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Sample records for bundles atomistic simulations

  1. Atomistic simulations of nanoindentation

    Directory of Open Access Journals (Sweden)

    Izabela Szlufarska

    2006-05-01

    Full Text Available Our understanding of mechanics is pushed to its limit when the functionality of devices is controlled at the nanometer scale. A fundamental understanding of nanomechanics is needed to design materials with optimum properties. Atomistic simulations can bring an important insight into nanostructure-property relations and, when combined with experiments, they become a powerful tool to move nanomechanics from basic science to the application area. Nanoindentation is a well-established technique for studying mechanical response. We review recent advances in modeling (atomistic and beyond of nanoindentation and discuss how they have contributed to our current state of knowledge.

  2. Parallel Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    HEFFELFINGER,GRANT S.

    2000-01-18

    Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.

  3. Numerical tools for atomistic simulations.

    Energy Technology Data Exchange (ETDEWEB)

    Fang, H. (Mississippi State University); Gullett, Philip Michael; Slepoy, Alexander (Sandia National Laboratories, Albuquerque, NM); Horstemeyer, Mark F. (Mississippi State University); Baskes, Michael I. (Los Alamos National Laboratory, Los Alamos, NM); Wagner, Gregory John; Li, Mo (Materials Science and Engineering, Atlanta, GA)

    2004-01-01

    The final report for a Laboratory Directed Research and Development project entitled 'Parallel Atomistic Computing for Failure Analysis of Micromachines' is presented. In this project, atomistic algorithms for parallel computers were developed to assist in quantification of microstructure-property relations related to weapon micro-components. With these and other serial computing tools, we are performing atomistic simulations of various sizes, geometries, materials, and boundary conditions. These tools provide the capability to handle the different size-scale effects required to predict failure. Nonlocal continuum models have been proposed to address this problem; however, they are phenomenological in nature and are difficult to validate for micro-scale components. Our goal is to separately quantify damage nucleation, growth, and coalescence mechanisms to provide a basis for macro-scale continuum models that will be used for micromachine design. Because micro-component experiments are difficult, a systematic computational study that employs Monte Carlo methods, molecular statics, and molecular dynamics (EAM and MEAM) simulations to compute continuum quantities will provide mechanism-property relations associated with the following parameters: specimen size, number of grains, crystal orientation, strain rates, temperature, defect nearest neighbor distance, void/crack size, chemical state, and stress state. This study will quantify sizescale effects from nanometers to microns in terms of damage progression and thus potentially allow for optimized micro-machine designs that are more reliable and have higher fidelity in terms of strength. In order to accomplish this task, several atomistic methods needed to be developed and evaluated to cover the range of defects, strain rates, temperatures, and sizes that a material may see in micro-machines. Therefore we are providing a complete set of tools for large scale atomistic simulations that include pre

  4. Atomistic Simulations of Nanotube Fracture

    CERN Document Server

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

    2002-01-01

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

  5. Atomistic computer simulations a practical guide

    CERN Document Server

    Brazdova, Veronika

    2013-01-01

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

  6. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss......Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction...... into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and...

  7. Quantum corrections to the `atomistic' MOSFET simulation

    OpenAIRE

    Asenov, A.

    2000-01-01

    In this paper we study the influence of the quantum effects in the inversion layer on the parameter fluctuation in decanano MOSFETs. The quantum mechanical effects are incorporated in our previously published 3D 'atomistic' simulation approach using a full 3D implementation of the density gradient formalism. This results in a consistent, fully 3D, quantum mechanical picture which incorporates the vertical inversion layer quantization, lateral confinement effects associated with the current fi...

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

    International Nuclear Information System (INIS)

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

  9. Atomistic simulations of dislocation processes in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Jacobsen, K.W.

    2002-01-01

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

  10. Scalable Atomistic Simulation Algorithms for Materials Research

    Directory of Open Access Journals (Sweden)

    Aiichiro Nakano

    2002-01-01

    Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

  11. Free energy of steps using atomistic simulations

    Science.gov (United States)

    Freitas, Rodrigo; Frolov, Timofey; Asta, Mark

    The properties of solid-liquid interfaces are known to play critical roles in solidification processes. Particularly special importance is given to thermodynamic quantities that describe the equilibrium state of these surfaces. For example, on the solid-liquid-vapor heteroepitaxial growth of semiconductor nanowires the crystal nucleation process on the faceted solid-liquid interface is influenced by the solid-liquid and vapor-solid interfacial free energies, and also by the free energies of associated steps at these faceted interfaces. Crystal-growth theories and mesoscale simulation methods depend on quantitative information about these properties, which are often poorly characterized from experimental measurements. In this work we propose an extension of the capillary fluctuation method for calculation of the free energy of steps on faceted crystal surfaces. From equilibrium atomistic simulations of steps on (111) surfaces of Copper we computed accurately the step free energy for different step orientations. We show that the step free energy remains finite at all temperature up to the melting point and that the results obtained agree with the more well established method of thermodynamic integration if finite size effects are taken into account. The research of RF and MA at UC Berkeley were supported by the US National Science Foundation (Grant No. DMR-1105409). TF acknowledges support through a postdoctoral fellowship from the Miller Institute for Basic Research in Science.

  12. Atomistic simulations of caloric effects in ferroelectrics

    Science.gov (United States)

    Lisenkov, Sergey; Ponomareva, Inna

    2013-03-01

    The materials that exhibit large caloric effects have emerged as promising candidates for solid-state refrigeration which is an energy-efficient and environmentally friendly alternative to the conventional refrigeration technology. However, despite recent ground breaking discoveries of giant caloric effects in some materials they appear to remain one of nature's rarities. Here we use atomistic simulations to study electrocaloric and elastocaloric effects in Ba0.5Sr0.5TiO3 and PbTiO3 ferroelectrics. Our study reveals the intrinsic features of such caloric effects in ferroelectrics and their potential to exhibit giant caloric effects. Some of the findings include the coexistence of negative and positive electrocaloric effects in one material and an unusual field-driven transition between them as well as the coexistence of multiple giant caloric effects in Ba0.5Sr0.5TiO3 alloys. These findings could potentially lead to new paradigms for cooling devices. This work is partially supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0005245.

  13. A robust, coupled approach for atomistic-continuum simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Aubry, Sylvie; Webb, Edmund Blackburn, III (Sandia National Laboratories, Albuquerque, NM); Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John (Sandia National Laboratories, Albuquerque, NM); Kimmer, Christopher J.

    2004-09-01

    This report is a collection of documents written by the group members of the Engineering Sciences Research Foundation (ESRF), Laboratory Directed Research and Development (LDRD) project titled 'A Robust, Coupled Approach to Atomistic-Continuum Simulation'. Presented in this document is the development of a formulation for performing quasistatic, coupled, atomistic-continuum simulation that includes cross terms in the equilibrium equations that arise due to kinematic coupling and corrections used for the calculation of system potential energy to account for continuum elements that overlap regions containing atomic bonds, evaluations of thermo-mechanical continuum quantities calculated within atomistic simulations including measures of stress, temperature and heat flux, calculation used to determine the appropriate spatial and time averaging necessary to enable these atomistically-defined expressions to have the same physical meaning as their continuum counterparts, and a formulation to quantify a continuum 'temperature field', the first step towards constructing a coupled atomistic-continuum approach capable of finite temperature and dynamic analyses.

  14. An object oriented Python interface for atomistic simulations

    Science.gov (United States)

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

    2016-01-01

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

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

    OpenAIRE

    Asenov, A.; Brown, A. R.; J. H. Davies; S Saini

    1999-01-01

    We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1-μm MOSFETs. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have de...

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  17. Definition and detection of contact in atomistic simulations

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    2015-01-01

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

  18. Numerical simulations of square arrayed rod bundles

    International Nuclear Information System (INIS)

    Highlights: ► CFD simulations with square arrayed rod bundles. ► Mesh dependency and turbulence model study by comparison with experiments. ► Gibson and Launder Reynolds stress model shows good agreement with experiments. ► Effect of pitch to diameter ratio and Reynolds number is correctly captured. - Abstract: Computational fluid dynamics (CFD) simulations were performed with square arrayed rod bundles featuring pitch to diameter (P/D) ratio of 1.194 and 1.326 in order to find an optimal mesh and turbulence model for simulations with more complex geometries in the future. With the tighter lattice a mesh sensitivity and turbulence model study were accomplished and the post processed turbulence quantities, velocity field and wall shear stress were compared with experimental data ( Developed single phase turbulent flow through a square-pitch rod cluster. Nuclear Engineering and Design 60, 365–379.). The comparisons show that Reynolds-Averaged Navier–Stokes method with the Reynolds stress model of Gibson and Launder in conjunction with an appropriate mesh can provide reasonable agreement with the experiment for this lattice. For pure bundle simulations the body fitted structured meshes are suggested, since slightly better agreement can be captured considering all quantities with the same number of cells. Based on the drawn conclusions the procession was repeated for P/D = 1.326, where, due to lack of experiment, just the correct tendencies of the turbulence quantities and velocity field were established. The results show Reynolds number independency correctly and the increase of P/D issues in more similar flow to axisymmetric pipe flow.

  19. Atomistic simulations of Mg-Cu metallic glasses: Mechanical properties

    DEFF Research Database (Denmark)

    Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel

    2004-01-01

    The atomistic mechanisms of plastic deformation in amorphous metals are far from being understood. We have derived potential parameters for molecular dynamics simulations of Mg-Cu amorphous alloys using the Effective Medium Theory. We have simulated the formation of alloys by cooling from the melt......, and have used these glassy configurations to carry out simulations of plastic deformation. These involved different compositions, temperatures (including zero), and types of deformation (uniaxial strain/pure shear), and yielded stress-strain curves and values of flow stress. Separate simulations were...

