data Exchange (ETDEWEB)

Fan, Houfu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States); Ren, Bo [Livermore Software Technology Corporation, 7374 Las Positas Road, Livermore, CA 94551 (United States); Li, Shaofan, E-mail: shaofan@berkeley.edu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)

2015-12-01

In this work, we have developed a novel multiscale computational contact formulation based on the generalized Derjuguin approximation for continua that are characterized by atomistically enriched constitutive relations in order to study macroscopic interaction between arbitrarily shaped deformable continua. The proposed adhesive contact formulation makes use of the microscopic interaction forces between individual particles in the interacting bodies. In particular, the double-layer volume integral describing the contact interaction (energy, force vector, matrix) is converted into a double-layer surface integral through a mathematically consistent approach that employs the divergence theorem and a special partitioning technique. The proposed contact model is formulated in the nonlinear continuum mechanics framework and implemented using the standard finite element method. With no large penalty constant, the stiffness matrix of the system will in general be well-conditioned, which is of great significance for quasi-static analysis. Three numerical examples are presented to illustrate the capability of the proposed method. Results indicate that with the same mesh configuration, the finite element computation based on the surface integral approach is faster and more accurate than the volume integral based approach. In addition, the proposed approach is energy preserving even in a very long dynamic simulation.

Molecular dynamics simulations of the atomistic structure of the intergranular film between silicon nitride grains: Effect of composition, thickness, and surface vacancies

International Nuclear Information System (INIS)

Garofalini, Stephen H.

2006-01-01

Molecular dynamics computer simulations were used to study the atomistic structure of intergranular films (IGFs) between two basal oriented Si 3 N 4 crystals or between combined basal and prism oriented crystals. Ordering of the ions into the IGF induced by the crystal surfaces was observed using density profiles of the ions, although that ordering is effected by the roughness of the crystal surface. Density profiles of the sum of all ions misleadingly shows a rapid decay in the density oscillations and apparent ordering into the IGF. However, this is an artifact of the coincidence of the maximum in the peaks of one species with the minimum of another species and the actual oscillations of individual species extend into the IGF farther than the sum profile indicates. This result would have important implications regarding the density oscillations observed in physical experiments with regard to the actual extent of ordering into the IGF induced by the crystal surface

Atomistic modeling of defect evolution in Si for amorphizing and subamorphizing implants

International Nuclear Information System (INIS)

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

2004-01-01

Solid phase epitaxial regrowth of pre-amorphizing implants has received significant attention as a method to achieve high dopant activation with minimal diffusion at low implant temperatures and suppress channelling. Therefore, a good understanding of the amorphization and regrowth mechanisms is required in process simulators. We present an atomistic amorphization and recrystallization model that uses the interstitial-vacancy (I-V) pair as a building block to describe the amorphous phase. I-V pairs are locally characterized by the number of neighbouring I-V pairs. This feature captures the damage generation and the dynamical annealing during ion implantation, and also explains the annealing behaviour of amorphous layers and amorphous pockets

Simulations for Making On-farm Decisions in Relation to ENSO in Semi-arid Areas, South Africa

Science.gov (United States)

Tesfuhuney, W. A.; Crespo, O. O.; Walker, S. S.; Steyn, S. A.

2017-12-01

The study was employed to investigate and improve on-farm decision making on planting dates and fertilization by relating simulated yield and seasonal outlook information. The Agricultural Production Systems SIMulator model (APSIM) was used to explore ENSO/SOI effects for small-scale farmers to represent weather conditions and soil forms of semi-arid areas of Bothaville, Bethlehem and Bloemfontein regions in South Africa. The relationships of rainfall and SOI anomalies indicate a positive correlation, signifies ENSO/SOI as seasonal outlooks for study areas. Model evaluation results showed higher degree of bias (RMSEs/RMSE value of 0.88-0.98). The D-index of agreement in the range 0.61-0.71 indicate the ability of the APSIM-Maize model is an adequate tool in evaluating relative changes in maize yield in relation to various management practices and seasonal variations. During rainy, La Niño years (SOI > +5), highest simulated yields were found for Bethlehem in November with addition of 100 - 150 kg ha-1 N fertilization and up to 50 kg ha-1 for both Bothaville and Bloemfontein. With respect to various levels of fertilization, the dry El Niño years (SOI risk for dryland farming in semi-arid regions. Key word: Semi-arid; APSIM; SOI; El Niño / La Niña; On-farm Decisions

Experimentally driven atomistic model of 1,2 polybutadiene

Energy Technology Data Exchange (ETDEWEB)

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

2014-02-07

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

Atomistic simulations of void migration under thermal gradient in UO2

International Nuclear Information System (INIS)

Desai, Tapan G.; Millett, Paul; Tonks, Michael; Wolf, Dieter

2010-01-01

It is well known that within a few hours after startup of a nuclear reactor, the temperature gradient within a fuel element causes migration of voids/bubbles radially inwards to form a central hole. To understand the atomic processes that control this migration of voids, we performed molecular dynamics (MD) simulations on single crystal UO 2 with voids of diameter 2.2 nm. An external temperature gradient was applied across the simulation cell. At the end of the simulation run, it was observed that the voids had moved towards the hot end of the simulation cell. The void migration velocity obtained from the simulations was compared with the available phenomenological equations for void migration due to different transport mechanisms. Surface diffusion of the slowest moving specie, i.e. uranium, was found to be the dominant mechanism for void migration. The contribution from lattice diffusion and the thermal stress gradient to the void migration was analyzed and found to be negligible. By extrapolation, a crossover from the surface-diffusion-controlled mechanism to the lattice-diffusion-controlled mechanism was found to occur for voids with sizes in the μm range.

Simulation and experimental verification of the filling process of semi-solid die forging for cup shell

Directory of Open Access Journals (Sweden)

Jianbo TAN

2015-06-01

Full Text Available The filling mold process of semi-solid alloy blank influences severely the forming and properties of finished piece. In this paper, DEFORM is applied to simulate the process of cup-type 6061 alloy die forging casting. The influences of the temperature of semi-solid alloy blank, preheating temperature, and downward press speed of pressure head on process of mold filling and velocity field are investigated. The results show that the mold filling of semi-solid alloy paste smoothly fills along the whole of mould cavity in “total wall thickness” form when the temperature of semi-solid alloy blank is 620 ℃, preheating temperature of pressure head is 200 ℃ and speed of pressure head is 40 mm/s. Along with the increase of the preheating temperature of pressure head, the filling process of the semi-solid alloy paste trends toward stable when the temperature of semi-solid alloy blank is 620 ℃ and the speed of pressure head is 20 mm/s. Along with the increasing of the temperature of semi-solid alloy, the process of mould filling becomes off balance and the liquid becomes turbulent flow. The velocity field in the process of mould filling affects severely the structure uniformity of the finished product.

Atomistic modeling of metal surfaces under electric fields: direct coupling of electric fields to a molecular dynamics algorithm

CERN Document Server

Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

2011-01-01

The effect of electric fields on metal surfaces is fairly well studied, resulting in numerous analytical models developed to understand the mechanisms of ionization of surface atoms observed at very high electric fields, as well as the general behavior of a metal surface in this condition. However, the derivation of analytical models does not include explicitly the structural properties of metals, missing the link between the instantaneous effects owing to the applied field and the consequent response observed in the metal surface as a result of an extended application of an electric field. In the present work, we have developed a concurrent electrodynamic–molecular dynamic model for the dynamical simulation of an electric-field effect and subsequent modification of a metal surface in the framework of an atomistic molecular dynamics (MD) approach. The partial charge induced on the surface atoms by the electric field is assessed by applying the classical Gauss law. The electric forces acting on the partially...

Systematic and efficient navigating potential energy surface: Data for silver doped gold clusters

Directory of Open Access Journals (Sweden)

Vitaly V. Chaban

2016-06-01

Full Text Available Locating global minimum of certain atomistic ensemble is known to be a highly challenging and resource consuming task. This dataset represents joint usage of the semi-empirical PM7 Hamiltonian, Broyden–Fletcher–Goldfarb–Shanno algorithm and basin hopping scheme to navigate a potential energy surface. The Au20 nanocluster was used for calibration as its global minimum structure is well-known. Furthermore, Au18Ag2 and Au15Ag5 were simulated for illustration of the algorithm performance. The work shows encouraging results and, particularly, underlines proper accuracy of PM7 as applied to this type of heavy metal systems. The reported dataset motivates to use the benchmarked method for studying potential energy surfaces of manifold systems and locate their global-minimum atomistic configurations.

Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.

Directory of Open Access Journals (Sweden)

Yunqiang Bian

2014-04-01

Full Text Available In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and K(+ ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes.

Numerical simulation of shock absorbers heat load for semi-active vehicle suspension system

Directory of Open Access Journals (Sweden)

Demić Miroslav D.

2016-01-01

Full Text Available Dynamic simulation, based on modelling, has a significant role during to the process of vehicle development. It is especially important in the first design stages, when relevant parameters are to be defined. Shock absorber, as an executive part of a semi-active suspension system, is exposed to thermal loads which can lead to its damage and degradation of characteristics. Therefore, this paper attempts to analyze a conversion of mechanical work into heat energy by use of a method of dynamic simulation. The issue of heat dissipation from the shock absorber has not been taken into consideration.

Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: Insights from atomistic simulations

Science.gov (United States)

Kumari, Pratibha; Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

2018-04-01

Modulation of lipid membrane properties due to the permeation of amphiphiles is an important biological process pertaining to many applications in the field of pharmaceutics, toxicology, and biotechnology. Sphingolipids are both structural and functional lipids that constitute an important component of mechanically stable and chemically resistant outer leaflets of plasma membranes. Here, we present an atomistic molecular dynamics simulation study to appreciate the concentration-dependent effects of small amphiphilic molecules, such as ethanol, acetone, and dimethyl sulfoxide (DMSO), on the structure and stability of a fully hydrated homogeneous N-palmitoyl-sphingomyelin (PSM) bilayer. The study reveals an increase in the lateral expansion of the bilayer along with disordering of the hydrophobic lipid tails on increasing the concentration of ethanol. At higher concentrations of ethanol, rupturing of the bilayer is quite evident through the analysis of partial electron density profiles and lipid tail order parameters. For ethanol containing systems, permeation of water molecules in the hydrophobic part of the bilayer is allowed through local defects made due to the entry of ethanol molecules via ethanol-ethanol and ethanol-PSM hydrogen bonds. Moreover, the extent of PSM-PSM hydrogen bonding decreases with increasing ethanol concentration. On the other hand, acetone and DMSO exhibit minimal effects on the stability of the PSM bilayer at their lower concentrations, but at higher concentrations they tend to enhance the stability of the bilayer. The simulated potential of mean force (PMF) profiles for the translocation of the three solutes studied reveal that the free-energy of transfer of an ethanol molecule across the PSM lipid head region is lower than that for acetone and DMSO molecules. However, highest free-energy rise in the core hydrophobic part of the bilayer is observed for the DMSO molecule, whereas the ethanol and acetone PMF profiles show a lower barrier in

An atomistic fingerprint algorithm for learning ab initio molecular force fields

Science.gov (United States)

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

2018-01-01

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

Viscosity of nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation.

Science.gov (United States)

Eslami, Hossein; Müller-Plathe, Florian

2010-01-14

Our new simulation scheme in isosurface-isothermal-isobaric ensemble [Eslami, H.; Mozaffari, F.; Moghadasi, J.; Müller-Plathe, F. J. Chem. Phys. 2008, 129, 194702], developed to simulate confined fluids in equilibrium with bulk, is applied to simulate polyamide-6,6 oligomers confined between graphite surfaces. The reverse nonequilibrium molecular dynamics simulation technique is employed to shear the graphite surfaces. In this work, six confined systems, with different surface separations, as well as the bulk fluid are simulated. Our results show a viscosity increase with respect to the bulk fluid, with decreasing distance between surfaces. Also, the calculated viscosities of the confined systems show an oscillatory behavior with maxima corresponding to well-formed layers between the surfaces. We observe a substantial slip at the surfaces, with the slip length depending on the shear rate and on the slit width. The slip length and the slip velocity show oscillatory behavior with out-of-phase oscillations with respect to the solvation force oscillations. Moreover, the temperature difference between coldest and hottest parts of the simulation box depends on the shear rate and on the layering effect (solvation force oscillations). An analysis of oligomer deformation under flow shows preferential alignment of oligomers parallel to the surfaces with increasing shear rate.

How Well Does BODIPY-Cholesteryl Ester Mimic Unlabeled Cholesteryl Esters in High Density Lipoprotein Particles?

DEFF Research Database (Denmark)

Karilainen, Topi; Vuorela, Timo; Vattulainen, Ilpo

2015-01-01

We compare the behavior of unlabeled and BODIPY-labeled cholesteryl ester (CE) in high density lipoprotein by atomistic molecular dynamics simulations. We find through replica exchange umbrella sampling and unbiased molecular dynamics simulations that BODIPY labeling has no significant effect...... on the partitioning of CE between HDL and the water phase. However, BODIPY-CE was observed to diffuse more slowly and locate itself closer to the HDL-water interface than CE due to the BODIPY probe that is constrained to the surface region, and because the CE body in BODIPY-CE prefers to align itself away from...... the HDL surface. The implications as to the suitability of BODIPY to explore lipoprotein properties are discussed....

VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

Energy Technology Data Exchange (ETDEWEB)

Orlić, Ivica; Mekterović, Darko [Department of Physics, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka (Croatia); Mekterović, Igor [Faculty of Electrical Engineering and Computing, University of Zagreb (Croatia); Ivošević, Tatjana [Faculty of Engineering, University of Rijeka, Vukovarska 58, HR-51000 Rijeka (Croatia)

2015-11-15

VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster–Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By “running” a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

International Nuclear Information System (INIS)

Orlić, Ivica; Mekterović, Darko; Mekterović, Igor; Ivošević, Tatjana

2015-01-01

VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster–Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By “running” a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

Science.gov (United States)

Orlić, Ivica; Mekterović, Darko; Mekterović, Igor; Ivošević, Tatjana

2015-11-01

VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster-Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By "running" a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

Science.gov (United States)

Hong, Bingbing

Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic

A semi-nested PCR assay for molecular detection of Paracoccidioides brasiliensis in tissue samples Semi-nested PCR para a detecção molecular de Paracoccidioides brasiliensis em amostras de tecido

Directory of Open Access Journals (Sweden)

Andrea Cristine Koishi

2010-12-01

Full Text Available INTRODUCTION: Paracoccidioidomycosis is a systemic infection caused by Paracoccidioides brasiliensis. METHODS: In this study, a semi-nested PCR for paracoccidioidomycosis diagnosis was developed. The primers ITS1 and ITS4 were used in the first reaction, while the primers MJ03 and ITS1 primer were used in the second reaction. The semi-nested PCR was used to investigate biopsies of five patients with oral lesions that resembled paracoccidioidomycosis. RESULTS: The semi-nested PCR was positive for four samples and negative for a sample from a patient later diagnosed with leishmaniasis. CONCLUSIONS: The new semi-nested PCR describe is useful for paracoccidioidomycosis diagnosis.INTRODUÇÃO: A paracoccidioidomicose é uma infecção sistêmica causada pelo Paracoccidioides brasiliensis. MÉTODOS: Neste estudo, uma semi-nested PCR foi desenvolvida para o diagnóstico da paracoccidioidomicose. Os oligonucleotídeos iniciadores ITS1 e ITS4 foram usados na primeira reação, enquanto os oligonucleotídeos iniciadores MJ03 e ITS1 foram usados na segunda reação. A semi-nested PCR foi usada para investigar biopsias de cinco pacientes com lesões orais que se assemelhavam a paracoccidioidomicose. RESULTADOS: A semi-nested PCR foi positiva para quatro amostras e negativa para a amostra de um paciente, posteriormente diagnosticado com leishmaniose. CONCLUSÕES: A semi-nested PCR descrita aqui é útil para o diagnóstico da paracoccidioidomicose.

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-06-15

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

How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers?

DEFF Research Database (Denmark)

Kulig, W.; Tynkkynen, J.; Javanainen, M.

2014-01-01

Cholesteryl hemisuccinate is a detergent that is often used to replace cholesterol in crystallization of membrane proteins. Here we employ atomistic molecular dynamics simulations to characterize how well the properties of cholesteryl hemisuccinate actually match those of cholesterol in saturated...... protein-free lipid membranes. We show that the protonated form of cholesteryl hemisuccinate mimics many of the membrane properties of cholesterol quite well, while the deprotonated form of cholesteryl hemisuccinate is less convincing in this respect. Based on the results, we suggest that cholesteryl...... hemisuccinate in its protonated form is a quite faithful mimic of cholesterol for membrane protein crystallization, if specific cholesterol-protein interactions (not investigated here) are not playing a crucial role....

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

International Nuclear Information System (INIS)

Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

2015-01-01

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

Energy Technology Data Exchange (ETDEWEB)

Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de; Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

2015-05-21

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

Monte Carlo simulations towards semi-quantitative prompt gamma activation imaging

International Nuclear Information System (INIS)

Kis, Zoltan; Belgya, Tamas; Szentmiklosi, Laszlo

2011-01-01

Numerous non-destructive techniques utilize neutron attenuation, scattering or capture to gain morphological, structural or elemental information about the material under study. However, few attempts have been made so far to use neutron-induced gamma radiation for 3D element mapping. The first ever facility using direct scanning for element imaging was set up at the Budapest Research Reactor. It was shown that the position-sensitive prompt-gamma detection (PGAI) enables us to determine the spatial distribution of major elements. Iterative Monte Carlo simulation technique has also been developed to provide not only qualitative but also semi-quantitative element distribution of a simple object.

Dynamics of Surfactant Clustering at Interfaces and Its Influence on the Interfacial Tension: Atomistic Simulation of a Sodium Hexadecane-Benzene Sulfonate-Tetradecane-Water System.