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

    OpenAIRE

    Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

    2014-01-01

    Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DM...

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

    Science.gov (United States)

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394

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

    CERN Document Server

    Rapaport, D C

    2009-01-01

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

  3. Structure identification methods for atomistic simulations of crystalline materials

    OpenAIRE

    Stukowski, Alexander

    2012-01-01

    We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as Common Neighbor Analysis, Centrosymmetry Analysis, Bond Angle Analysis, Bond Order Analysis, and Voronoi Analysis. In addition we propose a simple extension to the Common Neighbor Analysis method that makes it suitable for multi-phase systems...

  4. 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.

  5. Atomistic simulations of plasma-wall interactions in fusion reactors

    International Nuclear Information System (INIS)

    Atomistic computer simulations, especially molecular dynamics, but also kinetic Monte Carlo simulations and electronic structure calculations, have proven to be a valuable tool for studying radiation effects in fusion reactor materials. In this paper, I will first review a few cases where these methods have given additional insights into the interaction between a fusion plasma and the first wall of a reactor. Then I will, in the spirit of the workshop theme of 'new directions in plasma-wall interactions' discuss some possible future avenues of research

  6. 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)

  7. Nanostructured surfaces described by atomistic simulation methods

    International Nuclear Information System (INIS)

    Three separate simulation techniques have been applied to study different problems involving nanostructured surfaces. In the first investigation the bonding of fullerene molecules on silicon and Ag adatoms and dimers on graphite are investigated using the PLATO density functional code. It is shown that in the first case there are strong covalent bonds formed whereas in the latter there are relatively weak bonds with small energy barriers between adjacent sites. Classical MD is used to show how energetic (∼ keV) Ag clusters can be pinned on or implanted into a graphite surface and that the pinning thresholds and implantation depths agree with experiment. Finally a Monte Carlo model for cluster motion over a surface is described and related to pattern formation in the early stages of thin film growth

  8. Atomistic approach for simulating plasmons in nanostructures

    Science.gov (United States)

    Sakko, Arto; Rossi, Tuomas P.; Enkovaara, Jussi; Nieminen, Risto M.

    2014-05-01

    Recent experimental and theoretical works have demonstrated that quantum mechanical effects play an important role in materials design of some novel nano-plasmonic materials. In this work, electronic structure calculations are used to study these effects for the optical properties of metal nanostructures and small flakes of graphene. Their optical response is shown to depend on their exact atomic composition, and their similarities (size-dependent resonance frequency) and differences (metallic vs. semiconducting material) are discussed. The open-source computer code GPAW is used for the simulations, which can be done for systems of thousands of valence electrons. The calculations automatically include quantum effects such as tunneling, nonlocal response, and molecular orbital hybridization.

  9. Nuclear wasteform materials: Atomistic simulation case studies

    Energy Technology Data Exchange (ETDEWEB)

    Chroneos, A., E-mail: alex.chroneos@open.ac.uk [Materials Engineering, The Open University, Milton Keynes MK7 6AA (United Kingdom); Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Institute of Materials Science, NCSR Demokritos, GR-15310 Athens (Greece); Rushton, M.J.D. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Jiang, C. [State Key Laboratory of Powder Metallurgy, Central South University, Changsha 410083 (China); Tsoukalas, L.H. [Department of Nuclear Engineering, Purdue University, West Lafayette, IN 47907 (United States)

    2013-10-15

    Ever increasing global energy demand combined with a requirement to reduce CO{sub 2} emissions has rekindled an interest in nuclear power generation. In order that nuclear energy remains publicly acceptable and therefore a sustainable source of power it is important that nuclear waste is dealt with in a responsible manner. To achieve this, improved materials for the long-term immobilisation of waste should be developed. The extreme conditions experienced by nuclear wasteforms necessitate the detailed understanding of their properties and the mechanisms acting within them at the atomic scale. This latter issue is the focus of the present review. Atomic scale simulation techniques can accelerate the development of new materials for nuclear wasteform applications and provide detailed information on their physical properties that cannot be easily accessed by experiment. The present article introduces examples of how atomic scale, computational modelling techniques have led to an improved understanding of current nuclear wasteform materials and also suggest how they may be used in the development of new wasteforms.

  10. Atomistic simulations of jog migration on extended screw dislocations

    DEFF Research Database (Denmark)

    Vegge, T.; Leffers, T.; Pedersen, O.B.; Jacobsen, K.W.

    Effective Medium Theory, The minimum energy path through configuration space and the corresponding transition state energy are obtained using the Nudged Elastic Band path technique. We find very similar migration properties for elementary jogs on the (110){110} octahedral slip systems and the (110){110} non......We have performed large-scale atomistic simulations of the migration of elementary jogs on dissociated screw dislocations in Cu. The local crystalline configurations, transition paths. effective masses. and migration barriers for the jogs are determined using an interatomic potential based on the...

  11. Atomistic Kinetic Monte Carlo Simulations of Polycrystalline Copper Electrodeposition

    CERN Document Server

    Treeratanaphitak, Tanyakarn; Abukhdeir, Nasser Mohieddin

    2014-01-01

    A high-fidelity kinetic Monte Carlo (KMC) simulation method (T. Treeratanaphitak, M. Pritzker, N. M. Abukhdeir, Electrochim. Acta 121 (2014) 407--414) using the semi-empirical multi-body embedded-atom method (EAM) potential has been extended to model polycrystalline metal electrodeposition. The presented KMC-EAM method enables true three-dimensional atomistic simulations of electrodeposition over experimentally relevant timescales. Simulations using KMC-EAM are performed over a range of overpotentials to predict the effect on deposit texture evolution. Results show strong agreement with past experimental results both with respect to deposition rates on various copper surfaces and roughness-time power law behaviour. It is found that roughness scales with time $\\propto t^\\beta$ where $\\beta=0.62 \\pm 0.12$, which is in good agreement with past experimental results. Furthermore, the simulations provide insights into sub-surface deposit morphologies which are not directly accessible from experimental measurements.

  12. Atomistic Simulation of High-Density Uranium Fuels

    Directory of Open Access Journals (Sweden)

    Jorge Eduardo Garcés

    2011-01-01

    Full Text Available We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1 the trend indicating formation of interfacial compounds, (2 much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3 Si depletion in the Al matrix, (4 an unexpected interaction between Mo and Si which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5 the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.

  13. Atomistic simulations of material damping in amorphous silicon nanoresonators

    Science.gov (United States)

    Mukherjee, Sankha; Song, Jun; Vengallatore, Srikar

    2016-06-01

    Atomistic simulations using molecular dynamics (MD) are emerging as a valuable tool for exploring dissipation and material damping in nanomechanical resonators. In this study, we used isothermal MD to simulate the dynamics of the longitudinal-mode oscillations of an amorphous silicon nanoresonator as a function of frequency (2 GHz–50 GHz) and temperature (15 K–300 K). Damping was characterized by computing the loss tangent with an estimated uncertainty of 7%. The dissipation spectrum displays a sharp peak at 50 K and a broad peak at around 160 K. Damping is a weak function of frequency at room temperature, and the loss tangent has a remarkably high value of ~0.01. In contrast, at low temperatures (15 K), the loss tangent increases monotonically from 4× {{10}-4} to 4× {{10}-3} as the frequency increases from 2 GHz to 50 GHz. The mechanisms of dissipation are discussed.

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

    Science.gov (United States)

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

    2016-09-01

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

  15. Atomistic simulation of mineral surfaces: Their structure, hydration and growth

    International Nuclear Information System (INIS)

    In this thesis, we have used atomistic simulation techniques to investigate the surface structure and stability of the biomineral barium sulfate and a number of important iron oxides, namely hematite, magnetite and goethite. We have studied the effect of the molecular adsorption of water on the surface structures and stabilities of all four minerals, and dissociative adsorption of water on the iron oxides. In addition, we have investigated the segregation of foreign ions to the surfaces of barium sulfate. Chapter 1 gives an overview of some previous studies of surfaces, employing both atomistic simulations and electronic structure calculations. Also discussed are some popular experimental analysis techniques used in surface characterisation. Chapter 2 describes the theoretical methods used in atomistic simulations and the mathematical methods used in the calculations, including the evaluation of surface energies. Chapter 3 introduces the potential model and discusses their reliability and transferability between structures. The potential parameters used in chapters 4-7 are given and where possible, compared with experiment. Chapter 4 describes the structures and stabilities of the pure surfaces of barium sulfate, and after the overgrowth of segregation of a layer of impurity ions at the surface. The modified crystal morphologies are discussed. Chapter 5 follows the work in the previous chapter by discussing the effect of the molecular adsorption of water at different coverages on the structure and stabilities of barium sulfate surfaces. The hydrated energies and surface energies are calculated. The second section of chapter 5 investigates structural influences on the growth of barium sulfate. In Chapter 6, the pure surfaces of hematite, magnetite and goethite are described. The surface relaxation are studied and equilibrium crystal morphologies compared with experimental findings. The surface structure of Fe2O3(00.1) under reducing conditions is also investigated

  16. Atomistic simulations for multiscale modeling in bcc metal

    Energy Technology Data Exchange (ETDEWEB)

    Belak, J.; Moriarty, J.A.; Soderlind, P.; Xu, W.; Yang, L.H.; Zhu

    1998-09-25

    Quantum-based atomistic simulations are being used to study fundamental deformation and defect properties relevant to the multiscale modeling of plasticity in bcc metals at both ambient and extreme conditions. Ab initio electronic-structure calculations on the elastic and ideal-strength properties of Ta and Mo help constrain and validate many-body interatomic potentials used to study grain boundaries and dislocations. The predicted C(capital Sigma)5 (310)[100] grain boundary structure for Mo has recently been confirmed in HREM measurements. The core structure, (small gamma) surfaces, Peierls stress, and kink-pair formation energies associated with the motion of a/2(111) screw dislocations in Ta and Mo have also been calculated. Dislocation mobility and dislocation junction formation and breaking are currently under investigation.

  17. Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

    Energy Technology Data Exchange (ETDEWEB)

    Ogawa, Hiroshi, E-mail: h.ogawa@aist.go.jp

    2015-10-05

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

  18. Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

    International Nuclear Information System (INIS)

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

  19. Atomistic Molecular Dynamics Simulations of Shock Compressed Quartz

    CERN Document Server

    Farrow, Matthew R

    2011-01-01

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

  20. Tracking Microstructure of Crystalline Materials: A Post-Processing Algorithm for Atomistic Simulations

    Science.gov (United States)

    Panzarino, Jason F.; Rupert, Timothy J.

    2014-03-01

    Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. To understand the fundamental principles that govern material behavior at the atomic scale and directly connect to experimental works, it is necessary to quantify the microstructure of materials simulated with atomistics. Specifically, quantitative tools for identifying crystallites, their crystallographic orientation, and overall sample texture do not currently exist. Here, we develop a post-processing algorithm capable of characterizing such features, while also documenting their evolution during a simulation. In addition, the data is presented in a way that parallels the visualization methods used in traditional experimental techniques. The utility of this algorithm is illustrated by analyzing several types of simulation cells that are commonly found in the atomistic modeling literature but could also be applied to a variety of other atomistic studies that require precise identification and tracking of microstructure.

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

    Science.gov (United States)

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

    2016-01-01

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

  2. Nanosculpt: A methodology for generating complex realistic configurations for atomistic simulations

    Science.gov (United States)

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

    2016-01-01

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

  3. Simulation of bundle test Quench-12 with integral code MELCOR

    International Nuclear Information System (INIS)

    The past NRI analyses cover the Quench-01, Quench-03 and Quench-06 with version MELCOR 1.8.5 (including reflood model), and Quench-01 and Quench-11 tests with the latest version MELCOR 1.8.6. The Quench-12 test is specific, because it has different bundle configuration related to the VVER bundle configuration with hexagonal grid of pins and also used E110 cladding material. Specificity of Quench-12 test is also in the used material of fuel rod cladding - E110. The test specificities are a reason for the highest concern, because the VVER reactors are operated in the Czech Republic. The new input model was developed with the taking into account all experience from previous simulations of the Quench bundle tests. The recent version MELCOR 1.8.6 YU2911 was used for the simulation with slightly modified ELHEAT package. Sensitivity studies on input parameters and oxidation kinetics were performed. (author)

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

    Science.gov (United States)

    Abbott, Lauren J.; Stevens, Mark J.

    2015-03-01

    The amphiphilic polymer poly(N-isopropylacrylamide) (PNIPAM) displays a sharp phase transition at its LCST around 32 °C, which results from competing interactions of the hydrophobic and hydrophilic groups with water. This thermoresponsive behavior can be exploited in more complex architectures, such as block copolymers or surfactants, to provide responsive PNIPAM head groups. In these systems, however, changes to the hydrophobic/hydrophilic balance can alter the transition behavior. In this work, we perform atomistic simulations of PNIPAM-alkyl surfactants to study the temperature dependence of their structures. A single chain of the surfactant does not show temperature-responsive behavior. Instead, below and above the LCST of PNIPAM, the surfactant folds to bring the hydrophobic alkyl tail in contact with the PNIPAM backbone, shielding it from water. In addition to single chains, we explore the self-assembly of multiple surfactants into micelles and how the temperature-dependent behavior is changed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  5. Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Wijesinghe, S; Hornung, R; Garcia, A; Hadjiconstantinou, N

    2004-04-15

    We present an adaptive mesh and algorithmic refinement (AMAR) scheme for modeling multi-scale hydrodynamics. The AMAR approach extends standard conservative adaptive mesh refinement (AMR) algorithms by providing a robust flux-based method for coupling an atomistic fluid representation to a continuum model. The atomistic model is applied locally in regions where the continuum description is invalid or inaccurate, such as near strong flow gradients and at fluid interfaces, or when the continuum grid is refined to the molecular scale. The need for such ''hybrid'' methods arises from the fact that hydrodynamics modeled by continuum representations are often under-resolved or inaccurate while solutions generated using molecular resolution globally are not feasible. In the implementation described herein, Direct Simulation Monte Carlo (DSMC) provides an atomistic description of the flow and the compressible two-fluid Euler equations serve as our continuum-scale model. The AMR methodology provides local grid refinement while the algorithm refinement feature allows the transition to DSMC where needed. The continuum and atomistic representations are coupled by matching fluxes at the continuum-atomistic interfaces and by proper averaging and interpolation of data between scales. Our AMAR application code is implemented in C++ and is built upon the SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) framework developed at Lawrence Livermore National Laboratory. SAMRAI provides the parallel adaptive gridding algorithm and enables the coupling between the continuum and atomistic methods.

  6. 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 ...

  7. Investigations on flow induced vibration of simulated CANDU fuel bundles in a pipe

    International Nuclear Information System (INIS)

    In this paper, vibration of a two-bundle string consisting of simulated CANDU fuel bundles subjected to turbulent liquid flow is investigated through numerical simulations and experiments. Large eddy simulation is used to solve the three-dimensional turbulent flow surrounding the fuel bundles for determining fluid excitations. The CFD model includes pipe flow, flow through the inlet fuel bundle along with its two endplates, half of the second bundle and its upstream endplate. The fluid excitation obtained from the fluid model is subsequently fed into a fuel bundle vibration code written in FORTRAN. Fluid structure interaction terms for the fuel elements are approximated using the slender body theory. Simulation results are compared to measurements conducted on the simulated fuel bundles in a testing hydraulic loop. (author)

  8. Numerical simulation of flow-induced vibrations in tube bundles

    International Nuclear Information System (INIS)

    Full text of publication follows: In many industrial components mechanical structures like rod cluster control assembly, fuel assembly and heat exchanger tube bundles are submitted to complex flows causing possible vibrations and damage. Fluid forces are usually split into two parts: structure motion independent forces and fluid-elastic forces coupled with tube motion and responsible for possible dynamic instability development leading to possible short term failures through high amplitude vibrations. Most classical fluid force identification methods rely on structure response experimental measurements associated with convenient data processes. Owing to recent improvements in Computational Fluid Dynamics (C.F.D.), numerical fluid force identification is now practicable in the presence of industrial configurations. The present paper is devoted to numerical simulation of flow-induced vibrations of tube bundles submitted to single-phase cross flows by using C.F.D. codes. Direct Numerical Simulation (D.N.S.), Arbitrary Lagrange Euler formulation (A.L.E.) and code coupling process are involved to predict fluid forces responsible for tube bundle vibrations in the presence of fluid structure and fluid-elastic coupling effects. In the presence of strong multi-physics coupling, simulation of flow-induced vibrations requires a fluid structure code coupling process. The methodology consists in solving in the same time thermohydraulics and mechanics problems by using an A.L.E. formulation for the fluid computation. The purpose is to take into account coupling between flow and structure motions in order to be able to capture coupling effects. From a numerical point of view, there are three steps in the computation: the fluid problem is solved on the computational domain; fluid forces acting on the moving tube are estimated; finally they are introduced in the structure solver providing the tube displacement that is used to actualize the fluid computational domain. Specific

  9. Hybrid Atomistic and Coarse-Grained Molecular Dynamics Simulations of Polyethylene Glycol (PEG) in Explicit Water.

    Science.gov (United States)

    Stanzione, Francesca; Jayaraman, Arthi

    2016-05-01

    In-silico design of polymeric biomaterials requires molecular dynamics (MD) simulations that retain essential atomistic/molecular details (e.g., explicit water around the biofunctional macromolecule) while simultaneously achieving large length and time scales pertinent to macroscale function. Such large-scale atomistically detailed macromolecular MD simulations with explicit solvent representation are computationally expensive. One way to overcome this limitation is to use an adaptive resolution scheme (AdResS) in which the explicit solvent molecules dynamically adopt either atomistic or coarse-grained resolution depending on their location (e.g., near or far from the macromolecule) in the system. In this study we present the feasibility and the limitations of AdResS methodology for studying polyethylene glycol (PEG) in adaptive resolution water, for varying PEG length and architecture. We first validate the AdResS methodology for such systems, by comparing PEG and solvent structure with that from all-atom simulations. We elucidate the role of the atomistic zone size and the need for calculating thermodynamic force correction within this AdResS approach to correctly reproduce the structure of PEG and water. Lastly, by varying the PEG length and architecture, we study the hydration of PEG, and the effect of PEG architectures on the structural properties of water. Changing the architecture of PEG from linear to multiarm star, we observe reduction in the solvent accessible surface area of the PEG, and an increase in the order of water molecules in the hydration shells. PMID:27108869

  10. CFD and DNS methodologies development for fuel bundle simulations

    International Nuclear Information System (INIS)