Science.gov (United States)

Paredes, Ricardo; Fariñas-Sánchez, Ana Isabel; Medina-Rodrı Guez, Bryan; Samaniego, Samantha; Aray, Yosslen; Álvarez, Luis Javier

2018-03-06

The process of equilibration of the tetradecane-water interface in the presence of sodium hexadecane-benzene sulfonate is studied using intensive atomistic molecular dynamics simulations. Starting as an initial point with all of the surfactants at the interface, it is obtained that the equilibration time of the interface (several microseconds) is orders of magnitude higher than previously reported simulated times. There is strong evidence that this slow equilibration process is due to the aggregation of surfactants molecules on the interface. To determine this fact, temporal evolution of interfacial tension and interfacial formation energy are studied and their temporal variations are correlated with cluster formation. To study cluster evolution, the mean cluster size and the probability that a molecule of surfactant chosen at random is free are obtained as a function of time. Cluster size distribution is estimated, and it is observed that some of the molecules remain free, whereas the rest agglomerate. Additionally, the temporal evolution of the interfacial thickness and the structure of the surfactant molecules on the interface are studied. It is observed how this structure depends on whether the molecules agglomerate or not.

3D atomistic studies of fatigue behaviour of edge crack (0 0 1) in bcc iron loaded in mode i and II

Czech Academy of Sciences Publication Activity Database

Machová, Anna; Pokluda, J.; Uhnáková, Alena; Hora, Petr

2014-01-01

Roč. 66, September (2014), s. 11-19 ISSN 0142-1123 R&D Projects: GA ČR(CZ) GAP108/10/0698 Institutional support: RVO:61388998 Keywords : fatigue crack growth * bcc iron * 3D atomistic simulations * molecular dynamics Subject RIV: JQ - Machines ; Tools Impact factor: 2.275, year: 2014 www.elsevier.com/locate/ijfatigue

Software-In-the-Loop based Modeling and Simulation of Unmanned Semi-submersible Vehicle for Performance Verification of Autonomous Navigation

Science.gov (United States)

Lee, Kwangkook; Jeong, Mijin; Kim, Dong Hun

2017-12-01

Since an unmanned semi-submersible is mainly used for the purpose of carrying out dangerous missions in the sea, it is possible to work in a region where it is difficult to access due to safety reasons. In this study, an USV hull design was determined using Myring hull profile, and reinforcement work was performed by designing and implementing inner stiffener member for 3D printing. In order to simulate a sea state 5.0 or more at sea, which is difficult to implement in practice, a regular and irregular wave equation was implemented in Matlab / Simulink. We performed modeling and simulation of semi - submersible simulation based on DMWorks considering the rolling motion in wave. To verify and improve unpredicted errors, we implemented a numeric and physical simulation model of the USV based on software-in-the-loop (SIL) method. This simulation allows shipbuilders to participate in new value-added markets such as engineering, procurement, construction, installation, commissioning, operation, and maintenance for the USV.

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

Science.gov (United States)

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

2008-01-31

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

Modelling and simulation of superalloys. Book of abstracts

Energy Technology Data Exchange (ETDEWEB)

Rogal, Jutta; Hammerschmidt, Thomas; Drautz, Ralf (eds.)

2014-07-01

Superalloys are multi-component materials with complex microstructures that offer unique properties for high-temperature applications. The complexity of the superalloy materials makes it particularly challenging to obtain fundamental insight into their behaviour from the atomic structure to turbine blades. Recent advances in modelling and simulation of superalloys contribute to a better understanding and prediction of materials properties and therefore offer guidance for the development of new alloys. This workshop will give an overview of recent progress in modelling and simulation of materials for superalloys, with a focus on single crystal Ni-base and Co-base alloys. Topics will include electronic structure methods, atomistic simulations, microstructure modelling and modelling of microstructural evolution, solidification and process simulation as well as the modelling of phase stability and thermodynamics.

Study of plasticity in metals by numerical simulations

International Nuclear Information System (INIS)

Clouet, E.

2013-01-01

We present a study of the plastic behaviour in metals based on the modelling of dislocation properties. Different simulation tools have been used and developed to study plasticity in structural materials, in particular metals used in the nuclear industry. In iron or zirconium alloys, plasticity is controlled at low temperature by the glide of screw dislocations. Atomistic simulations can be used to model dislocation core properties and thus to obtain a better knowledge of the mechanisms controlling dislocation glide. Such atomistic simulations need nevertheless some special care because of the long range elastic field induced by the dislocations. We have therefore developed a modelling approach relying both on atomistic simulations, using either empirical interatomic potentials or ab initio calculations, and on elasticity theory. Such an approach has been used to obtain dislocation intrinsic core properties. These simulations allowed us to describe, in iron, the variations of these core properties with the dislocation character. In zirconium, we could identity the origin of the high lattice friction and obtain a better understanding of the competition between the different glide systems. At high temperature, dislocations do not only glide but can also cross-slip or climb. This leads to a motion of the dislocations out of their glide plane which needs to be considered when modelling the plastic flow. We performed a study of dislocation climb at different scales, leading to the implementation of a dislocation climb model in dislocation dynamics simulations. (author) [fr

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Giant electrocaloric response in the prototypical Pb(Mg,Nb)O3 relaxor ferroelectric from atomistic simulations

Science.gov (United States)

Jiang, Zhijun; Nahas, Y.; Prokhorenko, S.; Prosandeev, S.; Wang, D.; Íñiguez, Jorge; Bellaiche, L.

2018-03-01

An atomistic effective Hamiltonian is used to investigate electrocaloric (EC) effects of Pb (Mg1 /3Nb2 /3) O3 relaxor ferroelectrics in its ergodic regime, and subject to electric fields applied along the pseudocubic [111] direction. Such a Hamiltonian qualitatively reproduces (i) the electric field-versus-temperature phase diagram, including the existence of a critical point where first-order and second-order transitions meet each other; and (ii) a giant EC response near such a critical point. It also reveals that such giant response around this critical point is microscopically induced by field-induced percolation of polar nanoregions. Moreover, it is also found that, for any temperature above the critical point, the EC coefficient-versus-electric-field curve adopts a maximum (and thus larger electrocaloric response too), that can be well described by the general Landau-like model proposed by Jiang et al., [Phys. Rev. B 96, 014114 (2017)], 10.1103/PhysRevB.96.014114, and that is further correlated with specific microscopic features related to dipoles lying along different rhombohedral directions. Furthermore, for temperatures being at least 40 K higher than the critical temperature, the (electric field, temperature) line associated with this maximal EC coefficient is below both the Widom line and the line representing percolation of polar nanoregions.

A Table-Based Random Sampling Simulation for Bioluminescence Tomography

Directory of Open Access Journals (Sweden)

Xiaomeng Zhang

2006-01-01

Full Text Available As a popular simulation of photon propagation in turbid media, the main problem of Monte Carlo (MC method is its cumbersome computation. In this work a table-based random sampling simulation (TBRS is proposed. The key idea of TBRS is to simplify multisteps of scattering to a single-step process, through randomly table querying, thus greatly reducing the computing complexity of the conventional MC algorithm and expediting the computation. The TBRS simulation is a fast algorithm of the conventional MC simulation of photon propagation. It retained the merits of flexibility and accuracy of conventional MC method and adapted well to complex geometric media and various source shapes. Both MC simulations were conducted in a homogeneous medium in our work. Also, we present a reconstructing approach to estimate the position of the fluorescent source based on the trial-and-error theory as a validation of the TBRS algorithm. Good agreement is found between the conventional MC simulation and the TBRS simulation.

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses.

Science.gov (United States)

Huber, Roland G; Marzinek, Jan K; Holdbrook, Daniel A; Bond, Peter J

2017-09-01

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

2014-10-01

Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

Science.gov (United States)

2017-01-01

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

Semi-analytical treatment of fracture/matrix flow in a dual-porosity simulator for unsaturated fractured rock masses

International Nuclear Information System (INIS)

Zimmerman, R.W.; Bodvarsson, G.S.

1992-04-01

A semi-analytical dual-porosity simulator for unsaturated flow in fractured rock masses has been developed. Fluid flow between the fracture network and the matrix blocks is described by analytical expressions that have been derived from approximate solutions to the imbibition equation. These expressions have been programmed into the unsaturated flow simulator, TOUGH, as a source/sink term. Flow processes are then simulated using only fracture elements in the computational grid. The modified code is used to simulate flow along single fractures, and infiltration into pervasively fractured formations

Atomistic simulation of solid solution hardening in Mg/Al alloys: Examination of composition scaling and thermo-mechanical relationships

International Nuclear Information System (INIS)

Yi, Peng; Cammarata, Robert C.; Falk, Michael L.

2016-01-01

Dislocation mobility in a solid solution was studied using atomistic simulations of an Mg/Al system. The critical resolved shear stress (CRSS) for the dislocations on the basal plane was calculated at temperatures from 0 K to 500 K with solute concentrations from 0 to 7 at%, and with four different strain rates. Solute hardening of the CRSS is decomposed into two contributions: one scales with c 2/3 , where c is the solute concentration, and the other scales with c 1 . The former was consistent with the Labusch model for local solute obstacles, and the latter was related to the athermal plateau stress due to the long range solute effect. A thermo-mechanical model was then used to analyze the temperature and strain rate dependences of the CRSS, and it yielded self-consistent and realistic results. The scaling laws were confirmed and the thermo-mechanical model was successfully parameterized using experimental measurements of the CRSS for Mg/Al alloys under quasi-static conditions. The predicted strain rate sensitivity from the experimental measurements of the CRSS is in reasonable agreement with separate mechanical tests. The concentration scaling and the thermo-mechanical relationships provide a potential tool to analytically relate the structural and thermodynamic parameters on the microscopic level with the macroscopic mechanical properties arising from dislocation mediated deformation.

Statistical analysis of simulation-generated time series : Systolic vs. semi-systolic correlation on the Connection Machine

NARCIS (Netherlands)

Dontje, T.; Lippert, Th.; Petkov, N.; Schilling, K.

1992-01-01

Autocorrelation becomes an increasingly important tool to verify improvements in the state of the simulational art in Latice Gauge Theory. Semi-systolic and full-systolic algorithms are presented which are intensively used for correlation computations on the Connection Machine CM-2. The

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

International Nuclear Information System (INIS)

Yang, L.; Deng, H.Q.; Gao, F.; Heinisch, H.L.; Kurtz, R.J.; Hu, S.Y.; Li, Y.L.; Zu, X.T.

2013-01-01

Atomistic simulations of the nucleation of He clusters and bubbles in bcc iron at 800 K have been carried out using the newly developed Fe–Fe interatomic potential, along with Ackland potential for the Fe–Fe interactions. Microstructure changes were analyzed in detail. We found that a He cluster with four He atoms is able to push out an iron interstitial from the cluster, creating a Frenkel pair. Small He clusters and self-interstitial atom (SIA) can migrate in the matrix, but He-vacancy (He-V) clusters are immobile. Most SIAs form clusters, and only the dislocation loops with a Burgers vector of b = 1/2 appear in the simulations. SIA clusters (or loops) are attached to He-V clusters for He implantation up to 1372 appm, while the He-V cluster–loop complexes with more than one He-V cluster are formed at the He concentration of 2057 appm and larger

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

Directory of Open Access Journals (Sweden)

Radhakrishna Bettadapura

2015-10-01

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

Probability Sampling Method for a Hidden Population Using Respondent-Driven Sampling: Simulation for Cancer Survivors.

Science.gov (United States)

Jung, Minsoo

2015-01-01

When there is no sampling frame within a certain group or the group is concerned that making its population public would bring social stigma, we say the population is hidden. It is difficult to approach this kind of population survey-methodologically because the response rate is low and its members are not quite honest with their responses when probability sampling is used. The only alternative known to address the problems caused by previous methods such as snowball sampling is respondent-driven sampling (RDS), which was developed by Heckathorn and his colleagues. RDS is based on a Markov chain, and uses the social network information of the respondent. This characteristic allows for probability sampling when we survey a hidden population. We verified through computer simulation whether RDS can be used on a hidden population of cancer survivors. According to the simulation results of this thesis, the chain-referral sampling of RDS tends to minimize as the sample gets bigger, and it becomes stabilized as the wave progresses. Therefore, it shows that the final sample information can be completely independent from the initial seeds if a certain level of sample size is secured even if the initial seeds were selected through convenient sampling. Thus, RDS can be considered as an alternative which can improve upon both key informant sampling and ethnographic surveys, and it needs to be utilized for various cases domestically as well.

A Universal Semi-totalistic Cellular Automaton on Kite and Dart Penrose Tilings

Directory of Open Access Journals (Sweden)

Katsunobu Imai

2012-08-01

Full Text Available In this paper we investigate certain properties of semi-totalistic cellular automata (CA on the well known quasi-periodic kite and dart two dimensional tiling of the plane presented by Roger Penrose. We show that, despite the irregularity of the underlying grid, it is possible to devise a semi-totalistic CA capable of simulating any boolean circuit on this aperiodic tiling.

Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation.

Science.gov (United States)

Hu, Xiao Liang; Piccinin, Simone; Laio, Alessandro; Fabris, Stefano

2012-12-21

Solar-driven water splitting is a key photochemical reaction that underpins the feasible and sustainable production of solar fuels. An amorphous cobalt-phosphate catalyst (Co-Pi) based on earth-abundant elements has been recently reported to efficiently promote water oxidation to protons and dioxygen, a main bottleneck for the overall process. The structure of this material remains largely unknown. We here exploit ab initio and classical atomistic simulations combined with metadynamics to build a realistic and statistically meaningful model of Co-Pi nanoparticles. We demonstrate the emergence and stability of molecular-size ordered crystallites in nanoparticles initially formed by a disordered Co-O network and phosphate groups. The stable crystallites consist of bis-oxo-bridged Co centers that assemble into layered structures (edge-sharing CoO(6) octahedra) as well as in corner- and face-sharing cubane units. These layered and cubane motifs coexist in the crystallites, which always incorporate disordered phosphate groups at the edges. Our computational nanoparticles, although limited in size to ~1 nm, can contain more than one crystallite and incorporate up to 18 Co centers in the cubane/layered structures. The crystallites are structurally stable up to high temperatures. We simulate the extended X-ray absorption fine structure (EXAFS) of our nanoparticles. Those containing several complete and incomplete cubane motifs-which are believed to be essential for the catalytic activity-display a very good agreement with the experimental EXAFS spectra of Co-Pi grains. We propose that the crystallites in our nanoparticles are reliable structural models of the Co-Pi catalyst surface. They will be useful to reveal the origin of the catalytic efficiency of these novel water-oxidation catalysts.

Atomistic studies of cation transport in tetragonal ZrO2 during zirconium corrosion

International Nuclear Information System (INIS)

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

2015-01-01

Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is a significant degradation mechanism of these alloys. During corrosion, the transport of oxidizing species in zirconium dioxide (ZrO 2 ) determines the corrosion kinetics. Previously, it has been argued that the outward diffusion of cations is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO 2 is studied with temperature accelerated dynamics and molecular dynamics simulations. The results show that Zr interstitials have anisotropic diffusion and migrate preferentially along the [001] or c direction in tetragonal ZrO 2 . The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration of Zr interstitials at a grain boundary is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed. (authors)

Computer Graphics Simulations of Sampling Distributions.

Science.gov (United States)

Gordon, Florence S.; Gordon, Sheldon P.

1989-01-01

Describes the use of computer graphics simulations to enhance student understanding of sampling distributions that arise in introductory statistics. Highlights include the distribution of sample proportions, the distribution of the difference of sample means, the distribution of the difference of sample proportions, and the distribution of sample…

Drug design: Insights from atomistic simulations

International Nuclear Information System (INIS)

Collu, F.; Spiga, E.; Kumar, A.; Hajjar, E.; Vargiu, A.V.; Ceccarelli, M.; Ruggerone, P.

2009-01-01

Computer simulations have become a widely used and powerful tool to study the behaviour of many-particle and many-interaction systems and processes such as nucleic acid dynamics, drug-DNA interactions, enzymatic processes, membrane, antibiotics. The increased reliability of computational techniques has made possible to plane a bottom-up approach in drug design, i.e. designing molecules with improved properties starting from the knowledge of the molecular mechanisms. However, the in silico techniques have to face the fact that the number of degrees of freedom involved in biological systems is very large while the time scale of several biological processes is not accessible to standard simulations. Algorithms and methods have been developed and are still under construction to bridge these gaps. Here we review the activities of our group focussed on the time-scale bottleneck and, in particular, on the use of the meta dynamics scheme that allows the investigation of rare events in reasonable computer time without reducing the accuracy of the calculation. In particular, we have devoted particular attention to the characterization at microscopic level of translocation of antibiotics through membrane pores, aiming at the identification of structural and dynamical features helpful for a rational drug design.

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

Energy Technology Data Exchange (ETDEWEB)

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

2006-10-01

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

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

Science.gov (United States)

Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

2017-04-01

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

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

International Nuclear Information System (INIS)

Piochaud, Jean-Baptiste

2013-01-01

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

Groundwater sampling with well-points

International Nuclear Information System (INIS)

Laubacher, R.C.; Bailey, W.M.