    Development and application of Computational Fluid Dynamics (CFD) and Direct Numerical Simulation (DNS) approaches to the simulation of coolant flow inside nuclear fuel bundles are presented, focusing on the advantages and limitations of the different methodologies and on their synergetic potential. High Reynolds number flow cases are analyzed with the adoption of an improved anisotropic turbulence modeling, which adopts a non-linear stress strain correlation and an improved near wall treatment. The capability of the model of predicting the coolant flow distribution inside the bundles is shown and discussed on the base of comparison with experimental data for a variety of geometrical and Reynolds number conditions. In particular wall shear stresses, velocity, and secondary flow distributions comparisons are shown. Moreover, DNS computations are performed adopting an algorithm based on the finite difference method, extended to boundary fitted coordinate systems in order to efficiently concentrate grids near the distorted wall boundaries. The validity and significance of the results is discussed underlying the importance of the insights into the turbulence structure. The calculations are further extended to higher Reynolds numbers, which cannot in general be treated with DNS approach, renouncing to the estimation of the higher-order moments, but limited to the evaluation of the averaged velocity profiles, turbulence intensities and Reynolds stresses. (authors)

  11. Large scale atomistic simulation of size effects during nanoindentation: Dislocation length and hardness

    International Nuclear Information System (INIS)

    The present paper studies the size effects during nanoindentation in Ni thin films using large scale atomistic simulation. The main focus of this paper is to evaluate the available theoretical models of size effects during nanoindentation using atomistic simulation. First, the dislocation nucleation and evolution in the simulated samples are studied. In the next step, the plastic zone size is obtained for each sample at several indentation depths incorporating the dislocation visualization. The results show that the plastic zone size divided by the contact radius is not a constant factor and varies as the indentation depth changes. The total length of dislocations located in the plastic zone is measured in the simulated samples and compared to that of the corresponding theoretical models. The results obtained from the atomistic simulation verify the theoretical predictions of the dislocation length. Next, the variation of hardness obtained directly from the molecular dynamics outputs, which is the indentation force over the contact area, is studied. In the case of conical indenter, the theoretical predictions of hardness have been verified using both experiments and simulations, and the current simulation shows the same trend, i.e. the hardness decreases as the indentation depth increases. However, in the cases of flat indenters, the theoretical models have not been validated using any experiments or simulations. Here, in the cases of flat indenters, the simulation results verify the theoretical predictions of hardness. They show that the hardness increases as the indentation depth increases. The variation of dislocation density as a function of indentation depth is then studied. In the case of nanoindentation experiment, the validity of Taylor hardening model, i.e. the relation between the hardening and dislocation density, which has not been previously studied with full atomistic details, is investigated. Accordingly, the hardness obtained directly from the

  12. Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension

    OpenAIRE

    Muddana, Hari S.; Gullapalli, Ramachandra R.; Manias, Evangelos; Butler, Peter J.

    2010-01-01

    Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from −2.6 mN m−1 to 15.9 mN m−1. Simulations showed that th...

  13. 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....

  14. An atomistic-continuum hybrid simulation of fluid flows over superhydrophobic surfaces

    OpenAIRE

    LI Qiang; He, Guo-Wei

    2009-01-01

    Recent experiments have found that slip length could be as large as on the order of 1 μm for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper, an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces, in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption i...

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

    Science.gov (United States)

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

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

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

    Science.gov (United States)

    Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

    2016-07-01

    Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

  17. Cobra-TF simulation of BWR bundle dry out experiments

    International Nuclear Information System (INIS)

    The COBRA-TF computer code uses a two-fluid, three-field and three-dimensional formulation to model a two-phase flow field in a specific geometry. The liquid phase is divided in a continuous liquid field and a separate dispersed field, which is used to describe the entrained liquid drops. For each space dimension, the code solves three momentum equations, three mass conservation equations and two energy conservation equations. Entrainment and depositions models are implemented into the code to model the mass transfer between the two liquid fields. This study presents the results obtained with COBRA-TF for the simulation of the Siemens 9-9Q BWR Bundle Dryout experiments. The model includes 20 channels and 34 axial nodes in the heated section. The predicted critical power and dryout location is compared with the measured values. An assessment of the code entrainment and de-entrainment models is presented. (authors)

  18. 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.

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    Penazzi, G.; KWOK, YH; Aradi, B.; Pecchia, A.; Frauenheim, T.; Chen, G.; Markov, SN

    2015-01-01

    We establish the dependence of the permittivity of oxidized ultra-thin silicon films on the film thickness by means of atomistic simulations within the density-functional-based tight-binding theory (DFTB). This is of utmost importance for modeling ultra- and extremely-thin silicon-on-insulator MOSFETs, and for evaluating their scaling potential. We demonstrate that electronic contribution to the dielectric response naturally emerges from the DFTB Hamiltonian when coupled to Poisson equation s...

  1. Protein folding kinetics and thermodynamics from atomistic simulation

    DEFF Research Database (Denmark)

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

    2012-01-01

    Advances in simulation techniques and computing hardware have created a substantial overlap between the timescales accessible to atomic-level simulations and those on which the fastest-folding proteins fold. Here we demonstrate, using simulations of four variants of the human villin headpiece, how......¦-values, and folding pathways provides support for the notion that a norleucine double mutant of villin folds five times faster than the wild-type sequence, but following a slightly different pathway. This work showcases how computer simulation has now developed into a mature tool for the quantitative computational...

  2. Analysis of spurious image forces in atomistic simulations of dislocations

    International Nuclear Information System (INIS)

    Molecular dynamics simulations of dislocation/obstacle interactions are enhancing our physical understanding of plasticity. However, despite increasing computational power, the interaction between simulation cell boundaries and the long ranged fields of dislocations make spurious image effects inevitable. Here, these image effects are examined in detail, providing a general map of the spurious image stress as a function of simulation cell size, aspect ratio and bow-out for both nominally edge and screw dislocations. This is achieved using an approximate image solution of the resulting boundary value problem as well as an analytic model that captures most of the spurious image effects. A unique simulation cell shape is found to minimize spurious image effects for a fixed simulation volume (i.e. fixed total number of atoms) and specified initial dislocation line length. The results are used to estimate image stress effects in various literature studies involving dislocation bow-out. The image effects are non-negligible. Several case studies involving simulation cell dimensions are shown to converge due to a near-zero scaling of the image stress with respect to the simulation cell dimensions used. Finally, a direct comparison is made between a dislocation bow-out configuration under an applied load in a finite simulation cell and an image-free multiscale simulation of the same problem and the difference is shown to be consistent with our estimated image stresses. Overall, the results here provide guidance for both the development and interpretation of quantitative molecular dynamics studies involving curved dislocation structures. (paper)

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Liedke, Bartosz

    2011-03-24

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

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

    Science.gov (United States)

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

    2015-01-01

    The optical properties of metallic nanoparticles with nanometre dimensions exhibit features that cannot be described by classical electrodynamics. In this quantum size regime, the near-field properties are significantly modified and depend strongly on the geometric arrangements. However, simulating realistically sized systems while retaining the atomistic description remains computationally intractable for fully quantum mechanical approaches. Here we introduce an atomistic electrodynamics model where the traditional description of nanoparticles in terms of a macroscopic homogenous dielectric constant is replaced by an atomic representation with dielectric properties that depend on the local chemical environment. This model provides a unified description of bare and ligand-coated nanoparticles, as well as strongly interacting nanoparticle dimer systems. The non-local screening owing to an inhomogeneous ligand layer is shown to drastically modify the near-field properties. This will be important to consider in optimization of plasmonic nanostructures for near-field spectroscopy and sensing applications. PMID:26555179

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

    Energy Technology Data Exchange (ETDEWEB)

    Kielpinski, A.L.

    1995-03-01

    Glass formulation development depends on an understanding of the effects of glass composition on its processibility and product quality. Such compositional effects on properties in turn depend on the microscopic structure of the glass. Historically, compositional effects on macroscopic properties have been explored empirically, e.g., by measuring viscosity at various glass compositions. The relationship of composition to structure has been studied by microstructural experimental methods. More recently, computer simulation has proved a fruitful complement to these more traditional methods of study. By simulating atomic interaction over a period of time using the molecular dynamics method, a direct picture of the glass structure and dynamics is obtained which can verify existing concepts as well as permit ``measurement`` of quantities inaccessible to experiment. Atomistic simulation can be of particular benefit in the development of waste glasses. As vitrification is being considered for an increasing variety of waste streams, process and product models are needed to formulate compositions for an extremely wide variety of elemental species and composition ranges. The demand for process and product models which can predict over such a diverse composition space requires mechanistic understanding of glass behavior; atomistic simulation is ideally suited for providing this understanding. Moreover, while simulation cannot completely eliminate the need for treatability studies, it can play a role in minimizing the experimentation on (and therefore contact handling of) such materials. This paper briefly reviews the molecular dynamics method, which is the primary atomistic simulation tool for studying glass structure. We then summarize the current state of glass simulation, emphasizing areas of importance for waste glass process/product modeling. At SRS, glass process and product models have been formulated in terms of glass structural concepts.

  7. Concurrent atomistic and continuum simulation of strontium titanate

    International Nuclear Information System (INIS)

    This paper presents a concurrent atomistic–continuum methodology (CAC) to simulate the dynamic processes of dislocation nucleation and migration as well as crack initiation and propagation in complex crystals. The accuracy and efficiency of the method is tested with respect to the molecular dynamics (MD) method through simulations of the dynamic fracture processes in strontium titanate under a combination of tension and shear loading and the dislocation behavior under nanoindentation. CAC simulation results demonstrated a smooth passage of cracks and dislocations through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment. Although some accuracy is lost in CAC simulations as a consequence of a 98.4% reduction in the degrees of freedom, all the CAC results are qualitatively and quantitatively comparable with MD results. The stacking fault width and nanoindentation hardness measured in the CAC simulations agrees well with existing experimental data. Criteria for cleavage and slip in ionic materials are verified. The need to include the internal degrees of freedom of atoms in concurrent atomistic–continuum methods for polyatomic crystalline materials is confirmed.

  8. Atomistic simulations of diffusion mechanisms in stoichiometric Ni3Al

    International Nuclear Information System (INIS)

    The first molecular dynamics (MD) simulation of diffusion mechanisms in ordered stoichiometric Ni3Al with the Finnis-Sinclair interatomic potential is reported in this paper. Results show that Ni atoms mainly diffuse through Ni sublattices via the vacancy mechanism; Al atoms diffuse via both the antistructure bridge and the intrasublattice mechanism. Molecular statics (MS) simulations are carried out to estimate the migration energy barriers for the elementary jumps and the different diffusion mechanisms with both the 'embedded atom method' and Finnis-Sinclair interatomic potentials. It is proven that the six-jump cycle mechanism is not energetically favourable because of the high migration energy. Thus, MD and MS simulations yield the same results on the diffusion mechanism in stoichiometric Ni3Al. Ni diffusion mechanisms obtained in this work agree with experimental results and theoretical calculation

  9. Atomistic simulations of Au-silica nanocomposite film growth

    Science.gov (United States)

    Khan, Saif A.; Heinig, K.-H.; Avasthi, D. K.

    2011-05-01

    The growth of Au-silica nanocomposite film is simulated in the framework of kinetic three dimensional lattice Monte Carlo simulations considering the basic phenomena in the deposition process. In case of co-sputter deposition, the growth kinetics of nanoparticles has been studied taking into consideration the effect of the energetic sputtered species reaching the surface of the film during deposition. Formation of Au nanorod like structures are predicted under certain growth conditions particularly when surface diffusion assisted phase separation plays the dominant role and bulk kinetics is frozen. The observed dependence of the Au nanoparticle size on Au/silica ratio is in agreement with the experimental results.

  10. Atomistic simulations of mechanical properties of graphene nanoribbons

    International Nuclear Information System (INIS)

    The mechanical behavior of graphene nanoribbons (GNRs) was investigated by molecular dynamics (MD) simulations. The simulation results showed that GNRs behave nonlinear elastically under tensile loads. When the strain exceeds 18%, the stress stiffening causes an increase in the Young's modulus. The width of a GNR has slight effects on the Young modulus and fracture strength. The maximum strain at which fracture occurs can reach 30.26% with an intrinsic strength of about 0.175 TPa. The excellent flexibility is attributed to the elongation of the C-C bonds and the variations of the bond angles.

  11. CFD simulation of critical heat flux in a rod bundle

    International Nuclear Information System (INIS)

    The critical heat flux (CHF) condition is characterized by a sharp reduction of the local heat transfer coefficient which results from the replacement of liquid by vapour adjacent to the heat transfer surface. If the surface heat flux is the independent variable, the condition manifests itself as a sharp increase in surface temperature as the critical heat flux value is reached. The critical heat flux forms an important boundary for the performance of the heat exchange equipment. Determination of the critical heat flux is one of the key issues in nuclear reactor safety. This paper presents numerical simulations of boiling flow in a rod bundle with Departure from Nucleate Boiling (DNB) condition at the end of the middle rod. Large Water Loop CHF tests were used as a data set for our simulations. The Large Water Loop (LWL) is non-active pressurised-water equipment with technological and thermal parameters corresponding to those of PWR. The CHF experimental facility (a part of the Large Water Loop) has been designed for research into CHF in water flow through a bundle of electrically heated vertical rods. The critical conditions were determined under constant pressure, inlet water temperature and mass flux and for quasi steady-state - by gradually increasing the heat input. The rods are modelled by hollow tubes with direct heating of the wall. NEPTUNE-CFD code was used for numerical simulations. The computational domain covered a 30 deg. quasi-symmetric section of the actual channel. Simplified grid spacers were included in the domain. Calculations were performed with two-fluid approach with models for drag, lift, added mass and turbulent dispersion forces as well as for interfacial heat and mass transfer. Turbulent dispersion coefficient was based on void fraction gradient and on drag and mass forces. K-epsilon model was used for the prediction of the liquid turbulence, the flow of vapour was assumed to be laminar. Generalized wall heat-flux-splitting model was used

  12. Insights into prion protein function from atomistic simulations.

    Science.gov (United States)

    Hodak, Miroslav; Bernholc, Jerzy

    2010-01-01

    Computer simulations are a powerful tool for studies of biological systems. They have often been used to study prion protein (PrP), a protein responsible for neurodegenerative diseases, which include "mad cow disease" in cattle and Creutzfeldt-Jacob disease in humans. An important aspect of the prion protein is its interaction with copper ion, which is thought to be relevant for PrP's yet undetermined function and also potentially play a role in prion diseases. for studies of copper attachment to the prion protein, computer simulations have often been used to complement experimental data and to obtain binding structures of Cu-PrP complexes. This paper summarizes the results of recent ab initio calculations of copper-prion protein interactions focusing on the recently discovered concentration-dependent binding modes in the octarepeat region of this protein. In addition to determining the binding structures, computer simulations were also used to make predictions about PrP's function and the role of copper in prion diseases. The results demonstrate the predictive power and applicability of ab initio simulations for studies of metal-biomolecular complexes. PMID:20118658

  13. Voltage equilibration for reactive atomistic simulations of electrochemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Onofrio, Nicolas; Strachan, Alejandro, E-mail: strachan@purdue.edu [School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47906 (United States)

    2015-08-07

    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.

  14. Recent progress in atomistic simulation of electrical current DNA sequencing.

    Science.gov (United States)

    Kim, Han Seul; Kim, Yong-Hoon

    2015-07-15

    We review recent advances in the DNA sequencing method based on measurements of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices. PMID:25744599

  15. Atomistic simulation of detonation initiation by ultra-short impact

    Science.gov (United States)

    Murzov, S. A.; Zhakhovsky, V. V.

    2015-11-01

    We present results of the classical molecular dynamics simulation of detonation initiation in simple AB model of a high explosive compressed by ultra-short shock wave (SW). The simplified reactive empirical bond order potential (REBO) defines interatomic forces in the AB model explosive made up of diatomic AB molecules. Simulation of ultra-short piston-driven compression of AB explosive with duration of picoseconds represents an indirect initiation via a thin metal foil irradiated by a femtosecond laser pulse. We studied transition of SW to a detonation wave (DW), including evolution of calculated pressure profile in a sample. A run distance to detonation of such AB explosive film, which is required for detonation initiation, was obtained. Variation of loading time and piston velocity gives a 2D region of transition from SW to DW. The influence of pores on detonation initiation threshold is discussed.

  16. Thermal stability of silicon nanowires:atomistic simulation study

    Institute of Scientific and Technical Information of China (English)

    Liu Wen-Liang; Zhang Kai-Wang; Zhong Jian-Xin

    2009-01-01

    Using the Stillinger-Weber (SW) potential model, we investigate the thermal stability of pristine silicon nanowires based on classical molecular dynamics (MD) simulations. We explore the structural evolutions and the Lindemann indices of silicon nanowires at different temperatures in order to unveil atomic-level melting behaviour of silicon nanowires.The simulation results show that silicon nanowires with surface reconstructions have higher thermal stability than those without surface reconstructions, and that silicon nanowires with perpendicular dimmer rows on the two (100) surfaces have somewhat higher thermal stability than nanowires with parallel dimmer rows on the two (100) surfaces. Furthermore, the melting temperature of silicon nanowires increases as their diameter increases and reaches a saturation value close to the melting temperature of bulk silicon. The value of the Lindemann index for melting silicon nanowires is 0.037.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  18. Atomistic simulations of oleic imidazolines bound to ferric clusters

    Energy Technology Data Exchange (ETDEWEB)

    Ramachandran, S.; Tsai, B.L.; Blanco, M.; Goddard, W.A. III [California Inst. of Technology, Pasadena, CA (United States); Chen, H.; Tang, Y. [Chevron Petroleum Technology Company, La Habra, CA (United States)

    1997-01-02

    The oleic imidazoline (OI) class of molecules is used extensively for corrosion inhibitor oil field pipeline applications. However, there is no model for understanding how they work. As a first step in elucidating this mechanism we carried out quantum mechanical calculations on clusters involving Fe{sup 3+}, H{sub 2}O, OH, and OI. These calculations are used to determine the MS force field for molecular dynamics simulations. 17 refs., 5 figs., 6 tabs.

  19. Insights into prion protein function from atomistic simulations

    OpenAIRE

    Hodak, Miroslav; Bernholc, Jerzy

    2010-01-01

    Computer simulations are a powerful tool for studies of biological systems. They have often been used to study prion protein (PrP), a protein responsible for neurodegenerative diseases, which include “mad cow disease” in cattle and Creutzfeldt-Jacob disease in humans. An important aspect of the prion protein is its interaction with copper ion, which is thought to be relevant for PrP’s yet undetermined function and also potentially play a role in prion diseases. For studies of copper attachmen...

  20. Atomistic simulations of swift ion tracks in diamond and graphite

    International Nuclear Information System (INIS)

    We have used molecular dynamics simulations to study ion tracks in diamond and graphite. Tracks are included using a thermal spike model, i.e. a certain number of atoms within an initial track radius are given an initial excitation energy. The total energy given to the excited atoms and the length of the track determine an 'effective' stopping power dE/dx. Electronic excitations in semiconductors and semimetals like diamond and graphite can diffuse far from each other or be quenched before they couple to the lattice. This effect is included by varying the number of atoms that are effectively energized within the track. We use an initial track radius of 3 nm and we find that full amorphization of this region during the first few ps only occurs when the 'effective' dE/dx is larger than 6 ± 0.9 keV/nm for graphite and 10.5 ± 1.5 keV/nm for diamond. Since the 'effective' dE/dx depends on the electron-phonon coupling, our simulations set bounds on the efficiency of the coupling between the electronic excitations and the lattice in this highly non-equilibrium scenario

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

    Science.gov (United States)

    Yu, Miao; Kenny, Steven D.