1992-01-01

This paper reports that BP Oil Company and Engineering-Science (ES) conducted a groundwater investigation at a BP Oil Distribution facility in the coastal plain of south central Alabama. The predominant lithologies include unconsolidated Quaternary-aged gravels, sands, silts and clay. Wellpoints were used to determine the vertical and horizontal extent of volatile hydrocarbons in the water table aquifer. To determine the vertical extent of contaminant migration, the hollow-stem augers were advanced approximately 10 feet into the aquifer near a suspected source. The drill stem and bit were removed very slowly to prevent sand heaving. The well-point was again driven ahead of the augers and four volumes (18 liters) of groundwater were purged. A sample was collected and the headspace vapor was analyzed as before. Groundwater from a total of seven borings was analyzed using these techniques. Permanent monitoring wells were installed at four boring locations which had volatile concentrations less than 1 part per million. Later groundwater sampling and laboratory analysis confirmed the wells had been installed near or beyond both the horizontal and vertical plume boundaries

Atomistic simulation of nanoformed metallic glass

Energy Technology Data Exchange (ETDEWEB)

Wu, Cheng-Da, E-mail: nanowu@cycu.edu.tw

2015-07-15

Highlights: • STZ forms at substrate surface underneath punch. • Atoms underneath punch have higher speeds at larger mold displacement. • Stick-slip phenomenon becomes more obvious with increasing imprint speed. • Great pattern transfer is obtained with unloading at low temperatures. - Abstract: The effects of forming speed and temperature on the forming mechanism and mechanics of Cu{sub 50}Zr{sub 25}Ti{sub 25} metallic glass are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. These effects are investigated in terms of atomic trajectories, flow field, slip vectors, internal energy, radial distribution function, and elastic recovery of nanoimprint lithography (NIL) patterns. The simulation results show that a shear transformation zone (STZ) forms at the substrate surface underneath the mold during the forming process. The STZ area increases with mold displacement (D). The movement speed of substrate atoms underneath the mold increases with increasing D value. The movement directions of substrate atoms underneath the mold are more agreeable for a larger D value. The stick-slip phenomenon becomes more obvious with increasing D value and imprint speed. The substrate energy increases with increasing imprint speed and temperature. Great NIL pattern transfer is obtained with unloading at low temperatures (e.g., room temperature)

Fast sampling algorithm for the simulation of photon Compton scattering

International Nuclear Information System (INIS)

Brusa, D.; Salvat, F.

1996-01-01

A simple algorithm for the simulation of Compton interactions of unpolarized photons is described. The energy and direction of the scattered photon, as well as the active atomic electron shell, are sampled from the double-differential cross section obtained by Ribberfors from the relativistic impulse approximation. The algorithm consistently accounts for Doppler broadening and electron binding effects. Simplifications of Ribberfors' formula, required for efficient random sampling, are discussed. The algorithm involves a combination of inverse transform, composition and rejection methods. A parameterization of the Compton profile is proposed from which the simulation of Compton events can be performed analytically in terms of a few parameters that characterize the target atom, namely shell ionization energies, occupation numbers and maximum values of the one-electron Compton profiles. (orig.)

Analysis and Comparison on the Flood Simulation in Typical Hilly & Semi-mountainous Region

Science.gov (United States)

Luan, Qinghua; Wang, Dong; Zhang, Xiang; Liu, Jiahong; Fu, Xiaoran; Zhang, Kun; Ma, Jun

2017-12-01

Water-logging and flood are both serious in hilly and semi-mountainous cities of China, but the related research is rare. Lincheng Economic Development Zone (EDZ) in Hebei Province as the typical city was selected and storm water management model (SWMM) was applied for flood simulation in this study. The regional model was constructed through calibrating and verifying the runoff coefficient of different flood processes. Different designed runoff processes in five-year, ten-year and twenty-year return periods in basic scenario and in the low impact development (LID) scenario, respectively, were simulated and compared. The result shows that: LID measures have effect on peak reduction in the study area, but the effectiveness is not significant; the effectiveness of lagging peak time is poor. These simulation results provide decision support for the rational construction of LID in the study area, and provide the references for regional rain flood management.

Microcanonical Monte Carlo approach for computing melting curves by atomistic simulations

OpenAIRE

Davis, Sergio; Gutiérrez, Gonzalo

2017-01-01

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

Preview-based sampling for controlling gaseous simulations

KAUST Repository

Huang, Ruoguan; Melek, Zeki; Keyser, John

2011-01-01

to maintain. During the high resolution simulation, a matching process ensures that the properties sampled from the low resolution simulation are maintained. This matching process keeps the different resolution simulations aligned even for complex systems

Direct and semi-direct effects of aerosol climatologies on long-term climate simulations over Europe

Science.gov (United States)

Schultze, Markus; Rockel, Burkhardt

2017-08-01

This study compares the direct and semi-direct aerosol effects of different annual cycles of tropospheric aerosol loads for Europe from 1950 to 2009 using the regional climate model COSMO-CLM, which is laterally forced by reanalysis data and run using prescribed, climatological aerosol optical properties. These properties differ with respect to the analysis strategy and the time window, and are then used for the same multi-decadal period. Five simulations with different aerosol loads and one control simulation without any tropospheric aerosols are integrated and compared. Two common limitations of our simulation strategy, to fully assess direct and semi-direct aerosol effects, are the applied observed sea surface temperatures and sea ice conditions, and the lack of short-term variations in the aerosol load. Nevertheless, the impact of different aerosol climatologies on common regional climate model simulations can be assessed. The results of all aerosol-including simulations show a distinct reduction in solar irradiance at the surface compared with that in the control simulation. This reduction is strongest in the summer season and is balanced primarily by a weakening of turbulent heat fluxes and to a lesser extent by a decrease in longwave emissions. Consequently, the seasonal mean surface cooling is modest. The temperature profile responses are characterized by a shallow near-surface cooling and a dominant warming up to the mid-troposphere caused by aerosol absorption. The resulting stabilization of stratification leads to reduced cloud cover and less precipitation. A decrease in cloud water and ice content over Central Europe in summer possibly reinforce aerosol absorption and thus strengthen the vertical warming. The resulting radiative forcings are positive. The robustness of the results was demonstrated by performing a simulation with very strong aerosol forcing, which lead to qualitatively similar results. A distinct added value over the default aerosol

Tunable thermodynamic stability of Au-CuPt core-shell trimetallic nanoparticles by controlling the alloy composition: insights from atomistic simulations.

Science.gov (United States)

Huang, Rao; Shao, Gui-Fang; Wen, Yu-Hua; Sun, Shi-Gang

2014-11-07

A microscopic understanding of the thermal stability of metallic core-shell nanoparticles is of importance for their synthesis and ultimately application in catalysis. In this article, molecular dynamics simulations have been employed to investigate the thermodynamic evolution of Au-CuPt core-shell trimetallic nanoparticles with various Cu/Pt ratios during heating processes. Our results show that the thermodynamic stability of these nanoparticles is remarkably enhanced upon rising Pt compositions in the CuPt shell. The melting of all the nanoparticles initiates at surface and gradually spreads into the core. Due to the lattice mismatch among Au, Cu and Pt, stacking faults have been observed in the shell and their numbers are associated with the Cu/Pt ratios. With the increasing temperature, they have reduced continuously for the Cu-dominated shell while more stacking faults have been produced for the Pt-dominated shell because of the significantly different thermal expansion coefficients of the three metals. Beyond the overall melting, all nanoparticles transform into a trimetallic mixing alloy coated by an Au-dominated surface. This work provides a fundamental perspective on the thermodynamic behaviors of trimetallic, even multimetallic, nanoparticles at the atomistic level, indicating that controlling the alloy composition is an effective strategy to realize tunable thermal stability of metallic nanocatalysts.

Automated sampling and control of gaseous simulations

KAUST Repository

Huang, Ruoguan; Keyser, John

2013-01-01

In this work, we describe a method that automates the sampling and control of gaseous fluid simulations. Several recent approaches have provided techniques for artists to generate high-resolution simulations based on a low-resolution simulation

Simulated Job Samples: A Student-Centered Approach to Vocational Exploration and Evaluation.

Science.gov (United States)

Richter-Stein, Caryn; Stodden, Robert A.

1981-01-01

Incorporating simulated job samples into the junior high school curriculum can provide vocational exploration opportunities as well as assessment data on special needs students. Students can participate as active learners and decision makers. (CL)

Simulated Sampling of Estuary Plankton

Science.gov (United States)

Fortner, Rosanne W.; Jenkins, Deborah Bainer

2009-01-01

To find out about the microscopic life in the valuable estuary environment, it is usually necessary to be near the water. This dry lab offers an alternative, using authentic data and a simulation of plankton sampling. From the types of organisms found in the sample, middle school students can infer relationships in the biological and physical…

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

DEFF Research Database (Denmark)

Papaleo, Elena

2015-01-01

that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

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

Science.gov (United States)

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

2018-04-16

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

Simulated Optimum Sowing Date for Forage Pearl Millet Cultivars in Multilocation Trials in Brazilian Semi-Arid Region.

Science.gov (United States)

Santos, Rafael D; Boote, Kenneth J; Sollenberger, Lynn E; Neves, Andre L A; Pereira, Luiz G R; Scherer, Carolina B; Gonçalves, Lucio C

2017-01-01

Forage production is primarily limited by weather conditions under dryland production systems in Brazilian semi-arid regions, therefore sowing at the appropriate time is critical. The objectives of this study were to evaluate the CSM-CERES-Pearl Millet model from the DSSAT software suite for its ability to simulate growth, development, and forage accumulation of pearl millet [ Pennisetum glaucum (L.) R.] at three Brazilian semi-arid locations, and to use the model to study the impact of different sowing dates on pearl millet performance for forage. Four pearl millet cultivars were grown during the 2011 rainy season in field experiments conducted at three Brazilian semi-arid locations, under rainfed conditions. The genetic coefficients of the four pearl millet cultivars were calibrated for the model, and the model performance was evaluated with experimental data. The model was run for 14 sowing dates using long-term historical weather data from three locations, to determine the optimum sowing window. Results showed that performance of the model was satisfactory as indicated by accurate simulation of crop phenology and forage accumulation against measured data. The optimum sowing window varied among locations depending on rainfall patterns, although showing the same trend for cultivars within the site. The best sowing windows were from 15 April to 15 May for the Bom Conselho location; 12 April to 02 May for Nossa Senhora da Gloria; and 17 April to 25 May for Sao Bento do Una. The model can be used as a tool to evaluate the effect of sowing date on forage pearl millet performance in Brazilian semi-arid conditions.

Preview-based sampling for controlling gaseous simulations

KAUST Repository

Huang, Ruoguan

2011-01-01

In this work, we describe an automated method for directing the control of a high resolution gaseous fluid simulation based on the results of a lower resolution preview simulation. Small variations in accuracy between low and high resolution grids can lead to divergent simulations, which is problematic for those wanting to achieve a desired behavior. Our goal is to provide a simple method for ensuring that the high resolution simulation matches key properties from the lower resolution simulation. We first let a user specify a fast, coarse simulation that will be used for guidance. Our automated method samples the data to be matched at various positions and scales in the simulation, or allows the user to identify key portions of the simulation to maintain. During the high resolution simulation, a matching process ensures that the properties sampled from the low resolution simulation are maintained. This matching process keeps the different resolution simulations aligned even for complex systems, and can ensure consistency of not only the velocity field, but also advected scalar values. Because the final simulation is naturally similar to the preview simulation, only minor controlling adjustments are needed, allowing a simpler control method than that used in prior keyframing approaches. Copyright © 2011 by the Association for Computing Machinery, Inc.

Semi-automatic watershed medical image segmentation methods for customized cancer radiation treatment planning simulation

International Nuclear Information System (INIS)

Kum Oyeon; Kim Hye Kyung; Max, N.

2007-01-01

A cancer radiation treatment planning simulation requires image segmentation to define the gross tumor volume, clinical target volume, and planning target volume. Manual segmentation, which is usual in clinical settings, depends on the operator's experience and may, in addition, change for every trial by the same operator. To overcome this difficulty, we developed semi-automatic watershed medical image segmentation tools using both the top-down watershed algorithm in the insight segmentation and registration toolkit (ITK) and Vincent-Soille's bottom-up watershed algorithm with region merging. We applied our algorithms to segment two- and three-dimensional head phantom CT data and to find pixel (or voxel) numbers for each segmented area, which are needed for radiation treatment optimization. A semi-automatic method is useful to avoid errors incurred by both human and machine sources, and provide clear and visible information for pedagogical purpose. (orig.)

Land Surface Model and Particle Swarm Optimization Algorithm Based on the Model-Optimization Method for Improving Soil Moisture Simulation in a Semi-Arid Region.

Science.gov (United States)

Yang, Qidong; Zuo, Hongchao; Li, Weidong

2016-01-01

Improving the capability of land-surface process models to simulate soil moisture assists in better understanding the atmosphere-land interaction. In semi-arid regions, due to limited near-surface observational data and large errors in large-scale parameters obtained by the remote sensing method, there exist uncertainties in land surface parameters, which can cause large offsets between the simulated results of land-surface process models and the observational data for the soil moisture. In this study, observational data from the Semi-Arid Climate Observatory and Laboratory (SACOL) station in the semi-arid loess plateau of China were divided into three datasets: summer, autumn, and summer-autumn. By combing the particle swarm optimization (PSO) algorithm and the land-surface process model SHAW (Simultaneous Heat and Water), the soil and vegetation parameters that are related to the soil moisture but difficult to obtain by observations are optimized using three datasets. On this basis, the SHAW model was run with the optimized parameters to simulate the characteristics of the land-surface process in the semi-arid loess plateau. Simultaneously, the default SHAW model was run with the same atmospheric forcing as a comparison test. Simulation results revealed the following: parameters optimized by the particle swarm optimization algorithm in all simulation tests improved simulations of the soil moisture and latent heat flux; differences between simulated results and observational data are clearly reduced, but simulation tests involving the adoption of optimized parameters cannot simultaneously improve the simulation results for the net radiation, sensible heat flux, and soil temperature. Optimized soil and vegetation parameters based on different datasets have the same order of magnitude but are not identical; soil parameters only vary to a small degree, but the variation range of vegetation parameters is large.

Atomistic simulation study of short pulse laser interactions with a metal target under conditions of spatial confinement by a transparent overlayer

Energy Technology Data Exchange (ETDEWEB)

Karim, Eaman T.; Shugaev, Maxim; Wu, Chengping; Zhigilei, Leonid V., E-mail: lz2n@virginia.edu [Department of Materials Science and Engineering, University of Virginia, 395 McCormick Road, Charlottesville, Virginia 22904-4745 (United States); Lin, Zhibin; Hainsey, Robert F. [Electro Scientific Industries, Inc., 13900 NW Science Park Drive, Portland, Oregon 97229 (United States)

2014-05-14

The distinct characteristics of short pulse laser interactions with a metal target under conditions of spatial confinement by a solid transparent overlayer are investigated in a series of atomistic simulations. The simulations are performed with a computational model combining classical molecular dynamics (MD) technique with a continuum description of the laser excitation, electron-phonon equilibration, and electronic heat transfer based on two-temperature model (TTM). Two methods for incorporation of the description of a transparent overlayer into the TTM-MD model are designed and parameterized for Ag-silica system. The material response to the laser energy deposition is studied for a range of laser fluences that, in the absence of the transparent overlayer, covers the regimes of melting and resolidification, photomechanical spallation, and phase explosion of the overheated surface region. In contrast to the irradiation in vacuum, the spatial confinement by the overlayer facilitates generation of sustained high-temperature and high-pressure conditions near the metal-overlayer interface, suppresses the generation of unloading tensile wave, decreases the maximum depth of melting, and prevents the spallation and explosive disintegration of the surface region of the metal target. At high laser fluences, when the laser excitation brings the surface region of the metal target to supercritical conditions, the confinement prevents the expansion and phase decomposition characteristic for the vacuum conditions leading to a gradual cooling of the hot compressed supercritical fluid down to the liquid phase and eventual solidification. The target modification in this case is limited to the generation of crystal defects and the detachment of the metal target from the overlayer.

Four Mile Creek semi-annual sampling report, January 1993 sampling event

International Nuclear Information System (INIS)

1993-05-01

From 1955 to 1988 low-level radioactive wastewater generated by chemical separation processes within the General Separations Area (GSA) was discharged to seepage basins in the F and H Areas of the Savannah River Site (SRS). These basins were designed to permit the infiltration of the process wastewaters. As wastewater percolated downward through the basins, chemical and radioactive constituents were retained or sequestered in the subsoils. An extensive study aimed at characterizing the groundwater seeping into Four Mile Creek and its associated seepline was conducted in 1988 and 1989 (Haselow et al. 1990). Results of this study suggested that contaminants leaching from the F and H Area seepage basins were impacting the Four Mile Creek wetland system. The seepage basins were closed in 1988 and capped and sealed in 1990. This effectively eliminated the source of the contaminants and the hydraulic head driving the migration of contaminants from the basins. It has been hypothesized that, after the elimination of the source and head, annual rainfall amounts would be sufficient to dilute and flush out contaminants remaining in the subsoils and groundwaters beneath the basins. Westinghouse Savannah River Company has designed a semi-annual sampling and analytical program for the Four Mile Creek (FMC) seepline and stream water to test the hypothesis. This report summarizes field monitoring activities from January 25, 1993 to February 4, 1993

Improving blood sample logistics using simulation

DEFF Research Database (Denmark)

Jørgensen, Pelle Morten Thomas; Jacobsen, Peter

2012-01-01

Using simulation as an approach to display and improve internal logistics and handling at hospitals has great potential. This research will show how a simulation model can be used to evaluate changes made to two different cases of transportation of blood samples at a hospital, by evaluating...

Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting.

Science.gov (United States)

Goel, Saurav; Luo, Xichun; Reuben, Robert L; Rashid, Waleed Bin

2011-11-11

Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear.

The impact of repeated simulation on health and healthcare perceptions of simulated patients.

NARCIS (Netherlands)

Boerjan, M.; Boone, F.; Anthierens, S.; Weel-Baumgarten, E.M. van; Deveugele, M.

2008-01-01

OBJECTIVE: To explore the effect of simulating medical conditions on simulated patients (SPs). Main points of interest are influence on: perception of personal health and perception of their relation with the health care provider (HCP), personal well being. METHODS: Semi-structured interviews were

Atomistic Molecular Dynamics Simulations of the Electrical Double

Science.gov (United States)

Li, Zifeng; Milner, Scott; Fichthorn, Kristen

2015-03-01

The electrical double layer (EDL) near the polymer/water interface plays a key role in the colloidal stability of latex paint. To elucidate the structure of the EDL at the molecular level, we conducted an all-atom molecular dynamics simulations. We studied two representative surface charge groups in latex, the ionic surfactant sodium dodecyl sulfate (SDS) and the grafted short polyelectrolyte charged by dissociated methyl methacrylic acid (MAA) monomers. Our results confirm that the Poisson-Boltzmann theory works well outside the Stern layer. Our calculated electrostatic potential at the Outer Helmholtz Plane (OHP) is close to the zeta potential measured experimentally, which suggests that the potential at the OHP is a good estimate of the zeta potential. We found that the position of the OHP for the MAA polyelectrolyte system extends much further into the aqueous phase than that in the SDS system, resulting in a Stern layer that is twice as thick. This model will allow for future investigations of the interactions of the surface with different surfactants and rheology modifiers, which may serve as a guide to tune the rheology of latex formulations. We thank Dow Chemical Company for financial support.

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.

Science.gov (United States)

Rauscher, Sarah; Neale, Chris; Pomès, Régis

2009-10-13

Generalized-ensemble algorithms in temperature space have become popular tools to enhance conformational sampling in biomolecular simulations. A random walk in temperature leads to a corresponding random walk in potential energy, which can be used to cross over energetic barriers and overcome the problem of quasi-nonergodicity. In this paper, we introduce two novel methods: simulated tempering distributed replica sampling (STDR) and virtual replica exchange (VREX). These methods are designed to address the practical issues inherent in the replica exchange (RE), simulated tempering (ST), and serial replica exchange (SREM) algorithms. RE requires a large, dedicated, and homogeneous cluster of CPUs to function efficiently when applied to complex systems. ST and SREM both have the drawback of requiring extensive initial simulations, possibly adaptive, for the calculation of weight factors or potential energy distribution functions. STDR and VREX alleviate the need for lengthy initial simulations, and for synchronization and extensive communication between replicas. Both methods are therefore suitable for distributed or heterogeneous computing platforms. We perform an objective comparison of all five algorithms in terms of both implementation issues and sampling efficiency. We use disordered peptides in explicit water as test systems, for a total simulation time of over 42 μs. Efficiency is defined in terms of both structural convergence and temperature diffusion, and we show that these definitions of efficiency are in fact correlated. Importantly, we find that ST-based methods exhibit faster temperature diffusion and correspondingly faster convergence of structural properties compared to RE-based methods. Within the RE-based methods, VREX is superior to both SREM and RE. On the basis of our observations, we conclude that ST is ideal for simple systems, while STDR is well-suited for complex systems.

Prediction of irradiation induced microstructures in the AgCu model alloy using a multiscale method coupling atomistic and phase field modelling

OpenAIRE

Demange, Gilles; Pontikis, Vassilis; Lunéville, Laurence; Simeone, David

2016-01-01

In this work, a multiscale approach based on phase field was developed to simulate the microstructure's evolution under irradiation in binary systems, from atomic to microstructural scale. For that purpose, an efficient numerical scheme was developed. In the case of AgCu alloy under Krypton ions irradiation, phenomenological parameters were computed using atomistic methods, as a function of the temperature and the irradiation flux. As a result, we predicted the influence of the irradiation fl...

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

Directory of Open Access Journals (Sweden)

Helgi Adalsteinsson

2008-01-01

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

Towards a physically-based multi-scale ecohydrological simulator for semi-arid regions

Science.gov (United States)

Caviedes-Voullième, Daniel; Josefik, Zoltan; Hinz, Christoph

2017-04-01

The use of numerical models as tools for describing and understanding complex ecohydrological systems has enabled to test hypothesis and propose fundamental, process-based explanations of the system system behaviour as a whole as well as its internal dynamics. Reaction-diffusion equations have been used to describe and generate organized pattern such as bands, spots, and labyrinths using simple feedback mechanisms and boundary conditions. Alternatively, pattern-matching cellular automaton models have been used to generate vegetation self-organization in arid and semi-arid regions also using simple description of surface hydrological processes. A key question is: How much physical realism is needed in order to adequately capture the pattern formation processes in semi-arid regions while reliably representing the water balance dynamics at the relevant time scales? In fact, redistribution of water by surface runoff at the hillslope scale occurs at temporal resolution of minutes while the vegetation development requires much lower temporal resolution and longer times spans. This generates a fundamental spatio-temporal multi-scale problem to be solved, for which high resolution rainfall and surface topography are required. Accordingly, the objective of this contribution is to provide proof-of-concept that governing processes can be described numerically at those multiple scales. The requirements for a simulating ecohydrological processes and pattern formation with increased physical realism are, amongst others: i. high resolution rainfall that adequately captures the triggers of growth as vegetation dynamics of arid regions respond as pulsed systems. ii. complex, natural topography in order to accurately model drainage patterns, as surface water redistribution is highly sensitive to topographic features. iii. microtopography and hydraulic roughness, as small scale variations do impact on large scale hillslope behaviour iv. moisture dependent infiltration as temporal

A simulative comparison of respondent driven sampling with incentivized snowball sampling--the "strudel effect".

Science.gov (United States)

Gyarmathy, V Anna; Johnston, Lisa G; Caplinskiene, Irma; Caplinskas, Saulius; Latkin, Carl A

2014-02-01

Respondent driven sampling (RDS) and incentivized snowball sampling (ISS) are two sampling methods that are commonly used to reach people who inject drugs (PWID). We generated a set of simulated RDS samples on an actual sociometric ISS sample of PWID in Vilnius, Lithuania ("original sample") to assess if the simulated RDS estimates were statistically significantly different from the original ISS sample prevalences for HIV (9.8%), Hepatitis A (43.6%), Hepatitis B (Anti-HBc 43.9% and HBsAg 3.4%), Hepatitis C (87.5%), syphilis (6.8%) and Chlamydia (8.8%) infections and for selected behavioral risk characteristics. The original sample consisted of a large component of 249 people (83% of the sample) and 13 smaller components with 1-12 individuals. Generally, as long as all seeds were recruited from the large component of the original sample, the simulation samples simply recreated the large component. There were no significant differences between the large component and the entire original sample for the characteristics of interest. Altogether 99.2% of 360 simulation sample point estimates were within the confidence interval of the original prevalence values for the characteristics of interest. When population characteristics are reflected in large network components that dominate the population, RDS and ISS may produce samples that have statistically non-different prevalence values, even though some isolated network components may be under-sampled and/or statistically significantly different from the main groups. This so-called "strudel effect" is discussed in the paper. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Atomistic Properties of Solids

CERN Document Server

Sirdeshmukh, Dinker B; Subhadra, K G

2011-01-01

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

Zinc adsorption on clays inferred from atomistic simulations and EXAFS spectroscopy

International Nuclear Information System (INIS)

Churakov, S.V.; Daehn, R.

2012-01-01

Document available in extended abstract form only. Clay minerals such as illite and montmorillonite are ubiquitous in the environment. Because of their large specific area and high structural charge, they control the migration of heavy metals in the geosphere via different uptake mechanisms. The main processes for the sequestration of trace concentrations of heavy metals are sorption to clay edge sites and incorporation into clay structures. Whereas, sorption is a fast process occurring nearly instantaneously, the incorporation of metal ions into clay minerals occurs over geological time scales. Zn is a divalent transition metal, which shows similar chemical behavior to Ni and Co and can thus also be considered as a natural analogue for radioactive Ni and Co arising from nuclear fuel and radioactive waste from the decommissioning of nuclear power plants. The release of radionuclides from a repository can be considerably retarded due to interactions with clay minerals. For example, bentonite containing >70 wt% di-octahedral alumino-silicate clays is foreseen as a backfill material in the Swiss concept for a high level radioactive waste repository (NAGRA, 2002). Knowing the uptake mechanism of these elements on clays can help to protect the natural environment. In this study ab initio molecular dynamics (MD) calculations were applied to simulate the molecular mechanism of Zn uptake on the edge surfaces of montmorillonite, a di-octahedral clay, and to explain the measured K-edge extended X-ray absorption fine structure (EXAFS) spectra of Zn adsorbed on montmorillonite at different loadings. Two different montmorillonites were chosen for the experimental part of this study: Milos (Island of Milos, Greece) and STx-1 (Gonzales County, Texas, USA) (VANTELON et al., 2003). As a reference for Zn substituted for Al in the clay octahedral sheet a MILOS sample was prepared without adding any Zn. Milos was chosen because it contains 1.8 [mmol/kg] Zn incorporated into the

Transient subchannel simulation of sodium boiling in a 37 rods bundle with semi implicit and full implicit algorithms

Energy Technology Data Exchange (ETDEWEB)

Azad, Hamed Moslehi; Shirani, A.S. [Shahid Beheshti Univ., Tehran (Iran, Islamic Republic of). Dept. of Nuclear Engineering

2017-07-15

Thermal hydraulic analysis of sodium boiling in fuel assemblies is an important issue in safety of sodium cooled reactors and subchannel method is an efficient approach in transient two phase flow analyses. Almost all of the subchannel codes which use two-fluid model in two phase flow analysis, are based on semi implicit algorithm. With the full implicit method it is possible to use larger time steps. In order to compare the semi implicit algorithm with full implicit algorithm, two transient subchannel numerical programs which one is based on semi implicit algorithm and the other is based on full implicit algorithm have been written in FORTRAN in this work for simulation of transients in sodium cooled Kompakter-Natriumsiede-Kreislauf (KNS) at the former Kernforschungszentrum Karlsruhe (KfK) in Germany.

Development and Demonstration of a Method to Evaluate Bio-Sampling Strategies Using Building Simulation and Sample Planning Software.

Science.gov (United States)

Dols, W Stuart; Persily, Andrew K; Morrow, Jayne B; Matzke, Brett D; Sego, Landon H; Nuffer, Lisa L; Pulsipher, Brent A

2010-01-01

In an effort to validate and demonstrate response and recovery sampling approaches and technologies, the U.S. Department of Homeland Security (DHS), along with several other agencies, have simulated a biothreat agent release within a facility at Idaho National Laboratory (INL) on two separate occasions in the fall of 2007 and the fall of 2008. Because these events constitute only two realizations of many possible scenarios, increased understanding of sampling strategies can be obtained by virtually examining a wide variety of release and dispersion scenarios using computer simulations. This research effort demonstrates the use of two software tools, CONTAM, developed by the National Institute of Standards and Technology (NIST), and Visual Sample Plan (VSP), developed by Pacific Northwest National Laboratory (PNNL). The CONTAM modeling software was used to virtually contaminate a model of the INL test building under various release and dissemination scenarios as well as a range of building design and operation parameters. The results of these CONTAM simulations were then used to investigate the relevance and performance of various sampling strategies using VSP. One of the fundamental outcomes of this project was the demonstration of how CONTAM and VSP can be used together to effectively develop sampling plans to support the various stages of response to an airborne chemical, biological, radiological, or nuclear event. Following such an event (or prior to an event), incident details and the conceptual site model could be used to create an ensemble of CONTAM simulations which model contaminant dispersion within a building. These predictions could then be used to identify priority area zones within the building and then sampling designs and strategies could be developed based on those zones.

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

DEFF Research Database (Denmark)

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

2011-01-01

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

Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

Science.gov (United States)

Soisson, F.; Becquart, C. S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

2010-11-01

Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using "on-the-fly" calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

International Nuclear Information System (INIS)

Soisson, F.; Becquart, C.S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

2010-01-01

Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using 'on-the-fly' calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

Transient productivity index for numerical well test simulations

Energy Technology Data Exchange (ETDEWEB)

Blanc, G.; Ding, D.Y.; Ene, A. [Institut Francais du Petrole, Pau (France)] [and others

1997-08-01

The most difficult aspect of numerical simulation of well tests is the treatment of the Bottom Hole Flowing (BHF) Pressure. In full field simulations, this pressure is derived from the Well-block Pressure (WBP) using a numerical productivity index which accounts for the grid size and permeability, and for the well completion. This productivity index is calculated assuming a pseudo-steady state flow regime in the vicinity of the well and is therefore constant during the well production period. Such a pseudo-steady state assumption is no longer valid for the early time of a well test simulation as long as the pressure perturbation has not reached several grid-blocks around the well. This paper offers two different solutions to this problem: (1) The first one is based on the derivation of a Numerical Transient Productivity Index (NTPI) to be applied to Cartesian grids; (2) The second one is based on the use of a Corrected Transmissibility and Accumulation Term (CTAT) in the flow equation. The representation of the pressure behavior given by both solutions is far more accurate than the conventional one as shown by several validation examples which are presented in the following pages.

Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics

Energy Technology Data Exchange (ETDEWEB)

Alekseeva, Uliana, E-mail: Alekseeva@itc.rwth-aachen.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); German Research School for Simulation Sciences (GRS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Winkler, Roland G., E-mail: r.winkler@fz-juelich.de [Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Sutmann, Godehard, E-mail: g.sutmann@fz-juelich.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); ICAMS, Ruhr-University Bochum, D-44801 Bochum (Germany)

2016-06-01

A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations.

Cross-Domain Semi-Supervised Learning Using Feature Formulation.

Science.gov (United States)

Xingquan Zhu

2011-12-01

Semi-Supervised Learning (SSL) traditionally makes use of unlabeled samples by including them into the training set through an automated labeling process. Such a primitive Semi-Supervised Learning (pSSL) approach suffers from a number of disadvantages including false labeling and incapable of utilizing out-of-domain samples. In this paper, we propose a formative Semi-Supervised Learning (fSSL) framework which explores hidden features between labeled and unlabeled samples to achieve semi-supervised learning. fSSL regards that both labeled and unlabeled samples are generated from some hidden concepts with labeling information partially observable for some samples. The key of the fSSL is to recover the hidden concepts, and take them as new features to link labeled and unlabeled samples for semi-supervised learning. Because unlabeled samples are only used to generate new features, but not to be explicitly included in the training set like pSSL does, fSSL overcomes the inherent disadvantages of the traditional pSSL methods, especially for samples not within the same domain as the labeled instances. Experimental results and comparisons demonstrate that fSSL significantly outperforms pSSL-based methods for both within-domain and cross-domain semi-supervised learning.

Mechanism of crack healing at room temperature revealed by atomistic simulations

International Nuclear Information System (INIS)

Li, J.; Fang, Q.H.; Liu, B.; Liu, Y.; Liu, Y.W.; Wen, P.H.

2015-01-01

Three dimensional molecular dynamics (MD) simulations are systematically carried out to reveal the mechanism of the crack healing at room temperature, in terms of the dislocation shielding and the atomic diffusion to control the crack closure, in a copper (Cu) plate suffering from a shear loading. The results show that the process of the crack healing is actualized through the dislocation emission at a crack tip accompanied with intrinsic stacking faults ribbon forming in the crack tip wake, the dislocation slipping in the matrix and the dislocation annihilation in the free surface. Dislocation included stress compressing the crack tip is examined from the MD simulations and the analytical models, and then the crack closes rapidly due to the assistance of the atomic diffusion induced by the thermal activation when the crack opening displacement is less than a threshold value. This phenomenon is very different from the previous results for the crack propagation under the external load applied because of the crack healing (advancing) largely dependent on the crystallographic orientations of crack and the directions of external loading. Furthermore, based on the energy characteristic and considering the crack size effect, a theoretical model is established to predict the relationships between the crack size and the shear stress which qualitatively agree well with that obtained in the MD simulations

Simulation of sampling effects in FPAs

Science.gov (United States)

Cook, Thomas H.; Hall, Charles S.; Smith, Frederick G.; Rogne, Timothy J.

1991-09-01

The use of multiplexers and large focal plane arrays in advanced thermal imaging systems has drawn renewed attention to sampling and aliasing issues in imaging applications. As evidenced by discussions in a recent workshop, there is no clear consensus among experts whether aliasing in sensor designs can be readily tolerated, or must be avoided at all cost. Further, there is no straightforward, analytical method that can answer the question, particularly when considering image interpreters as different as humans and autonomous target recognizers (ATR). However, the means exist for investigating sampling and aliasing issues through computer simulation. The U.S. Army Tank-Automotive Command (TACOM) Thermal Image Model (TTIM) provides realistic sensor imagery that can be evaluated by both human observers and TRs. This paper briefly describes the history and current status of TTIM, explains the simulation of FPA sampling effects, presents validation results of the FPA sensor model, and demonstrates the utility of TTIM for investigating sampling effects in imagery.

Interval sampling methods and measurement error: a computer simulation.

Science.gov (United States)

Wirth, Oliver; Slaven, James; Taylor, Matthew A

2014-01-01

A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.

Semi-physiologic model validation and bioequivalence trials simulation to select the best analyte for acetylsalicylic acid.

Science.gov (United States)

Cuesta-Gragera, Ana; Navarro-Fontestad, Carmen; Mangas-Sanjuan, Victor; González-Álvarez, Isabel; García-Arieta, Alfredo; Trocóniz, Iñaki F; Casabó, Vicente G; Bermejo, Marival

2015-07-10

The objective of this paper is to apply a previously developed semi-physiologic pharmacokinetic model implemented in NONMEM to simulate bioequivalence trials (BE) of acetyl salicylic acid (ASA) in order to validate the model performance against ASA human experimental data. ASA is a drug with first-pass hepatic and intestinal metabolism following Michaelis-Menten kinetics that leads to the formation of two main metabolites in two generations (first and second generation metabolites). The first aim was to adapt the semi-physiological model for ASA in NOMMEN using ASA pharmacokinetic parameters from literature, showing its sequential metabolism. The second aim was to validate this model by comparing the results obtained in NONMEM simulations with published experimental data at a dose of 1000 mg. The validated model was used to simulate bioequivalence trials at 3 dose schemes (100, 1000 and 3000 mg) and with 6 test formulations with decreasing in vivo dissolution rate constants versus the reference formulation (kD 8-0.25 h (-1)). Finally, the third aim was to determine which analyte (parent drug, first generation or second generation metabolite) was more sensitive to changes in formulation performance. The validation results showed that the concentration-time curves obtained with the simulations reproduced closely the published experimental data, confirming model performance. The parent drug (ASA) was the analyte that showed to be more sensitive to the decrease in pharmaceutical quality, with the highest decrease in Cmax and AUC ratio between test and reference formulations. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiscale Simulation of Thermo-mechanical Processes in Irradiated Fission-reactor Materials

International Nuclear Information System (INIS)

Phillpot, Simon R.