    2016-03-01

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

  2. Membrane pore formation in atomistic and coarse-grained simulations.

    Science.gov (United States)

    Kirsch, Sonja A; Böckmann, Rainer A

    2016-10-01

    Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26748016

  3. Comparative study of embedded atom potentials for atomistic simulations of fracture in α-iron

    International Nuclear Information System (INIS)

    Atomistic simulations play a crucial role in advancing our understanding of the crack-tip processes that take place during fracture of semi-brittle materials like α-iron. As with all atomistic simulations, the results of such simulations however depend critically on the underlying atomic interaction model. Here, we present a systematic study of eight α-iron embedded atom method potentials used to model cracks subjected to plane strain mode-I loading conditions in six different crystal orientations. Molecular statics simulations are used to determine the fracture behavior (cleavage, dislocation emission, twinning) and the critical stress intensity factor KIc. The structural transformations in front of the crack tips, and in particular the occurrence of {1 1 0} planar faults, are analyzed in detail and related to the strain-dependent generalized stacking fault energy curve. The simulation results are discussed in terms of theoretical fracture criteria and compared to recent experimental data. The different potentials are ranked according to their capability to model the experimentally observed fracture behavior. (paper)

  4. Electron transfer, decoherence, and protein dynamics: insights from atomistic simulations.

    Science.gov (United States)

    Narth, Christophe; Gillet, Natacha; Cailliez, Fabien; Lévy, Bernard; de la Lande, Aurélien

    2015-04-21

    Electron transfer in biological systems drives the processes of life. From cellular respiration to photosynthesis and enzymatic catalysis, electron transfers (ET) are chemical processes on which essential biological functions rely. Over the last 40 years, scientists have sought understanding of how these essential processes function in biology. One important breakthrough was the discovery that Marcus theory (MT) of electron transfer is applicable to biological systems. Chemists have experimentally collected both the reorganization energies (λ) and the driving forces (ΔG°), two parameters of Marcus theory, for a large variety of ET processes in proteins. At the same time, theoretical chemists have developed computational approaches that rely on molecular dynamics and quantum chemistry calculations to access numerical estimates of λ and ΔG°. Yet another crucial piece in determining the rate of an electron transfer is the electronic coupling between the initial and final electronic wave functions. This is an important prefactor in the nonadiabatic rate expression, since it reflects the probability that an electron tunnels from the electron donor to the acceptor through the intervening medium. The fact that a protein matrix supports electron tunneling much more efficiently than vacuum is now well documented, both experimentally and theoretically. Meanwhile, many chemists have provided examples of the rich physical chemistry that can be induced by protein dynamics. This Account describes our studies of the dynamical effects on electron tunneling. We present our analysis of two examples of natural biological systems through MD simulations and tunneling pathway analyses. Through these examples, we show that protein dynamics sustain efficient tunneling. Second, we introduce two time scales: τcoh and τFC. The former characterizes how fast the electronic coupling varies with nuclear vibrations (which cause dephasing). The latter reflects the time taken by the system

  5. Atomistic simulations of the mechanical properties of 'super' carbon nanotubes

    International Nuclear Information System (INIS)

    The mechanical properties of the so-called 'super' carbon nanotubes (STs) are investigated using classical molecular dynamics simulations. The STs are built from single-walled carbon nanotubes (SWCNTs) connected by Y-like junctions forming an ordered carbon nanotube network that is then rolled into a seamless cylinder. We observed that the ST behaviour under tensile tests is similar to the one presented by fishing nets. This interesting behaviour provides a way to vary the accessible channels to the inner parts of STs by applying an external mechanical load. The Young's modulus is dependent on the ST chirality and it inversely varies with the ST radius. Smaller reduction of breaking strain values due to temperature increase is predicted for zigzag STs compared to SWCNTs. The results show that, for STs with radius ∼5 nm, the junctions between the constituent SWCNTs play an important role in the fracture process. The Young's modulus and tensile strength were estimated for hierarchical higher-order STs using scaling laws related to the ST fractal dimension. The obtained mechanical properties suggest that STs may be used in the development of new porous, flexible, and high-strength materials

  6. Atomistic simulation of diffusion of hydrocarbons in carbon nano tubes

    International Nuclear Information System (INIS)

    Full Text:As an important research direction in nano science and nano technology, carbon nano tubes have aroused great interest, due to their unique structure and stability. This project deals with the transport of hydrocarbons inside Single Wall Carbon Nano tubes, which can be imagined to be rolled up rectangular strips of hexagonal graphite. We will present a simulation of diffusion of methane molecules inside carbon nano tubes using the Dual Control Volume Grand Canonical Molecular Dynamics method, in which a steady state chemical potential gradient is applied over the tube that enables us to calculate the transport diffusion coefficients Dt according to Fick Law. The trajectory of the particles allows the calculation of self diffusion coefficients, Ds , which are given by Einstein's relation. We used Equilibrium Molecular Dynamics to determine Ds of methane molecules taking into account their tetrahedral structure, modeled using the Bond Order Empirical Potential (Brenner potential). Transport phenomena in carbon depend on the pore size, the pore network structure, the molecule dimensions, the temperature of the gas and the interaction between the transported gas and the tube. Selections of these parameters were made for different runs, in order to explore their significance. The Atomic Visualization program was used to animate diffusion of hydrocarbons inside the carbon nano tube, in order to observe typical features. For example we observed that small pores lead to single file diffusion

  7. Surface patterning by ion bombardment: predictions of large-scale atomistic simulations

    International Nuclear Information System (INIS)

    Despite of intense studies in recent years, atomistic understanding of surface evolution during ion irradiation is still under discussion. Continuum models, like the Bradley and Harper theory, cannot explain microscopic processes during ion irradiation. So far, atomistic simulations could not describe pattern dynamics on spatiotemporal scales of experiments. We present a novel program package that unifies the simulation of collision cascades with kinetic Monte-Carlo simulations. The 3D atom relocations were calculated in the Binary Collision Approximation (BCA), whereas the thermally activated relaxation of energetically unstable atomic configurations as well as diffusive processes were simulated by a very efficient bit-coded kinetic 3D Monte Carlo code. Our studies show that: (i) bulk defects continuously created within the collision cascade are responsible for local surface topography fluctuations and induce surface mass currents. These currents smooth the surface from normal incidence up to θ=40 , whereas at θ>40 ripple patterns appear; (ii) sputtering is not the dominant driving force for the ripple formation at non-grazing incidence angles. Surface patterning is caused by processes like bulk and surface defect migration, recombination, bulk and surface diffusion and ion induced diffusion.

  8. 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.

  9. Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    McCarty, Keven F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Zhou, Xiaowang [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ward, Donald K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schultz, Peter A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Foster, Michael E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bartelt, Norman Charles [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expand the number of potential types of graphene electronic devices.

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

    International Nuclear Information System (INIS)

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

  11. Heterogeneous plastic deformation and Bauschinger effect in ultrafine-grained metals: atomistic simulations

    Science.gov (United States)

    Tsuru, Tomohito; Aoyagi, Yoshiteru; Kaji, Yoshiyuki; Shimokawa, Tomotsugu

    2016-03-01

    The effect of the dislocation density on yield strength and subsequent plastic deformation of ultrafine-grained metals was investigated in large-scale atomistic simulations. Polycrystalline models were constructed and uniaxial tension and compression were applied to elucidate the heterogeneous plastic deformation and the Bauschinger effect. The initial yield becomes heterogeneous as the dislocation density decreases owing to a wide range of Schmid factors of activated slip systems in each grain. A different mechanism of the Bauschinger effect was proposed, where the Bauschinger effect of ultrafine-grained metals is caused by the change in dislocation density in the process of forward and backward loadings.

  12. Adaptive resolution simulation of supramolecular water : The concurrent making, breaking, and remaking of water bundles

    NARCIS (Netherlands)

    Zavadlav, Julija; Marrink, Siewert J; Praprotnik, Matej

    2016-01-01

    The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to

  13. A fully atomistic computer simulation study of cold denaturation of a β-hairpin

    Science.gov (United States)

    Yang, Changwon; Jang, Soonmin; Pak, Youngshang

    2014-12-01

    Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in molecular details can provide a new insight into the detailed natures of hydrophobic forces governing the stability of proteins in water. We show that the cold-denaturation-like phenomenon can be directly observed at low temperatures using a fully atomistic molecular dynamics simulation method. Using a highly optimized protein force field in conjunction with three different explicit water models, a replica exchange molecular dynamics simulation scheme at constant pressures allows for the computation of the melting profile of an experimentally well-characterized β-hairpin peptide. For all three water models tested, the simulated melting profiles are indicative of possible cold denaturation. From the analysis of simulation ensembles, we find that the most probable cold-denatured structure is structurally compact, with its hydrogen bonds and native hydrophobic packing substantially disrupted.

  14. 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.

  15. Simulation of flow across complicated domain between tube bundles by the discrete vortex method

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    On the basis of the analysis of numerical simulation methods for the complicated domain between tube bundles, an improved Lagragian discrete vortex method (DVM) and corresponding algorithm are put forward to solve the practical difficulties of flow across tube bundles. With this method the amount of vortices can be reduced considerably, which makes quick calculation possible. Applied to the practical configuration of horizontal tube bundles, the DVM simulation is carried out and compared with the experimental results. Both the transient flow field and the profile of mean velocity and fluctuations are in good agreement with experimental results, which indicate that the DVM is suitable for the simulation of single-phase flow across tube bundles.