2012-01-01

The work funded from this project has been published in six papers, with two more in draft form, with submission planned for the near future. The papers are: (1) Kinetically-Evolving Irradiation-Induced Point-Defect Clusters in UO 2 by Molecular-Dynamics Simulation; (2) Kinetically driven point-defect clustering in irradiated MgO by molecular-dynamics simulation; (3) Grain-Boundary Source/Sink Behavior for Point Defect: An Atomistic Simulation Study; (4) Energetics of intrinsic point defects in uranium dioxide from electronic structure calculations; (5) Thermodynamics of fission products in UO 2±x ; and (6) Atomistic study of grain boundary sink strength under prolonged electron irradiation. The other two pieces of work that are currently being written-up for publication are: (1) Effect of Pores and He Bubbles on the Thermal Transport Properties of UO2 by Molecular Dynamics Simulation; and (2) Segregation of Ruthenium to Edge Dislocations in Uranium Dioxide.

Atomistic simulations of the formation of -component dislocation loops in α-zirconium

Energy Technology Data Exchange (ETDEWEB)

Dai, Cong, E-mail: dai.cong@queensu.ca; Balogh, Levente; Yao, Zhongwen; Daymond, Mark R., E-mail: mark.daymond@queensu.ca

2016-09-15

The formation of -component dislocation loops in α-Zr is believed to be responsible for the breakaway irradiation growth experimentally observed under high irradiation fluences. However, while -loop growth is well described by existing models, the atomic mechanisms responsible for the nucleation of -component dislocation loops are still not clear. In the present work, both interstitial and vacancy -type dislocation loops are initially equilibrated at different temperatures. Cascades simulations in the vicinity of the -type loops are then performed by selecting an atom as the primary knock-on atoms (PKAs) with different kinetic energies, using molecular dynamics simulations. No -component dislocation loop was formed in cascades simulations with a 10 keV PKA, but -component interstitial loops were observed after the interaction between discontinuous 50 keV PKAs and pre-existing -type interstitial loops. The comparisons of cascades simulations in volumes having pre-existing -type interstitial and vacancy loops suggest that the reaction between the PKAs and -type interstitial loops is responsible for the formation of -component interstitial loops.

LibCPIXE: A PIXE simulation open-source library for multilayered samples

International Nuclear Information System (INIS)

Pascual-Izarra, C.; Barradas, N.P.; Reis, M.A.

2006-01-01

Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called 'LibCPIXE', for PIXE data analysis. It is written in standard C and implements functions for simulating X-ray yields of PIXE spectra taken from arbitrary samples, including multilayered targets. The library is designed to be fast, portable, modular and scalable, as well as to facilitate its incorporation into any existing program. In order to demonstrate the capabilities of the library, a program called CPIXE was developed and used to analyze various real samples involving both bulk and layered samples. Just as the library, the CPIXE source code is freely available under the General Public License. We demonstrate that it runs both under GNU/Linux systems as well as under MS Windows. There is in principle no limitation to port it to other platforms

spsann - optimization of sample patterns using spatial simulated annealing

Science.gov (United States)

Samuel-Rosa, Alessandro; Heuvelink, Gerard; Vasques, Gustavo; Anjos, Lúcia

2015-04-01

There are many algorithms and computer programs to optimize sample patterns, some private and others publicly available. A few have only been presented in scientific articles and text books. This dispersion and somewhat poor availability is holds back to their wider adoption and further development. We introduce spsann, a new R-package for the optimization of sample patterns using spatial simulated annealing. R is the most popular environment for data processing and analysis. Spatial simulated annealing is a well known method with widespread use to solve optimization problems in the soil and geo-sciences. This is mainly due to its robustness against local optima and easiness of implementation. spsann offers many optimizing criteria for sampling for variogram estimation (number of points or point-pairs per lag distance class - PPL), trend estimation (association/correlation and marginal distribution of the covariates - ACDC), and spatial interpolation (mean squared shortest distance - MSSD). spsann also includes the mean or maximum universal kriging variance (MUKV) as an optimizing criterion, which is used when the model of spatial variation is known. PPL, ACDC and MSSD were combined (PAN) for sampling when we are ignorant about the model of spatial variation. spsann solves this multi-objective optimization problem scaling the objective function values using their maximum absolute value or the mean value computed over 1000 random samples. Scaled values are aggregated using the weighted sum method. A graphical display allows to follow how the sample pattern is being perturbed during the optimization, as well as the evolution of its energy state. It is possible to start perturbing many points and exponentially reduce the number of perturbed points. The maximum perturbation distance reduces linearly with the number of iterations. The acceptance probability also reduces exponentially with the number of iterations. R is memory hungry and spatial simulated annealing is a

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

Science.gov (United States)

Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.

2013-12-01

In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations

Simulation and interpretation of inter-well tracer tests

Directory of Open Access Journals (Sweden)

Dugstad Øyvind

2013-05-01

Full Text Available In inter-well tracer tests (IWTT, chemical compounds or radioactive isotopes are used to label injection water and gas to establish well connections and fluid patterns in petroleum reservoirs. Tracer simulation is an invaluable tool to ease the interpretation of IWTT results and is also required for assisted history matching application of tracer data. In this paper we present a new simulation technique to analyse and interpret tracer results. Laboratory results are used to establish and test formulations of the tracer conservation equations, and the technique is used to provide simulated tracer responses that are compared with observed tracer data from an extensive tracer program. The implemented tracer simulation methodology use a fast post-processing of previously simulated reservoir simulation runs. This provides a fast, flexible and powerful method for analysing gas tracer behaviour in reservoirs. We show that simulation time for tracers can be reduced by factor 100 compared to solving the tracer flow equations simultaneously with the reservoir fluid flow equations. The post-processing technique, combined with a flexible built-in local tracer-grid refinement is exploited to reduce numerical smearing, particularly severe for narrow tracer pulses.

Semi-analytical model for hollow-core anti-resonant fibers

Directory of Open Access Journals (Sweden)

Wei eDing

2015-03-01

Full Text Available We detailedly describe a recently-developed semi-analytical method to quantitatively calculate light transmission properties of hollow-core anti-resonant fibers (HC-ARFs. Formation of equiphase interface at fiber’s outermost boundary and outward light emission ruled by Helmholtz equation in fiber’s transverse plane constitute the basis of this method. Our semi-analytical calculation results agree well with those of precise simulations and clarify the light leakage dependences on azimuthal angle, geometrical shape and polarization. Using this method, we show investigations on HC-ARFs having various core shapes (e.g. polygon, hypocycloid with single- and multi-layered core-surrounds. The polarization properties of ARFs are also studied. Our semi-analytical method provides clear physical insights into the light guidance in ARF and can play as a fast and useful design aid for better ARFs.

Spontaneous Formation of A Nanotube From A Square Ag Nanowire: An Atomistic View

Science.gov (United States)

Konuk Onat, Mine; Durukanoglu, Sondan

2012-02-01

We have performed molecular static calculations to investigate the recently observed phenomenon of the spontaneous formation of a nanotube from a regular, square Ag nanowire[1]. In the simulations, atoms are allowed to interact via the model potential obtained from the modified embedded atom method. Our simulations predict that this particular type of structural phase transformation is controlled by the nature of applied strain, length of the wire and initial cross-sectional shape. For such a perfect structural transformation, the axially oriented fcc nanowire needs (1) to be formed by stacking A and B layers of an fcc crystal, both possessing the geometry of two interpenetrating one-lattice-parameter-wide squares, containing four atoms each, (2) to have an optimum length of eight layers, and (3) to be exposed to a combination of low and high stress along the length direction. The results further offer insights into atomistic nature of this specific structural transformation into a nanotube with the smallest possible cross-section. [1] M.J. Lagos et al., Nature Nanotech. 4, 149 (2009).

Simulated tempering distributed replica sampling: A practical guide to enhanced conformational sampling

Energy Technology Data Exchange (ETDEWEB)

Rauscher, Sarah; Pomes, Regis, E-mail: pomes@sickkids.ca

2010-11-01

Simulated tempering distributed replica sampling (STDR) is a generalized-ensemble method designed specifically for simulations of large molecular systems on shared and heterogeneous computing platforms [Rauscher, Neale and Pomes (2009) J. Chem. Theor. Comput. 5, 2640]. The STDR algorithm consists of an alternation of two steps: (1) a short molecular dynamics (MD) simulation; and (2) a stochastic temperature jump. Repeating these steps thousands of times results in a random walk in temperature, which allows the system to overcome energetic barriers, thereby enhancing conformational sampling. The aim of the present paper is to provide a practical guide to applying STDR to complex biomolecular systems. We discuss the details of our STDR implementation, which is a highly-parallel algorithm designed to maximize computational efficiency while simultaneously minimizing network communication and data storage requirements. Using a 35-residue disordered peptide in explicit water as a test system, we characterize the efficiency of the STDR algorithm with respect to both diffusion in temperature space and statistical convergence of structural properties. Importantly, we show that STDR provides a dramatic enhancement of conformational sampling compared to a canonical MD simulation.

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

International Nuclear Information System (INIS)

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

2010-01-01

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

Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.

Directory of Open Access Journals (Sweden)

Kecheng Yang

Full Text Available Sampling enrichment toward a target state, an analogue of the improvement of sampling efficiency (SE, is critical in both the refinement of protein structures and the generation of near-native structure ensembles for the exploration of structure-function relationships. We developed a hybrid molecular dynamics (MD-Monte Carlo (MC approach to enrich the sampling toward the target structures. In this approach, the higher SE is achieved by perturbing the conventional MD simulations with a MC structure-acceptance judgment, which is based on the coincidence degree of small angle x-ray scattering (SAXS intensity profiles between the simulation structures and the target structure. We found that the hybrid simulations could significantly improve SE by making the top-ranked models much closer to the target structures both in the secondary and tertiary structures. Specifically, for the 20 mono-residue peptides, when the initial structures had the root-mean-squared deviation (RMSD from the target structure smaller than 7 Å, the hybrid MD-MC simulations afforded, on average, 0.83 Å and 1.73 Å in RMSD closer to the target than the parallel MD simulations at 310K and 370K, respectively. Meanwhile, the average SE values are also increased by 13.2% and 15.7%. The enrichment of sampling becomes more significant when the target states are gradually detectable in the MD-MC simulations in comparison with the parallel MD simulations, and provide >200% improvement in SE. We also performed a test of the hybrid MD-MC approach in the real protein system, the results showed that the SE for 3 out of 5 real proteins are improved. Overall, this work presents an efficient way of utilizing solution SAXS to improve protein structure prediction and refinement, as well as the generation of near native structures for function annotation.

The simulation approach to lipid-protein interactions.

Science.gov (United States)

Paramo, Teresa; Garzón, Diana; Holdbrook, Daniel A; Khalid, Syma; Bond, Peter J

2013-01-01

The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.

The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

Science.gov (United States)

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.

Artificial semi-rigid tissue sensitized with natural pigments: Effect of photon radiations

Directory of Open Access Journals (Sweden)

Adnan Jaradat

2011-01-01

Full Text Available Background: A new approach for evaluating the optical penetration depth and testing its validity with Monte Carlo simulations and Kubelka-Munk theory is used for artificial semi-rigid tissue sensitized with natural pigments. Photodynamic therapy is a promising cancer treatment in which a photosensitizing drug concentrates in malignant cells and is activated by visible light at certain wavelength. Materials and Methods: Cheap artificial semi-rigid tissue incorporated with scattering and absorbing materials along with some other composites comparable to normal human tissue has been performed. The optical parameters as measured with different conditions and calculated with various techniques are investigated. Results: The probability of interaction of light with tissue is very high when exposed to light in presence of Cichorium pumilum and RBCs followed by photohemolysis or/and photodegradation. The optical penetration depth calculated by linear absorption coefficient ranges from 0.63 to 2.85 mm is found to be comparable to those calculated using Kubelka-Munk theory or Monte Carlo simulation (range from 0.78 to 2.42 mm. The ratio of absorption to the scattering is independent of thickness and decreases with increasing irradiation time. Moreover, the optical parameters as well as their ratios are in very good agreement in the two approaches of calculation. The values of absorption and scattering coefficients are independent of thickness. Furthermore, the average photon ranges in the samples containing no scattering and absorbing materials are about three times greater than those samples containing scattering materials. Conclusion: Our results suggest that light propagation with optical properties presented in this work could be applicable in diagnostic and therapeutic of the human biological tissue for photodynamic therapy.

Stochastic semi-classical description of sub-barrier fusion reactions

Directory of Open Access Journals (Sweden)

Ayik Sakir

2011-10-01

Full Text Available A semi-classical method that incorporates the quantum effects of the low-lying vibrational modes is applied to fusion reactions. The quantum effect is simulated by stochastic sampling of initial zero-point fluctuations of the surface modes. In this model, dissipation of the relative energy into non-collective excitations of nuclei can be included straightforwardly. The inclusion of dissipation is shown to increase the agreement with the fusion cross section data of Ni isotopes.

Simulation of the optical coating deposition

Science.gov (United States)

Grigoriev, Fedor; Sulimov, Vladimir; Tikhonravov, Alexander

2018-04-01

A brief review of the mathematical methods of thin-film growth simulation and results of their applications is presented. Both full-atomistic and multi-scale approaches that were used in the studies of thin-film deposition are considered. The results of the structural parameter simulation including density profiles, roughness, porosity, point defect concentration, and others are discussed. The application of the quantum level methods to the simulation of the thin-film electronic and optical properties is considered. Special attention is paid to the simulation of the silicon dioxide thin films.

Multiscale Simulation of Thermo-mechancial Processes in Irradiated Fission-reactor Materials.

Energy Technology Data Exchange (ETDEWEB)

Simon R. Phillpot

2012-06-08

The work funded from this project has been published in six papers, with two more in draft form, with submission planned for the near future. The papers are: (1) Kinetically-Evolving Irradiation-Induced Point-Defect Clusters in UO{sub 2} by Molecular-Dynamics Simulation; (2) Kinetically driven point-defect clustering in irradiated MgO by molecular-dynamics simulation; (3) Grain-Boundary Source/Sink Behavior for Point Defect: An Atomistic Simulation Study; (4) Energetics of intrinsic point defects in uranium dioxide from electronic structure calculations; (5) Thermodynamics of fission products in UO{sub 2{+-}x}; and (6) Atomistic study of grain boundary sink strength under prolonged electron irradiation. The other two pieces of work that are currently being written-up for publication are: (1) Effect of Pores and He Bubbles on the Thermal Transport Properties of UO2 by Molecular Dynamics Simulation; and (2) Segregation of Ruthenium to Edge Dislocations in Uranium Dioxide.

Study on Applicability of Conceptual Hydrological Models for Flood Forecasting in Humid, Semi-Humid Semi-Arid and Arid Basins in China

Directory of Open Access Journals (Sweden)

Guangyuan Kan

2017-09-01

Full Text Available Flood simulation and forecasting in various types of watersheds is a hot issue in hydrology. Conceptual hydrological models have been widely applied to flood forecasting for decades. With the development of economy, modern China faces with severe flood disasters in all types of watersheds include humid, semi-humid semi-arid and arid watersheds. However, conceptual model-based flood forecasting in semi-humid semi-arid and arid regions is still challenging. To investigate the applicability of conceptual hydrological models for flood forecasting in the above mentioned regions, three typical conceptual models, include Xinanjiang (XAJ, mix runoff generation (MIX and northern Shannxi (NS, are applied to 3 humid, 3 semi-humid semi-arid, and 3 arid watersheds. The rainfall-runoff data of the 9 watersheds are analyzed based on statistical analysis and information theory, and the model performances are compared and analyzed based on boxplots and scatter plots. It is observed the complexity of drier watershed data is higher than that of the wetter watersheds. This indicates the flood forecasting is harder in drier watersheds. Simulation results indicate all models perform satisfactorily in humid watersheds and only NS model is applicable in arid watersheds. Model with consideration of saturation excess runoff generation (XAJ and MIX perform better than the infiltration excess-based NS model in semi-humid semi-arid watersheds. It is concluded more accurate mix runoff generation theory, more stable and efficient numerical solution of infiltration equation and rainfall data with higher spatial-temporal resolution are main obstacles for conceptual model-based flood simulation and forecasting.

The relative entropy is fundamental to adaptive resolution simulations

Science.gov (United States)

Kreis, Karsten; Potestio, Raffaello

2016-07-01

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy with respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.