  16. B and N ion implantation into carbon nanotubes: Insight from atomistic simulations

    International Nuclear Information System (INIS)

    By employing atomistic computer simulations with empirical potential and density functional force models, we study B/N ion implantation onto carbon nanotubes. We simulate irradiation of single-walled nanotubes with B and N ions and show that up to 40% of the impinging ions can occupy directly the sp2 positions in the nanotube atomic network. We further estimate the optimum ion energies for direct substitution. Ab initio simulations are used to get more insight into the structure of the typical atomic configurations which appear under the impacts of the ions. As annealing should further increase the number of sp2 impurities due to dopant atom migration and annihilation with vacancies, we also study migration of impurity atoms over the tube surface. Our results indicate that irradiation-mediated doping of nanotubes is a promising way to control the nanotube electronic and even mechanical properties due to impurity-stimulated crosslinking of nanotubes

  17. Atomistic simulation based prediction of the solvent effect on the molecular mobility and glass transition of poly (methyl methacrylate)

    Science.gov (United States)

    Mishra, Shawn; Keten, Sinan

    2013-01-01

    We present an investigation of the retained solvent effect on the glass transition temperature (Tg) of poly(methyl methacrylate) (PMMA) through all-atom molecular dynamics simulations. Addition of a weakly interactive solvent, tetrahydrofuran (THF), causes a depression of the PMMA Tg that can be identified through an analysis of the mean squared displacement of the polymer chains from atomistic trajectories. Our results are in very good agreement with an atomistically informed theoretical model based on free volume theory and demonstrate the applicability of molecular simulation to discern solvent effects on polymer thermomechanical behavior in silico.

  18. 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.

  19. 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.)

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

    Science.gov (United States)

    Carballo Pacheco, Martin; Ismail, Ahmed E.; Strodel, Birgit

    Amyloids are highly structured protein aggregates, normally associated with neurodegenerative diseases such as Alzheimer's disease. In recent years, a number of nontoxic amyloids with physiologically normal functions, called functional amyloids, have been found. It is known that soluble small oligomers are more toxic than large fibrils. Thus, we study with atomistic explicit-solvent molecular dynamics simulations the oligomer formation of the amyloid- β peptide Aβ25 - 35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Our simulations show that monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations. In addition, we observe faster aggregation by functional amyloids than toxic amyloids, which could explain their lack of toxicity.

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

    Science.gov (United States)

    Upadhyay, Sanjay K; Wang, Yukun; Zhao, Tangzhen; Ulmschneider, Jakob P

    2015-06-01

    The membrane disruption and pore-forming mechanism of melittin has been widely explored by experiments and computational studies. However, the precise mechanism is still enigmatic, and further study is required to turn antimicrobial peptides into future promising drugs against microbes. In this study, unbiased microsecond (µs) time scale (total 17 µs) atomistic molecular dynamics simulation were performed on multiple melittin systems in 1,2-dimyristoyl-sn-glycero-3-phosphocholine membrane to capture the various events during the membrane disorder produced by melittin. We observed bent U-shaped conformations of melittin, penetrated deeply into the membrane in all simulations, and a special double U-shaped structure. However, no peptide transmembrane insertion, nor pore formation was seen, indicating that these processes occur on much longer timescales, and suggesting that many prior computational studies of melittin were not sufficiently unbiased. PMID:25963936

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

    Science.gov (United States)

    Laktionov, Andrey; Chemineau-Chalaye, Emilie; Wesolowski, Tomasz A

    2016-08-21

    Besides molecular electron densities obtained within the Born-Oppenheimer approximation (ρB(r)) to represent the environment, the ensemble averaged density (〈ρB〉(r)) is also admissible in frozen-density embedding theory (FDET) [Wesolowski, Phys. Rev. A, 2008, 77, 11444]. This makes it possible to introduce an approximation in the evaluation of the solvent effect on quantum mechanical observables consisting of replacing the ensemble averaged observable by the observable evaluated at ensemble averaged ρB(r). This approximation is shown to affect negligibly the solvatochromic shift in the absorption of hydrated acetone. The proposed model provides a continuum type of representation of the solvent, which reflects nevertheless its local structure, and it is to be applied as a post-simulation analysis tool in atomistic level simulations. PMID:26984532

  3. Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation

    International Nuclear Information System (INIS)

    In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO2 and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature

  4. 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.

  5. Computer code for the atomistic simulation of lattice defects and dynamics

    International Nuclear Information System (INIS)

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

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

    CERN Document Server

    Mao, Yijin; Chen, C L

    2016-01-01

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

  7. Diffusive-to-ballistic transition in grain boundary motion studied by atomistic simulations

    International Nuclear Information System (INIS)

    An adapted simulation method is used to systematically study grain boundary motion at velocities and driving forces across more than five orders of magnitude. This analysis reveals that grain boundary migration can occur in two modes, depending upon the temperature (T) and applied driving force (P). At low P and T, grain boundary motion is diffusional, exhibiting the kinetics of a thermally activated system controlled by grain boundary self-diffusion. At high P and T, grain boundary migration exhibits the characteristic kinetic scaling behavior of a ballistic process. A rather broad transition range in both P and T lies between the regimes of diffusive and ballistic grain boundary motion, and is charted here in detail. The recognition and delineation of these two distinct modes of grain boundary migration also leads to the suggestion that many prior atomistic simulations might have probed a different kinetic regime of grain boundary motion (ballistic) as compared to that revealed in most experimental studies (diffusional).

  8. Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Dumpala, Santoshrupa; Broderick, Scott R.; Rajan, Krishna, E-mail: krajan@iastate.edu [Department of Materials Science and Engineering and Institute for Combinatorial Discovery, Iowa State University, 2220 Hoover Hall, Ames, Iowa 50011 (United States); Khalilov, Umedjon; Neyts, Erik C. [Department of Chemistry, PLASMANT Research Group, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk-Antwerp (Belgium); Duin, Adri C. T. van [Department of Mechanical and Nuclear Engineering, Penn State University, University Park, Pennsylvania 16801 (United States); Provine, J; Howe, Roger T. [Department of Electrical Engineering, Stanford University, 420 Via Palou Mall, Stanford, California 94305 (United States)

    2015-01-05

    In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO{sub 2} and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature.

  9. 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.

  10. 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; Biegel, Bryan (Technical Monitor)

    2002-01-01

    A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

  11. Hybrid Simulation Strategy for Simulating Self-Assembled Morphologies at the Atomistic Length Scales

    Science.gov (United States)

    Sethuraman, Vaidyanathan; Ganesan, Venkat

    In the context of Lithium-ion batteries, an enhancement in both ionic conductivity and mechanical properties, were observed for block copolymer electrolytes with increasing MW. On the contrary, when homopolymers were used as electrolytes, the ionic conductivity decreased with increasing MW. However, the origins of such increase in conductivity are unclear and are speculated to be tied to both the morphology and the atomistic details of the copolymer themselves. Motivated by such issues, we present a strategy to create ordered morphologies of block copolymers at the atomistic level using a combination of coarse-graining and inverse coarse-graining techniques. A mapping which is developed using the long-ranged structural mapping in the disordered phases will be utilized to generate self-assembled morphologies. In particular we focus on generating self-assembled morphologies of PS-PEO at the atomistic length scales. Statics and dynamics of such self-assembled morphologies will be presented and the effect of self assembly on the transport properties of ions will also be explored. Funded by NSF.

  12. Numerical simulation of turbulent flow in a rod bundle geometry

    International Nuclear Information System (INIS)

    This paper presents predictions of turbulent flows in a rod bundle geometry by using the k-ε turbulence model and the Reynolds stress model. Significant difference was not found in the predicted turbulence properties by the two models. The secondary flow predicted by the Reynolds stress model, which was nearly 1.2% of axial bulk velocity, changed the distribution of mean axial velocity, turbulence intensities and Reynolds shear stresses. The Reynolds stress model was unable to estimate the flow pulsation which is the main contribution of turbulent interchange mixing between subchannels. (author)

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

    International Nuclear Information System (INIS)

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

  14. Crystal Structures of Precise Functional Copolymers: Atomistic Molecular Dynamics Simulations and Comparisons with Experiments

    Science.gov (United States)

    Trigg, Edward B.; Stevens, Mark J.; Winey, Karen I.

    Layered crystal structures have been observed in linear poly(ethylene-co-acrylic acid) in which the carboxylic acid groups are placed precisely every 21 carbon atoms along the backbone. The alkane segments form structures resembling orthorhombic polyethylene crystals, while the acid groups form continuous domains that may act as pathways for ion conduction. Further details of the crystal structure have been difficult to elucidate experimentally, but could be important for understanding structure-property relationships. Here, two classes of crystal structures are evaluated via atomistic molecular dynamics: extended chain structures, wherein the polymer backbones are highly extended in near-trans conformations, and adjacent reentry structures, wherein the polymer backbones conform in adjacent reentry loops near the site of each covalently-bonded acid group. Energies of relaxed structures and hydrogen bonding states are compared, and X-ray scattering and other experimental data is compared with the simulation results.

  15. A Spectral Multiscale Method for Wave Propagation Analysis: Atomistic-Continuum Coupled Simulation

    CERN Document Server

    Patra, Amit K; Ganguli, Ranjan

    2014-01-01

    In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a ...