Grain scale simulation of multiphase flow through porous media; Simulacao em escala granular do escoamento multifasico em meio poroso

Energy Technology Data Exchange (ETDEWEB)

Domingos, Ricardo Golghetto; Cheng, Liang-Yee [Universidade de Sao Paulo (USP), SP (Brazil). Escola Politecnica

2012-07-01

Since the grain scale modeling of multi-phase flow in porous media is of great interest for the oil industry, the aim of the present research is to show an implementation of Moving Particle Semi-Implicit (MPS) method for the grain scale simulation of multi-phase flow in porous media. Geometry data obtained by a high-resolution CT scan of a sandstone sample has been used as input for the simulations. The results of the simulations performed considering different resolutions are given, the head loss and permeability obtained numerically, as well as the influence of the wettability of the fluids inside the sample of the reservoir's sandstone. (author)

Generative Adversarial Networks-Based Semi-Supervised Learning for Hyperspectral Image Classification

Directory of Open Access Journals (Sweden)

Zhi He

2017-10-01

Full Text Available Classification of hyperspectral image (HSI is an important research topic in the remote sensing community. Significant efforts (e.g., deep learning have been concentrated on this task. However, it is still an open issue to classify the high-dimensional HSI with a limited number of training samples. In this paper, we propose a semi-supervised HSI classification method inspired by the generative adversarial networks (GANs. Unlike the supervised methods, the proposed HSI classification method is semi-supervised, which can make full use of the limited labeled samples as well as the sufficient unlabeled samples. Core ideas of the proposed method are twofold. First, the three-dimensional bilateral filter (3DBF is adopted to extract the spectral-spatial features by naturally treating the HSI as a volumetric dataset. The spatial information is integrated into the extracted features by 3DBF, which is propitious to the subsequent classification step. Second, GANs are trained on the spectral-spatial features for semi-supervised learning. A GAN contains two neural networks (i.e., generator and discriminator trained in opposition to one another. The semi-supervised learning is achieved by adding samples from the generator to the features and increasing the dimension of the classifier output. Experimental results obtained on three benchmark HSI datasets have confirmed the effectiveness of the proposed method , especially with a limited number of labeled samples.

Semi-implicit magnetohydrodynamic calculations

International Nuclear Information System (INIS)

Schnack, D.D.; Barnes, D.C.; Mikic, Z.; Harned, D.S.; Caramana, E.J.

1987-01-01

A semi-implicit algorithm for the solution of the nonlinear, three-dimensional, resistive MHD equations in cylindrical geometry is presented. The specific model assumes uniform density and pressure, although this is not a restriction of the method. The spatial approximation employs finite differences in the radial coordinate, and the pseudo-spectral algorithm in the periodic poloidal and axial coordinates. A leapfrog algorithm is used to advance wave-like terms; advective terms are treated with a simple predictor--corrector method. The semi-implicit term is introduced as a simple modification to the momentum equation. Dissipation is treated implicitly. The resulting algorithm is unconditionally stable with respect to normal modes. A general discussion of the semi-implicit method is given, and specific forms of the semi-implicit operator are compared in physically relevant test cases. Long-time simulations are presented. copyright 1987 Academic Press, Inc

Semi-flexible polymer engendered aggregation/dispersion of fullerene (C60) nano-particles: An atomistic investigation

Science.gov (United States)

Kumar, Sunil; Pattanayek, Sudip K.

2018-06-01

Semi flexible polymer chain has been modeled by choosing various values of persistent length (stiffness). As the polymer chain stiffness increases, the shape of polymer chain changes from globule to extended cigar to toroid like structure during cooling from a high temperature. The aggregation of fullerene nano-particles is found to depend on the morphology of polymer chain. To maximize, the number of polymer bead-nanoparticle contacts, all nano-particle have positioned inside the polymer globule. To minimize, the energy penalty, due to bending of the polymer chain, all nano-particle have positioned on the surface of the polymer's cigar and toroid morphology.

Numerical simulation on void bubble dynamics using moving particle semi-implicit method

International Nuclear Information System (INIS)

Tian Wenxi; Ishiwatari, Yuki; Ikejiri, Satoshi; Yamakawa, Masanori; Oka, Yoshiaki

2009-01-01

In present study, the collapse of void bubble in liquid has been simulated using moving particle semi-implicit (MPS) code. The liquid is described using moving particles and the bubble-liquid interface was set to be vacuum pressure boundary without interfacial heat mass transfer. The topological shape of bubble can be traced according to the motion and location of interfacial particles. The time dependent bubble diameter, interfacial velocity and bubble collapse time were obtained under wide parametric range. The comparison with Rayleigh and Zababakhin's prediction showed a good agreement which validates the applicability and accuracy on MPS method in solving present momentum problems. The potential void induced water hammer pressure pulse was also evaluated which is instructive for further material erosion study. The bubble collapse with non-condensable gas has been further simulated and the rebound phenomenon was successfully captured which is similar with vapor-filled cavitation phenomenon. The present study exhibits some fundamental characteristics of void bubble hydrodynamics and it is also expected to be instructive for further applications of MPS method to complicated bubble dynamics problems.

Semi-empirical simulation of thermoluminescent response under different filter geometries

International Nuclear Information System (INIS)

Shammas, Gabriel Issa Jabra

2006-01-01

Many thermoluminescent materials has been developed and used for photon personal dosimetry but no one has all desired characteristics alone. These characteristics include robustness, high sensitivity, energy photon independence, large range of photon energy detection, good reproducibility, small fading and simple glow curve with peaks above 150 deg C. Calcium Sulfate Dysprosium doped (CaSO 4 :Dy) phosphor Thermoluminescent Dosimeter (TLD) has been used by many laboratories, mainly in Brazil and India. Another interesting phosphor is Calcium Fluoride (CaF 2 ). These phosphor advantages begin to be more required and its disadvantages have became more apparent, in a global market more and more competitive. These phosphors are used in environmental and area monitoring, once they present more sensibility than other phosphors, like LiF:Mg. Theirs mainly disadvantage is a strong energetic dependence response, which must be corrected for theirs application in the field, where photon radiation is unknown a priori. An interesting way do make this correction in orthogonal incidence of the radiation on the phosphor is to interject a plane leaked filter between the beam and the phosphor. In order to reduce the energetic dependence on any incidence angle, reducing the field dose measurement uncertainty too, this work presents a simulation study on spherical filter geometries. It was simulated photon irradiations with Gamma rays of 60 Co and x-rays of 33; 48 and 118 keV, on many incidence angles from zero to ninety degrees. These semi-empirical computational simulations using finite differences in three dimensions were done in spherical coordinates. The results pointed out the best filter thicknesses and widths, in order to optimize the correction on energetic dependence. (author)

Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

Science.gov (United States)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2012-10-01

Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

Multiscale Simulations of Lamellar PS–PEO Block Copolymers Doped with LiPF6 Ions

KAUST Repository

Sethuraman, Vaidyanathan; Mogurampelly, Santosh; Ganesan, Venkat

2017-01-01

We report the results of atomistic simulations of the structural equilibrium properties of PS–PEO block copolymer (BCP) melt in the ordered lamellar phase doped with LiPF6 salt. A hybrid simulation strategy, consisting of steps of coarse

Online ICPMS detection of the thermal release of fission products from nuclear fuel samples

International Nuclear Information System (INIS)

Guenther-Leopold, I.; Svedkauskaite-Le Gore, J.; Kivel, N.

2009-01-01

Full text: The release of volatile and semi-volatile fission products (like Cs, Tc, Mo etc.) from spent nuclear fuel by thermal and thermochemical treatment (oxidative or reductive conditions) as a head-end step for advanced reprocessing scenarios is studied in the Hot Laboratory of the Paul Scherrer Institut. For this purpose, a heated sampling cell online connected to an ICPMS (Element 2, Thermo Fisher Scientific) was designed and tested on simulated fuel samples up to 650 o C. The results of this study as well as technical perspectives for heating experiments up to 2000 o C will be presented. (author)

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

International Nuclear Information System (INIS)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian; Sugii, Taisuke

2015-01-01

We investigate the volumetric glass transition temperature T g in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T g increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T g in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T g is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment

EBR-II blanket fuel leaching test using simulated J-13 well water.

Energy Technology Data Exchange (ETDEWEB)

Fonnesbeck, J. E.

1998-05-15

A pulsed-flow leaching test is being conducted using three EBR-II blanket fuel segments. These samples are immersed in simulated J-13 well water. The samples are kept at a constant temperature of 90 C. Leachate is exchanged weekly and analyzed for various nuclides which are of interest from a mobility and longevity point of view. Our primary interest is in the longer-lived species such as {sup 99}Tc, {sup 237}Np, and {sup 241}Am. In addition, the behavior of U, Pu, {sup 90}Sr, and {sup 137}Cs are being analyzed. During the course of this experiment, an interesting observation has been made involving one of the samples which could indicate the possible rapid ''anoxic'' oxidation of uranium metal to UO{sub 2}.

Investigation of voltages and electric fields in silicon semi 3D radiation detectors using Silvaco/ATLAS simulation tool and a scanning electron microscope

CERN Document Server

Palviainen, T; Tuuva, T; Eranen, S; Härkönen, J; Luukka, P; Tuovinen, E

2006-01-01

The structure of silicon semi three-dimensional radiation detector is simulated on purpose to find out its electrical characteristics such as the depletion voltage and electric field. Two-dimensional simulation results are compared to voltage and electric field measurements done by a scanning electron microscope.

Compression deformation of WC: atomistic description of hard ceramic material

Science.gov (United States)

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.

Microscopic theory for coupled atomistic magnetization and lattice dynamics

Science.gov (United States)

Fransson, J.; Thonig, D.; Bessarab, P. F.; Bhattacharjee, S.; Hellsvik, J.; Nordström, L.

2017-12-01

A coupled atomistic spin and lattice dynamics approach is developed which merges the dynamics of these two degrees of freedom into a single set of coupled equations of motion. The underlying microscopic model comprises local exchange interactions between the electron spin and magnetic moment and the local couplings between the electronic charge and lattice displacements. An effective action for the spin and lattice variables is constructed in which the interactions among the spin and lattice components are determined by the underlying electronic structure. In this way, expressions are obtained for the electronically mediated couplings between the spin and lattice degrees of freedom, besides the well known interatomic force constants and spin-spin interactions. These former susceptibilities provide an atomistic ab initio description for the coupled spin and lattice dynamics. It is important to notice that this theory is strictly bilinear in the spin and lattice variables and provides a minimal model for the coupled dynamics of these subsystems and that the two subsystems are treated on the same footing. Questions concerning time-reversal and inversion symmetry are rigorously addressed and it is shown how these aspects are absorbed in the tensor structure of the interaction fields. By means of these results regarding the spin-lattice coupling, simple explanations of ionic dimerization in double-antiferromagnetic materials, as well as charge density waves induced by a nonuniform spin structure, are given. In the final parts, coupled equations of motion for the combined spin and lattice dynamics are constructed, which subsequently can be reduced to a form which is analogous to the Landau-Lifshitz-Gilbert equations for spin dynamics and a damped driven mechanical oscillator for the ionic motion. It is important to notice, however, that these equations comprise contributions that couple these descriptions into one unified formulation. Finally, Kubo-like expressions for

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

Science.gov (United States)

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

2013-08-07

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

Digital Rock Simulation of Flow in Carbonate Samples

Science.gov (United States)

Klemin, D.; Andersen, M.

2014-12-01

Reservoir engineering has becomes more complex to deal with current challenges, so core analysts must understand and model pore geometries and fluid behaviors at pores scales more rapidly and realistically. We introduce an industry-unique direct hydrodynamic pore flow simulator that operates on pore geometries from digital rock models obtained using microCT or 3D scanning electron microscope (SEM) images. The PVT and rheological models used in the simulator represent real reservoir fluids. Fluid-solid interactions are introduced using distributed micro-scale wetting properties. The simulator uses density functional approach applied for hydrodynamics of complex systems. This talk covers selected applications of the simulator. We performed microCT scanning of six different carbonate rock samples from homogeneous limestones to vuggy carbonates. From these, we constructed digital rock models representing pore geometries for the simulator. We simulated nonreactive tracer flow in all six digital models using a digital fluid description that included a passive tracer solution. During the simulation, we evaluated the composition of the effluent. Results of tracer flow simulations corresponded well with experimental data of nonreactive tracer floods for the same carbonate rock types. This simulation data of the non-reactive tracer flow can be used to calculate the volume of the rock accessible by the fluid, which can be further used to predict response of a porous medium to a reactive fluid. The described digital core analysis workflow provides a basis for a wide variety of activities, including input to design acidizing jobs and evaluating treatment efficiency and EOR economics. Digital rock multiphase flow simulations of a scanned carbonate rock evaluated the effect of wettability on flow properties. Various wetting properties were tested: slightly oil wet, slightly water wet, and water wet. Steady-state relative permeability simulations yielded curves for all three

Atomistic study of drag, surface and inertial effects on edge dislocations in face-centered cubic metals

International Nuclear Information System (INIS)

Bitzek, Erik; Gumbsch, Peter

2004-01-01

Atomistic simulations of an accelerating edge dislocation were carried out to study the effects of drag and inertia. Using an embedded atom potential for nickel, the Peierls stress, the effective mass and the drag coefficient of an edge dislocation were determined for different temperatures and stresses in a simple slab geometry. The effect of {1 1 1} surfaces on an intersecting edge dislocation were studied by appropriately cutting the slab. A dislocation intersecting a surface step was used as a model system to demonstrate the importance of inertial effects for dynamically overcoming short range obstacles. Significant effects were found even at room temperature. A simple model based on the dislocation-obstacle interaction energies was used to describe the findings

Anharmonic phonon-phonon scattering modeling of three-dimensional atomistic transport: An efficient quantum treatment

Science.gov (United States)

Lee, Y.; Bescond, M.; Logoteta, D.; Cavassilas, N.; Lannoo, M.; Luisier, M.

2018-05-01

We propose an efficient method to quantum mechanically treat anharmonic interactions in the atomistic nonequilibrium Green's function simulation of phonon transport. We demonstrate that the so-called lowest-order approximation, implemented through a rescaling technique and analytically continued by means of the Padé approximants, can be used to accurately model third-order anharmonic effects. Although the paper focuses on a specific self-energy, the method is applicable to a very wide class of physical interactions. We apply this approach to the simulation of anharmonic phonon transport in realistic Si and Ge nanowires with uniform or discontinuous cross sections. The effect of increasing the temperature above 300 K is also investigated. In all the considered cases, we are able to obtain a good agreement with the routinely adopted self-consistent Born approximation, at a remarkably lower computational cost. In the more complicated case of high temperatures (≫300 K), we find that the first-order Richardson extrapolation applied to the sequence of the Padé approximants N -1 /N results in a significant acceleration of the convergence.

Voltage equilibration for reactive atomistic simulations of electrochemical processes

International Nuclear Information System (INIS)

Onofrio, Nicolas; Strachan, Alejandro

2015-01-01

We introduce electrochemical dynamics with implicit degrees of freedom (EChemDID), a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and their effect on the self-consistent partial atomic charges used in reactive molecular dynamics. An additional variable assigned to each atom denotes the local potential in its vicinity and we use fictitious, but computationally convenient, dynamics to describe its equilibration within connected metallic structures on-the-fly during the molecular dynamics simulation. This local electrostatic potential is used to dynamically modify the atomic electronegativities used to compute partial atomic changes via charge equilibration. Validation tests show that the method provides an accurate description of the electric fields generated by the applied voltage and the driving force for electrochemical reactions. We demonstrate EChemDID via simulations of the operation of electrochemical metallization cells. The simulations predict the switching of the device between a high-resistance to a low-resistance state as a conductive metallic bridge is formed and resistive currents that can be compared with experimental measurements. In addition to applications in nanoelectronics, EChemDID could be useful to model electrochemical energy conversion devices

A compact skeletal mechanism for n -dodecane with optimized semi-global low-temperature chemistry for diesel engine simulations

Energy Technology Data Exchange (ETDEWEB)

Yao, Tong; Pei, Yuanjiang; Zhong, Bei-Jing; Som, Sibendu; Lu, Tianfeng; Luo, Kai Hong

2017-03-01

A skeletal mechanism with 54 species and 269 reactions was developed to predict pyrolysis and oxidation of n-dodecane as a diesel fuel surrogate involving both high-temperature (high-T) and low-temperature (low-T) conditions. The skeletal mechanism was developed from a semi-detailed mechanism developed at the University of Southern California (USC). Species and reactions for high-T pyrolysis and oxidation of C5-C12 were reduced by using reaction flow analysis (RFA), isomer lumping, and then merged into a skeletal C0-C4 core to form a high-T sub-mechanism. Species and lumped semi-global reactions for low-T chemistry were then added to the high-T sub-mechanism and a 54-species skeletal mechanism is obtained. The rate parameters of the low-T reactions were tuned against a detailed mechanism by the Lawrence Livermore National Laboratory (LLNL), as well as the Spray A flame experimental data, to improve the prediction of ignition delay at low-T conditions, while the high-T chemistry remained unchanged. The skeletal mechanism was validated for auto-ignition, perfectly stirred reactors (PSR), flow reactors and laminar premixed flames over a wide range of flame conditions. The skeletal mechanism was then employed to simulate three-dimensional turbulent spray flames at compression ignition engine conditions and validated against experimental data from the Engine Combustion Network (ECN).

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

International Nuclear Information System (INIS)

Akhmatskaya, Elena; Reich, Sebastian

2011-01-01

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

Campylobacter in Broiler Chicken and Broiler Meat in Sri Lanka: Influence of Semi-Automated vs. Wet Market Processing on Campylobacter Contamination of Broiler Neck Skin Samples

Directory of Open Access Journals (Sweden)

Kottawattage S. A. Kottawatta

2017-11-01

Full Text Available Broiler meat can become contaminated with Campylobacter of intestinal origin during processing. The present study aimed to identify the prevalence of Campylobacter in broiler flocks and meat contamination at retail shops, and determine the influence of semi-automated and wet market processing on Campylobacter contamination of neck skin samples. Samples were collected from semi-automated plants (n = 102 and wet markets (n = 25. From each batch of broilers, pooled caecal samples and neck skin samples were tested for Campylobacter. Broiler meat purchased from retail outlets (n = 37 was also tested. The prevalence of Campylobacter colonized broiler flocks was 67%. The contamination of meat at retail was 59%. Both semi-automated and wet market processing resulted to contaminate the broiler neck skins to the levels of 27.4% and 48%, respectively. When Campylobacter-free broiler flocks were processed in semi-automated facilities 15% (5/33 of neck skin samples became contaminated by the end of processing whereas 25% (2/8 became contaminated after wet market processing. Characterization of isolates revealed a higher proportion of C. coli compared to C. jejuni. Higher proportions of isolates were resistant to important antimicrobials. This study shows the importance of Campylobacter in poultry industry in Sri Lanka and the need for controlling antimicrobial resistance.

Campylobacter in Broiler Chicken and Broiler Meat in Sri Lanka: Influence of Semi-Automated vs. Wet Market Processing on Campylobacter Contamination of Broiler Neck Skin Samples.

Science.gov (United States)

Kottawatta, Kottawattage S A; Van Bergen, Marcel A P; Abeynayake, Preeni; Wagenaar, Jaap A; Veldman, Kees T; Kalupahana, Ruwani S

2017-11-29

Broiler meat can become contaminated with Campylobacter of intestinal origin during processing. The present study aimed to identify the prevalence of Campylobacter in broiler flocks and meat contamination at retail shops, and determine the influence of semi-automated and wet market processing on Campylobacter contamination of neck skin samples. Samples were collected from semi-automated plants ( n = 102) and wet markets ( n = 25). From each batch of broilers, pooled caecal samples and neck skin samples were tested for Campylobacter . Broiler meat purchased from retail outlets ( n = 37) was also tested. The prevalence of Campylobacter colonized broiler flocks was 67%. The contamination of meat at retail was 59%. Both semi-automated and wet market processing resulted to contaminate the broiler neck skins to the levels of 27.4% and 48%, respectively. When Campylobacter -free broiler flocks were processed in semi-automated facilities 15% (5/33) of neck skin samples became contaminated by the end of processing whereas 25% (2/8) became contaminated after wet market processing. Characterization of isolates revealed a higher proportion of C. coli compared to C. jejuni . Higher proportions of isolates were resistant to important antimicrobials. This study shows the importance of Campylobacter in poultry industry in Sri Lanka and the need for controlling antimicrobial resistance.

A simulative comparison of respondent driven sampling with incentivized snowball sampling – the “strudel effect”

Science.gov (United States)

Gyarmathy, V. Anna; Johnston, Lisa G.; Caplinskiene, Irma; Caplinskas, Saulius; Latkin, Carl A.

2014-01-01

Background Respondent driven sampling (RDS) and Incentivized Snowball Sampling (ISS) are two sampling methods that are commonly used to reach people who inject drugs (PWID). Methods We generated a set of simulated RDS samples on an actual sociometric ISS sample of PWID in Vilnius, Lithuania (“original sample”) to assess if the simulated RDS estimates were statistically significantly different from the original ISS sample prevalences for HIV (9.8%), Hepatitis A (43.6%), Hepatitis B (Anti-HBc 43.9% and HBsAg 3.4%), Hepatitis C (87.5%), syphilis (6.8%) and Chlamydia (8.8%) infections and for selected behavioral risk characteristics. Results The original sample consisted of a large component of 249 people (83% of the sample) and 13 smaller components with 1 to 12 individuals. Generally, as long as all seeds were recruited from the large component of the original sample, the simulation samples simply recreated the large component. There were no significant differences between the large component and the entire original sample for the characteristics of interest. Altogether 99.2% of 360 simulation sample point estimates were within the confidence interval of the original prevalence values for the characteristics of interest. Conclusions When population characteristics are reflected in large network components that dominate the population, RDS and ISS may produce samples that have statistically non-different prevalence values, even though some isolated network components may be under-sampled and/or statistically significantly different from the main groups. This so-called “strudel effect” is discussed in the paper. PMID:24360650

Atomistic Galois insertions for flow sensitive integrity

DEFF Research Database (Denmark)

Nielson, Flemming; Nielson, Hanne Riis

2017-01-01

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

A fast mollified impulse method for biomolecular atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)

2017-03-15

Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

Temperature Dependence of the OH- + CH3I Reaction Kinetics. Experimental and Simulation Studies and Atomic-Level Dynamics (Postprint)

Science.gov (United States)

2013-11-25

reaction time, the core of the flow was sampled through a small orifice in a rounded nose cone, while the bulk of the gas was pumped by an oil free...with direct dynamics simulations,6’ 10’ 11’ 13- 17 have provided an atomistic understanding of the dynamics of gas phase x- + CH3Y reactions. In...OH- was mass selected using a quadrupole mass filter, injected into the flow tube through a Venturi inlet, and carried downstream by a helium

Localisation accuracy of semi-dense monocular SLAM

Science.gov (United States)

Schreve, Kristiaan; du Plessies, Pieter G.; Rätsch, Matthias

2017-06-01

Understanding the factors that influence the accuracy of visual SLAM algorithms is very important for the future development of these algorithms. So far very few studies have done this. In this paper, a simulation model is presented and used to investigate the effect of the number of scene points tracked, the effect of the baseline length in triangulation and the influence of image point location uncertainty. It is shown that the latter is very critical, while the other all play important roles. Experiments with a well known semi-dense visual SLAM approach are also presented, when used in a monocular visual odometry mode. The experiments shows that not including sensor bias and scale factor uncertainty is very detrimental to the accuracy of the simulation results.

Polarization-dependent photoluminescence studies of semipolar and nonpolar InGaN quantum wells

Energy Technology Data Exchange (ETDEWEB)

Schade, Lukas; Schwarz, Ulrich [IAF, Freiburg (Germany); Wernicke, Tim; Weyers, Markus [FBH, Berlin (Germany); Kneissl, Michael [FBH, Berlin (Germany); Institute of Solid State Physics, TU Berlin (Germany)

2010-07-01

Light emitted from optical devices based on semi- and nonpolar GaN quantum well (QW) structures is partially or totally polarized, as a consequence of crystal symmetry and band structure. This can be an additional advantage over polar (0001)GaN in specific applications, e.g. in LED backlighting. Fundamentally, the polarized emission stems from breaking the isotropic symmetry of the hexagonal c-plane, resulting in two discrete semi- and nonpolar directions (parallel and normal to the projection of (0001)). We use the k.p method to simulate the crystal-direction dependent emission. The resulting transition matrix elements assign a specific (partial) polarization for each subband. The thermal occupation of the subbands results in a temperature dependent effective polarization of the light emission. We study MOVPE grown homoepitactical polar, semi- and nonpolar samples, measuring the polarization properties of the resonantly excited photoluminescence from the QW. With the complete polarization of the subbands for nonpolar devices it is possible to measure the energetic difference of the first two valence band levels. In contrast to our calculations we find a higher degree of polarization also in semipolar directions. A possible explanation could be a higher energetic subband difference than computed.

Predicting the long-term durability of hemp–lime renders in inland and coastal areas using Mediterranean, Tropical and Semi-arid climatic simulations

International Nuclear Information System (INIS)

Arizzi, Anna; Viles, Heather; Martín-Sanchez, Inés; Cultrone, Giuseppe

2016-01-01

Hemp-based composites are eco-friendly building materials as they improve energy efficiency in buildings and entail low waste production and pollutant emissions during their manufacturing process. Nevertheless, the organic nature of hemp enhances the bio-receptivity of the material, with likely negative consequences for its long-term performance in the building. The main purpose of this study was to study the response at macro- and micro-scale of hemp–lime renders subjected to weathering simulations in an environmental cabinet (one year was condensed in twelve days), so as to predict their long-term durability in coastal and inland areas with Mediterranean, Tropical and Semi-arid climates, also in relation with the lime type used. The simulated climatic conditions caused almost unnoticeable mass, volume and colour changes in hemp–lime renders. No efflorescence or physical breakdown was detected in samples subjected to NaCl, because the salt mainly precipitates on the surface of samples and is washed away by the rain. Although there was no visible microbial colonisation, alkaliphilic fungi (mainly Penicillium and Aspergillus) and bacteria (mainly Bacillus and Micrococcus) were isolated in all samples. Microbial growth and diversification were higher under Tropical climate, due to heavier rainfall. The influence of the bacterial activity on the hardening of samples has also been discussed here and related with the formation and stabilisation of vaterite in hemp–lime mixes. This study has demonstrated that hemp–lime renders show good durability towards a wide range of environmental conditions and factors. However, it might be useful to take some specific preventive and maintenance measures to reduce the bio-receptivity of this material, thus ensuring a longer durability on site. - Highlights: • Realistic simulations in the cabinet of one-year exposure to environmental conditions • Influence of the lime type on the durability of hemp–lime renders �

Predicting the long-term durability of hemp–lime renders in inland and coastal areas using Mediterranean, Tropical and Semi-arid climatic simulations

Energy Technology Data Exchange (ETDEWEB)

Arizzi, Anna, E-mail: anna.arizzi@ouce.ox.ac.uk [School of Geography and the Environment, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY (United Kingdom); Viles, Heather [School of Geography and the Environment, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY (United Kingdom); Martín-Sanchez, Inés [Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva s/n, 18002 Granada (Spain); Cultrone, Giuseppe [Departamento de Mineralogía y Petrología, Universidad de Granada, Avda. Fuentenueva s/n, 18002 Granada (Spain)

2016-01-15

Hemp-based composites are eco-friendly building materials as they improve energy efficiency in buildings and entail low waste production and pollutant emissions during their manufacturing process. Nevertheless, the organic nature of hemp enhances the bio-receptivity of the material, with likely negative consequences for its long-term performance in the building. The main purpose of this study was to study the response at macro- and micro-scale of hemp–lime renders subjected to weathering simulations in an environmental cabinet (one year was condensed in twelve days), so as to predict their long-term durability in coastal and inland areas with Mediterranean, Tropical and Semi-arid climates, also in relation with the lime type used. The simulated climatic conditions caused almost unnoticeable mass, volume and colour changes in hemp–lime renders. No efflorescence or physical breakdown was detected in samples subjected to NaCl, because the salt mainly precipitates on the surface of samples and is washed away by the rain. Although there was no visible microbial colonisation, alkaliphilic fungi (mainly Penicillium and Aspergillus) and bacteria (mainly Bacillus and Micrococcus) were isolated in all samples. Microbial growth and diversification were higher under Tropical climate, due to heavier rainfall. The influence of the bacterial activity on the hardening of samples has also been discussed here and related with the formation and stabilisation of vaterite in hemp–lime mixes. This study has demonstrated that hemp–lime renders show good durability towards a wide range of environmental conditions and factors. However, it might be useful to take some specific preventive and maintenance measures to reduce the bio-receptivity of this material, thus ensuring a longer durability on site. - Highlights: • Realistic simulations in the cabinet of one-year exposure to environmental conditions • Influence of the lime type on the durability of hemp–lime renders �

Semi-annual sampling of Fourmile Branch and its seeplines in the F and H Areas of SRS: July 1992

International Nuclear Information System (INIS)

Dixon, K.L.; Rogers, V.A.

1994-04-01

In July 1992, water samples were collected from Fourmile Branch (FMB) and its seeplines in the vicinity of the F and H-Area seepage basins. The samples were collected from five seepline locations in F Area, five seepline locations in H Area, and three stream locations on FMB. The sampling event was the first in a series of three semi-annual sampling event was the first in a series of three semi-annual sampling events aimed at characterizing the shallow groundwater outcropping into FMB and its wetlands. In the past, this groundwater has been shown to contain contaminants migrating from the F- and H-Area seepage basins. The samples were analyzed for Appendix 9 metals, various radionuclides, selected volatile compounds, and selected inorganic constituents and parameters. Results from the July 1992 sampling event suggest that the seeplines in both F and H Areas and FMB continue to be influenced by contaminants migrating from the F- and H-Area seepage basins. However, when compared to 1989 measurements, the concentrations of most of the constituents have declined. Contaminant concentration measured in July 1992 were compared to primary drinking water standards (PDWS), secondary drinking water standards (SDWS), and maximum contaminant levels (MCL) enforceable in 1993. Results were also compared to 1989 measurements at corresponding sampling locations and to background samples collected as part of the July 1992 sampling event. Using two different statistical tests, concentrations of selected F- and H-Area seepline analytes were compared to background samples. These tests were designed to detect if concentrations of contaminants along the F- and H-Area seeplines were greater than background concentrations

Assessing the fracture strength of geological and related materials via an atomistically based J-integral

Science.gov (United States)

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

Atomistic modeling of dropwise condensation

Energy Technology Data Exchange (ETDEWEB)

Sikarwar, B. S., E-mail: bssikarwar@amity.edu; Singh, P. L. [Department of Mechanical Engineering, Amity University Uttar Pradesh, Noida (India); Muralidhar, K.; Khandekar, S. [Department of Mechanical Engineering, IIT Kanpur (India)

2016-05-23

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

Massive quiescent galaxies at z > 3 in the Millennium simulation populated by a semi-analytic galaxy formation model

Science.gov (United States)

Rong, Yu; Jing, Yingjie; Gao, Liang; Guo, Qi; Wang, Jie; Sun, Shuangpeng; Wang, Lin; Pan, Jun

2017-10-01

We take advantage of the statistical power of the large-volume dark-matter-only Millennium simulation (MS), combined with a sophisticated semi-analytic galaxy formation model, to explore whether the recently reported z = 3.7 quiescent galaxy ZF-COSMOS-20115 (ZF) can be accommodated in current galaxy formation models. In our model, a population of quiescent galaxies with stellar masses and star formation rates comparable to those of ZF naturally emerges at redshifts z 3.5 massive QGs are rare (about 2 per cent of the galaxies with the similar stellar masses), the existing AGN feedback model implemented in the semi-analytic galaxy formation model can successfully explain the formation of the high-redshift QGs as it does on their lower redshift counterparts.

Probing the limits of metal plasticity with molecular dynamics simulations

Science.gov (United States)

Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.

2017-10-01

Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong

Modelling phase separation in Fe-Cr system using different atomistic kinetic Monte Carlo techniques

International Nuclear Information System (INIS)

Castin, N.; Bonny, G.; Terentyev, D.; Lavrentiev, M.Yu.; Nguyen-Manh, D.

2011-01-01

Atomistic kinetic Monte Carlo (AKMC) simulations were performed to study α-α' phase separation in Fe-Cr alloys. Two different energy models and two approaches to estimate the local vacancy migration barriers were used. The energy models considered are a two-band model Fe-Cr potential and a cluster expansion, both fitted to ab initio data. The classical Kang-Weinberg decomposition, based on the total energy change of the system, and an Artificial Neural Network (ANN), employed as a regression tool were used to predict the local vacancy migration barriers 'on the fly'. The results are compared with experimental thermal annealing data and differences between the applied AKMC approaches are discussed. The ability of the ANN regression method to accurately predict migration barriers not present in the training list is also addressed by performing cross-check calculations using the nudged elastic band method.

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

Energy Technology Data Exchange (ETDEWEB)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)

2015-12-28

We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

Stormwater Tank Performance: Design and Management Criteria for Capture Tanks Using a Continuous Simulation and a Semi-Probabilistic Analytical Approach

Directory of Open Access Journals (Sweden)

Flavio De Martino

2013-10-01

Full Text Available Stormwater tank performance significantly depends on management practices. This paper proposes a procedure to assess tank efficiency in terms of volume and pollutant concentration using four different capture tank management protocols. The comparison of the efficiency results reveals that, as expected, a combined bypass—stormwater tank system achieves better results than a tank alone. The management practices tested for the tank-only systems provide notably different efficiency results. The practice of immediately emptying after the end of the event exhibits significant levels of efficiency and operational advantages. All other configurations exhibit either significant operational problems or very low performances. The continuous simulation and semi-probabilistic approach for the best tank management practice are compared. The semi-probabilistic approach is based on a Weibull probabilistic model of the main characteristics of the rainfall process. Following this approach, efficiency indexes were established. The comparison with continuous simulations shows the reliability of the probabilistic approach even if this last is certainly very site sensitive.

A Long-Range Electric Field Solver for Molecular Dynamics Based on Atomistic-to-Continuum Modeling.

Science.gov (United States)

Templeton, Jeremy A; Jones, Reese E; Lee, Jonathan W; Zimmerman, Jonathan A; Wong, Bryan M

2011-06-14

Understanding charge transport processes at a molecular level is currently hindered by a lack of appropriate models for incorporating nonperiodic, anisotropic electric fields in molecular dynamics (MD) simulations. In this work, we develop a model for including electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and the algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. Our model represents the electric potential on a FE mesh satisfying a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagate to each atom through modified forces. The method is verified using simulations where analytical solutions are known or comparisons can be made to existing techniques. In addition, a calculation of a salt water solution in a silicon nanochannel is performed to demonstrate the method in a target scientific application in which ions are attracted to charged surfaces in the presence of electric fields and interfering media.

Atomistic Insight on the Charging Energetics in Sub-nanometer Pore Supercacitors

Energy Technology Data Exchange (ETDEWEB)

Qiao, Rui [ORNL; Huang, Jingsong [ORNL; Sumpter, Bobby G [ORNL; Meunier, Vincent [ORNL; Feng, Guang [Clemson University

2010-01-01

Electrodes featuring sub-nanometer pores can significantly enhance the capacitance and energy density of supercapacitors. However, ions must pay an energy penalty to enter sub-nanometer pores as they have to shed part of their solvation shell. The magnitude of such energy penalty plays a key role in determining the accessibility and charging/discharging of these sub-nanometer pores. Here we report on the atomistic simulation of Na+ and Cl ions entering a polarizable slit pore with a width of 0.82 nm. We show that the free energy penalty for these ions to enter the pore is less than 14 kJ/mol for both Na+ and Cl ions. The surprisingly small energy penalty is caused by the van der Waals attractions between ion and pore walls, the image charge effects, the moderate (19-26%) de-hydration of the ions inside the pore, and the strengthened interactions between ions and their hydration water molecules in the sub-nanometer pore. The results provide strong impetus for further developing nanoporous electrodes featuring sub- nanometer pores.

Communication: Predicting virial coefficients and alchemical transformations by extrapolating Mayer-sampling Monte Carlo simulations

Science.gov (United States)

Hatch, Harold W.; Jiao, Sally; Mahynski, Nathan A.; Blanco, Marco A.; Shen, Vincent K.

2017-12-01

Virial coefficients are predicted over a large range of both temperatures and model parameter values (i.e., alchemical transformation) from an individual Mayer-sampling Monte Carlo simulation by statistical mechanical extrapolation with minimal increase in computational cost. With this extrapolation method, a Mayer-sampling Monte Carlo simulation of the SPC/E (extended simple point charge) water model quantitatively predicted the second virial coefficient as a continuous function spanning over four orders of magnitude in value and over three orders of magnitude in temperature with less than a 2% deviation. In addition, the same simulation predicted the second virial coefficient if the site charges were scaled by a constant factor, from an increase of 40% down to zero charge. This method is also shown to perform well for the third virial coefficient and the exponential parameter for a Lennard-Jones fluid.

Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

Science.gov (United States)

Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

2016-03-01

Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

Computer simulation of RBS spectra from samples with surface roughness

Energy Technology Data Exchange (ETDEWEB)

Malinský, P., E-mail: malinsky@ujf.cas.cz [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, v. v. i., 250 68 Rez (Czech Republic); Department of Physics, Faculty of Science, J. E. Purkinje University, Ceske mladeze 8, 400 96 Usti nad Labem (Czech Republic); Hnatowicz, V., E-mail: hnatowicz@ujf.cas.cz [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, v. v. i., 250 68 Rez (Czech Republic); Macková, A., E-mail: mackova@ujf.cas.cz [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, v. v. i., 250 68 Rez (Czech Republic); Department of Physics, Faculty of Science, J. E. Purkinje University, Ceske mladeze 8, 400 96 Usti nad Labem (Czech Republic)

2016-03-15

A fast code for the simulation of common RBS spectra including surface roughness effects has been written and tested on virtual samples comprising either a rough layer deposited on a smooth substrate or smooth layer deposited on a rough substrate and simulated at different geometries. The sample surface or interface relief has been described by a polyline and the simulated RBS spectrum has been obtained as the sum of many particular spectra from randomly chosen particle trajectories. The code includes several procedures generating virtual samples with random and regular (periodical) roughness. The shape of the RBS spectra has been found to change strongly with increasing sample roughness and an increasing angle of the incoming ion beam.

Optimizing area under the ROC curve using semi-supervised learning.

Science.gov (United States)

Wang, Shijun; Li, Diana; Petrick, Nicholas; Sahiner, Berkman; Linguraru, Marius George; Summers, Ronald M

2015-01-01

Receiver operating characteristic (ROC) analysis is a standard methodology to evaluate the performance of a binary classification system. The area under the ROC curve (AUC) is a performance metric that summarizes how well a classifier separates two classes. Traditional AUC optimization techniques are supervised learning methods that utilize only labeled data (i.e., the true class is known for all data) to train the classifiers. In this work, inspired by semi-supervised and transductive learning, we propose two new AUC optimization algorithms hereby referred to as semi-supervised learning receiver operating characteristic (SSLROC) algorithms, which utilize unlabeled test samples in classifier training to maximize AUC. Unlabeled samples are incorporated into the AUC optimization process, and their ranking relationships to labeled positive and negative training samples are considered as optimization constraints. The introduced test samples will cause the learned decision boundary in a multidimensional feature space to adapt not only to the distribution of labeled training data, but also to the distribution of unlabeled test data. We formulate the semi-supervised AUC optimization problem as a semi-definite programming problem based on the margin maximization theory. The proposed methods SSLROC1 (1-norm) and SSLROC2 (2-norm) were evaluated using 34 (determined by power analysis) randomly selected datasets from the University of California, Irvine machine learning repository. Wilcoxon signed rank tests showed that the proposed methods achieved significant improvement compared with state-of-the-art methods. The proposed methods were also applied to a CT colonography dataset for colonic polyp classification and showed promising results.

Semi-empirical Determination of Detection Efficiency for Voluminous Source by Effective Solid Angle Method

Energy Technology Data Exchange (ETDEWEB)

Kang, M. Y.; Kim, J. H.; Choi, H. D. [Seoul National Univ., Seoul (Korea, Republic of); Sun, G. M. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2014-05-15

In the field of γ-ray measurements, the determination of full energy (FE) absorption peak efficiency for a voluminous sample is difficult, because the preparation of the certified radiation source with the same chemical composition and geometry for the original voluminous sample is not easy. In order to solve this inconvenience, simulation or semi-empirical methods are preferred in many cases. Effective Solid Angle (ESA) Code which includes semi-empirical approach has been developed by the Applied Nuclear Physics Group in Seoul National University. In this study, we validated ESA code by using Marinelli type voluminous KRISS (Korea Research Institute of Standards and Science) CRM (Certified Reference Materials) sources and IAEA standard γ-ray point sources. And semi-empirically determined efficiency curve for voluminous source by using the ESA code is compared with the experimental value. We calculated the efficiency curve of voluminous source from the measured efficiency of standard point source by using the ESA code. We will carry out the ESA code validation by measurement of various CRM volume sources with detector of different efficiency.

Semi-metallic polymers

DEFF Research Database (Denmark)

Bubnova, Olga; Khan, Zia Ullah; Wang, Hui

2014-01-01

Polymers are lightweight, flexible, solution-processable materials that are promising for low-cost printed electronics as well as for mass-produced and large-area applications. Previous studies demonstrated that they can possess insulating, semiconducting or metallic properties; here we report...... that polymers can also be semi-metallic. Semi-metals, exemplified by bismuth, graphite and telluride alloys, have no energy bandgap and a very low density of states at the Fermi level. Furthermore, they typically have a higher Seebeck coefficient and lower thermal conductivities compared with metals, thus being...... a Fermi glass to a semi-metal. The high Seebeck value, the metallic conductivity at room temperature and the absence of unpaired electron spins makes polymer semi-metals attractive for thermoelectrics and spintronics....

Advanced Techniques for Reservoir Simulation and Modeling of Non-Conventional Wells

Energy Technology Data Exchange (ETDEWEB)

Durlofsky, Louis J.

2000-08-28

This project targets the development of (1) advanced reservoir simulation techniques for modeling non-conventional wells; (2) improved techniques for computing well productivity (for use in reservoir engineering calculations) and well index (for use in simulation models), including the effects of wellbore flow; and (3) accurate approaches to account for heterogeneity in the near-well region.

Adaptive resolution simulation of salt solutions

International Nuclear Information System (INIS)

Bevc, Staš; Praprotnik, Matej; Junghans, Christoph; Kremer, Kurt

2013-01-01

We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point charge (SPC/E) and simple point charge (SPC) water models in combination with AMBER and GROMOS force fields for ion interactions in the atomistic domain. Electrostatics in our model are described by the generalized reaction field method. The effective interactions for water–water and water–ion interactions in the coarse-grained model are derived using structure-based coarse-graining approach while the Coulomb interactions between ions are appropriately screened. To ensure an even distribution of water molecules and ions across the simulation box we employ thermodynamic forces. We demonstrate that the equilibrium structural, e.g. radial distribution functions and density distributions of all the species, and dynamical properties are correctly reproduced by our adaptive resolution method. Our multiscale approach, which is general and can be used for any classical non-polarizable force-field and/or types of ions, will significantly speed up biomolecular simulation involving aqueous salt. (paper)

Quantifying the benefit of wellbore leakage potential estimates for prioritizing long-term MVA well sampling at a CO2 storage site.

Science.gov (United States)

Azzolina, Nicholas A; Small, Mitchell J; Nakles, David V; Glazewski, Kyle A; Peck, Wesley D; Gorecki, Charles D; Bromhal, Grant S; Dilmore, Robert M

2015-01-20

This work uses probabilistic methods to simulate a hypothetical geologic CO2 storage site in a depleted oil and gas field, where the large number of legacy wells would make it cost-prohibitive to sample all wells for all measurements as part of the postinjection site care. Deep well leakage potential scores were assigned to the wells using a random subsample of 100 wells from a detailed study of 826 legacy wells that penetrate the basal Cambrian formation on the U.S. side of the U.S./Canadian border. Analytical solutions and Monte Carlo simulations were used to quantify the statistical power of selecting a leaking well. Power curves were developed as a function of (1) the number of leaking wells within the Area of Review; (2) the sampling design (random or judgmental, choosing first the wells with the highest deep leakage potential scores); (3) the number of wells included in the monitoring sampling plan; and (4) the relationship between a well’s leakage potential score and its relative probability of leakage. Cases where the deep well leakage potential scores are fully or partially informative of the relative leakage probability are compared to a noninformative base case in which leakage is equiprobable across all wells in the Area of Review. The results show that accurate prior knowledge about the probability of well leakage adds measurable value to the ability to detect a leaking well during the monitoring program, and that the loss in detection ability due to imperfect knowledge of the leakage probability can be quantified. This work underscores the importance of a data-driven, risk-based monitoring program that incorporates uncertainty quantification into long-term monitoring sampling plans at geologic CO2 storage sites.

Semi-supervised sparse coding

KAUST Repository

Wang, Jim Jing-Yan; Gao, Xin

2014-01-01

Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

Semi-supervised sparse coding

KAUST Repository

Wang, Jim Jing-Yan

2014-07-06

Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

Comparing semi-analytic particle tagging and hydrodynamical simulations of the Milky Way's stellar halo

Science.gov (United States)

Cooper, Andrew P.; Cole, Shaun; Frenk, Carlos S.; Le Bret, Theo; Pontzen, Andrew

2017-08-01

Particle tagging is an efficient, but approximate, technique for using cosmological N-body simulations to model the phase-space evolution of the stellar populations predicted, for example, by a semi-analytic model of galaxy formation. We test the technique developed by Cooper et al. (which we call stings here) by comparing particle tags with stars in a smooth particle hydrodynamic (SPH) simulation. We focus on the spherically averaged density profile of stars accreted from satellite galaxies in a Milky Way (MW)-like system. The stellar profile in the SPH simulation can be recovered accurately by tagging dark matter (DM) particles in the same simulation according to a prescription based on the rank order of particle binding energy. Applying the same prescription to an N-body version of this simulation produces a density profile differing from that of the SPH simulation by ≲10 per cent on average between 1 and 200 kpc. This confirms that particle tagging can provide a faithful and robust approximation to a self-consistent hydrodynamical simulation in this regime (in contradiction to previous claims in the literature). We find only one systematic effect, likely due to the collisionless approximation, namely that massive satellites in the SPH simulation are disrupted somewhat earlier than their collisionless counterparts. In most cases, this makes remarkably little difference to the spherically averaged distribution of their stellar debris. We conclude that, for galaxy formation models that do not predict strong baryonic effects on the present-day DM distribution of MW-like galaxies or their satellites, differences in stellar halo predictions associated with the treatment of star formation and feedback are much more important than those associated with the dynamical limitations of collisionless particle tagging.

Convergence of sampling in protein simulations

NARCIS (Netherlands)

Hess, B

With molecular dynamics protein dynamics can be simulated in atomic detail. Current computers are not fast enough to probe all available conformations, but fluctuations around one conformation can be sampled to a reasonable extent. The motions with the largest fluctuations can be filtered out of a

Harnessing atomistic simulations to predict the rate at which dislocations overcome obstacles

Science.gov (United States)

Saroukhani, S.; Nguyen, L. D.; Leung, K. W. K.; Singh, C. V.; Warner, D. H.

2016-05-01

Predicting the rate at which dislocations overcome obstacles is key to understanding the microscopic features that govern the plastic flow of modern alloys. In this spirit, the current manuscript examines the rate at which an edge dislocation overcomes an obstacle in aluminum. Predictions were made using different popular variants of Harmonic Transition State Theory (HTST) and compared to those of direct Molecular Dynamics (MD) simulations. The HTST predictions were found to be grossly inaccurate due to the large entropy barrier associated with the dislocation-obstacle interaction. Considering the importance of finite temperature effects, the utility of the Finite Temperature String (FTS) method was then explored. While this approach was found capable of identifying a prominent reaction tube, it was not capable of computing the free energy profile along the tube. Lastly, the utility of the Transition Interface Sampling (TIS) approach was explored, which does not need a free energy profile and is known to be less reliant on the choice of reaction coordinate. The TIS approach was found capable of accurately predicting the rate, relative to direct MD simulations. This finding was utilized to examine the temperature and load dependence of the dislocation-obstacle interaction in a simple periodic cell configuration. An attractive rate prediction approach combining TST and simple continuum models is identified, and the strain rate sensitivity of individual dislocation obstacle interactions is predicted.

An atomistic study of the deformation behavior of tungsten nanowires

Energy Technology Data Exchange (ETDEWEB)

Xu, Shuozhi [University of California, California NanoSystems Institute, Santa Barbara, CA (United States); Su, Yanqing [University of California, Department of Mechanical Engineering, Santa Barbara, CA (United States); Chen, Dengke [Georgia Institute of Technology, GWW School of Mechanical Engineering, Atlanta, GA (United States); Li, Longlei [Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA (United States)

2017-12-15

Large-scale atomistic simulations are performed to study tensile and compressive left angle 112 right angle 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. (orig.)

Flexible manifold embedding: a framework for semi-supervised and unsupervised dimension reduction.

Science.gov (United States)

Nie, Feiping; Xu, Dong; Tsang, Ivor Wai-Hung; Zhang, Changshui

2010-07-01

We propose a unified manifold learning framework for semi-supervised and unsupervised dimension reduction by employing a simple but effective linear regression function to map the new data points. For semi-supervised dimension reduction, we aim to find the optimal prediction labels F for all the training samples X, the linear regression function h(X) and the regression residue F(0) = F - h(X) simultaneously. Our new objective function integrates two terms related to label fitness and manifold smoothness as well as a flexible penalty term defined on the residue F(0). Our Semi-Supervised learning framework, referred to as flexible manifold embedding (FME), can effectively utilize label information from labeled data as well as a manifold structure from both labeled and unlabeled data. By modeling the mismatch between h(X) and F, we show that FME relaxes the hard linear constraint F = h(X) in manifold regularization (MR), making it better cope with the data sampled from a nonlinear manifold. In addition, we propose a simplified version (referred to as FME/U) for unsupervised dimension reduction. We also show that our proposed framework provides a unified view to explain and understand many semi-supervised, supervised and unsupervised dimension reduction techniques. Comprehensive experiments on several benchmark databases demonstrate the significant improvement over existing dimension reduction algorithms.

Simulation of reactive geochemical transport in groundwater using a semi-analytical screening model

Science.gov (United States)

McNab, Walt W.

1997-10-01

A reactive geochemical transport model, based on a semi-analytical solution to the advective-dispersive transport equation in two dimensions, is developed as a screening tool for evaluating the impact of reactive contaminants on aquifer hydrogeochemistry. Because the model utilizes an analytical solution to the transport equation, it is less computationally intensive than models based on numerical transport schemes, is faster, and it is not subject to numerical dispersion effects. Although the assumptions used to construct the model preclude consideration of reactions between the aqueous and solid phases, thermodynamic mineral saturation indices are calculated to provide qualitative insight into such reactions. Test problems involving acid mine drainage and hydrocarbon biodegradation signatures illustrate the utility of the model in simulating essential hydrogeochemical phenomena.

Thermodynamic and Mechanical Properties of Epon 862 With Curing Agent Detda by Molecular Simulation

National Research Council Canada - National Science Library

Tack, Jeremy L

2006-01-01

Fully atomistic molecular dynamics (MD) simulations were used to predict the properties of EPON 862 cross-linked with curing agent DETDA, a potentially useful epoxy resin for future applications of nanocomposites...

Semi-analytical solutions for flow to a well in an unconfined-fractured aquifer system

Science.gov (United States)

Sedghi, Mohammad M.; Samani, Nozar

2015-09-01

Semi-analytical solutions of flow to a well in an unconfined single porosity aquifer underlain by a fractured double porosity aquifer, both of infinite radial extent, are obtained. The upper aquifer is pumped at a constant rate from a pumping well of infinitesimal radius. The solutions are obtained via Laplace and Hankel transforms and are then numerically inverted to time domain solutions using the de Hoog et al. algorithm and Gaussian quadrature. The results are presented in the form of dimensionless type curves. The solution takes into account the effects of pumping well partial penetration, water table with instantaneous drainage, leakage with storage in the lower aquifer into the upper aquifer, and storativity and hydraulic conductivity of both fractures and matrix blocks. Both spheres and slab-shaped matrix blocks are considered. The effects of the underlying fractured aquifer hydraulic parameters on the dimensionless drawdown produced by the pumping well in the overlying unconfined aquifer are examined. The presented solution can be used to estimate hydraulic parameters of the unconfined and the underlying fractured aquifer by type curve matching techniques or with automated optimization algorithms. Errors arising from ignoring the underlying fractured aquifer in the drawdown distribution in the unconfined aquifer are also investigated.

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

International Nuclear Information System (INIS)

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

2015-01-01

Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties

A generalized Poisson solver for first-principles device simulations

Energy Technology Data Exchange (ETDEWEB)

Bani-Hashemian, Mohammad Hossein; VandeVondele, Joost, E-mail: joost.vandevondele@mat.ethz.ch [Nanoscale Simulations, ETH Zürich, 8093 Zürich (Switzerland); Brück, Sascha; Luisier, Mathieu [Integrated Systems Laboratory, ETH Zürich, 8092 Zürich (Switzerland)

2016-01-28

Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative method in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated.

Sorption tubes packed with polydimethylsiloxane: a new and promising technique for the preconcentration of volatiles and semi-volatiles from air and gaseous samples