  16. Atomistic simulation of twin boundaries effect on nanoindentation of Ag(1 1 1) films

    International Nuclear Information System (INIS)

    Atomistic simulations were employed to study the effect of a single twin boundary parallel with the indented surface on nanoindentation of Ag(1 1 1) films. The results show that the twin boundary has little influence on the elastic modulus of films. The load for the initial yield is observably reduced when the twin boundary is very near the indented surface due to the nucleation of the glissile dislocations on the slip plane parallel to the surface, rather than the formation of the tetrahedral sessile lock when nanoindentation on the perfect film. Twin boundaries are effective obstacles to the motion of dislocations, and change the dislocation patterns dominating the deformation, resulting in the hardening of films. In addition, twin boundaries can act as dislocation sources before losing their coherency.

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

    Science.gov (United States)

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

    2016-05-01

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

  18. Atomistic Simulations of Functional Au-144(SR)(60) Gold Nanoparticles in Aqueous Environment

    DEFF Research Database (Denmark)

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

    2012-01-01

    Charged monolayer-protected gold nanoparticles (AuNPs) have been studied in aqueous solution by performing atomistic molecular dynamics simulations at physiological temperature (310 K). Particular attention has been paid to electrostatic properties that modulate the formation of a complex comprised...... of the nanoparticle together with surrounding ions and water. We focus on Au-144 nanoparticles that comprise a nearly spherical Au core (diameter similar to 2 nm), a passivating Au-S interface, and functionalized alkanethiol chains. Cationic and anionic AuNPs have been modeled with amine and carboxyl...... electrostatic potential displays a minimum for AuNP- at 1.9 nm from the center of the nanoparticle, marking a preferable location for Na+, while the AuNP+ potential (affecting the distribution of Cl-) rises almost monotonically with a local maximum. Comparison to Debye-Huckel theory shows very good agreement...

  19. Structures, nanomechanics, and disintegration of single-walled GaN nanotubes: atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Jeong Won; Hwang, Ho Jung; Song, Ki Oh; Choi, Won Young; Byun, Ki Ryang [Chung-Ang University, Seoul (Korea, Republic of); Kwon, Oh Keun [Semyung University, Jecheon (Korea, Republic of); Lee, Jun Ha [Sangmyung University, Chonan (Korea, Republic of); Kim, Won Woo [Juseong College, Cheongwon (Korea, Republic of)

    2003-09-15

    We have investigated the structural, mechanical, and thermal properties of single-walled GaN nanotubes by using atomistic simulations and a Tersoff-type potential. The Tersoff potential for GaN effectively describes the properties of GaN nanotubes. The nanomechanics of GaN nanotubes under tensile and compressive loadings have also been investigated, and Young's modulus has been calculated. The caloric curves of single-walled GaN nanotubes can be divided into three regions corresponding to nanotubes, the disintegrating range, and vapor. Since the stability or the stiffness of a tube decreases with increasing curving sheet-to-tube strain energy, the disintegration temperatures of GaN nanotubes are closely related to the curving sheet-to-tube strain energy.

  20. Structures, nanomechanics, and disintegration of single-walled GaN nanotubes: atomistic simulations

    International Nuclear Information System (INIS)

    We have investigated the structural, mechanical, and thermal properties of single-walled GaN nanotubes by using atomistic simulations and a Tersoff-type potential. The Tersoff potential for GaN effectively describes the properties of GaN nanotubes. The nanomechanics of GaN nanotubes under tensile and compressive loadings have also been investigated, and Young's modulus has been calculated. The caloric curves of single-walled GaN nanotubes can be divided into three regions corresponding to nanotubes, the disintegrating range, and vapor. Since the stability or the stiffness of a tube decreases with increasing curving sheet-to-tube strain energy, the disintegration temperatures of GaN nanotubes are closely related to the curving sheet-to-tube strain energy.

  1. Numerical Simulation of The Mechanical Properties of Carbon Nanotube Using the Atomistic-Continuum Mechanics

    OpenAIRE

    Wu, C. -J.; Chou, C. -Y.; Han, C. -N.; Chiang, K.-N.

    2006-01-01

    This paper the utilizes atomistic-continuum mechanics (ACM) to investigate the mechanical properties of single-walled carbon nanotubes (SWCNTs). By establishing a linkage between structural mechanics and molecular mechanics, not only the Young's moduli could be obtained but also the modal analysis could be achieved. In addition, according to atomistic-continuum mechanics and finite element method, an effective atomistic-continuum model is constructed to investigate the above two mechanical pr...

  2. Atomistic simulation of polymer/solid and polymer/polymer interfaces

    International Nuclear Information System (INIS)

    Atomistic simulation techniques have been used to provide a molecular level perspective on the phenomena which control adhesion at metal oxide/polymer and polymer/polymer interfaces relevant to steel coating systems. Two simulation methodologies illustrated by relevant examples will be discussed. The physisorption of an epoxy resin (widely used as the basis of primer paint systems for metallic structural materials) onto alumina and chromia surfaces was compared. Initial model conformations of an epoxy resin oligomer were generated using the Theodorou-Suter technique and the metal oxide surfaces were represented by the low index Miller planes of AlIII and CrIII oxides. The simulated complexes of a single oligomer and various metal oxide surfaces were compared both geometrically and energetically and revealed the basis for better adhesion to the chromia surface. In order to simulate adhesion at polymer/polymer interfaces fully periodic amorphous models of interfaces were constructed and submitted to molecular dynamics. The results of these studies are in general agreement with experimental observations and provide the basis for developing a better understanding of the factors controlling adhesion at metal oxide/polymer and polymer/polymer interfaces

  3. CFD simulation of vertical seven-rod bundle cooled with supercritical Freon-12

    Energy Technology Data Exchange (ETDEWEB)

    Huang, X.; Podila, K.; Rao, Y.F., E-mail: podilak@aecl.ca [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada)

    2014-06-15

    In this paper, a seven-rod bare bundle was simulated using ANSYS Fluent 6.3.26 to accurately predict the fluid flow and heat transfer behaviour under supercritical flow conditions. Seven turbulence models were compared to identify the appropriate model to predict the experiments performed at the Institute of Physics and Power Engineering on a vertically oriented seven-rod bare bundle cooled with supercritical Freon-12. It was found that predictions of wall temperatures and heat transfer coefficients are sensitive to the choice of turbulence model as well as to the near-wall treatment. Overall, the CFD simulations were able to predict the measured sheath temperature profiles along the length of the bundle within reasonable accuracy. (author)

  4. Advanced CFD simulations of turbulent flows around appendages in CANDU fuel bundles

    International Nuclear Information System (INIS)

    Computational Fluid Dynamics (CFD) was used to simulate the coolant flow in a modified 37-element CANDU fuel bundle, in order to investigate the effects of the appendages on the flow field. First, a subchannel model was created to qualitatively analyze the capabilities of different turbulence models such as k.ε, Reynolds Normalization Group (RNG), Shear Stress Transport (SST) and Large Eddy Simulation (LES). Then, the turbulence model with the acceptable quality was used to investigate the effects of positioning appendages, normally used in CANDU 37-element Critical Heat Flux (CHF) experiments, on the flow field. It was concluded that the RNG and SST models both show improvements over the k.ε method by predicting cross flow rates closer to those predicted by the LES model. Also the turbulence effects in the k.ε model dissipate quickly downstream of the appendages, while in the RNG and SST models appear at longer distances similar to the LES model. The RNG method simulation time was relatively feasible and as a result was chosen for the bundle model simulations. In the bundle model simulations it was shown that the tunnel spacers and leaf springs, used to position the bundles inside the pressure tubes in the experiments, have no measureable dominant effects on the flow field. The flow disturbances are localized and disappear at relatively short streamwise distances. (author)

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

    KAUST Repository

    French, William R.

    2013-01-01

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

  6. Dynamic bonding of metallic nanocontacts: Insights from experiments and atomistic simulations

    Science.gov (United States)

    Fernández, M. A.; Sabater, C.; Dednam, W.; Palacios, J. J.; Calvo, M. R.; Untiedt, C.; Caturla, M. J.

    2016-02-01

    The conductance across an atomically narrow metallic contact can be measured by using scanning tunneling microscopy. In certain situations, a jump in the conductance is observed right at the point of contact between the tip and the surface, which is known as "jump to contact" (JC). Such behavior provides a way to explore, at a fundamental level, how bonding between metallic atoms occurs dynamically. This phenomenon depends not only on the type of metal but also on the geometry of the two electrodes. For example, while some authors always find JC when approaching two atomically sharp tips of Cu, others find that a smooth transition occurs when approaching a Cu tip to an adatom on a flat surface of Cu. In an attempt to show that all these results are consistent, we make use of atomistic simulations; in particular, classical molecular dynamics together with density functional theory transport calculations to explore a number of possible scenarios. Simulations are performed for two different materials: Cu and Au in a [100] crystal orientation and at a temperature of 4.2 K. These simulations allow us to study the contribution of short- and long-range interactions to the process of bonding between metallic atoms, as well as to compare directly with experimental measurements of conductance, giving a plausible explanation for the different experimental observations. Moreover, we show a correlation between the cohesive energy of the metal, its Young's modulus, and the frequency of occurrence of a jump to contact.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-02-17

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Sutthibutpong, Thana; Noy, Agnes; Harris, Sarah

    2016-01-01

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

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

    Science.gov (United States)

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

    2000-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-08-01

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

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

    Science.gov (United States)

    Oakes, V; Furini, S; Domene, C

    2016-01-01

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

  13. Atomistic simulation of MgO nanowires subject to electromagnetic wave

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

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

    2016-05-21

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

  15. Extracting dislocations and non-dislocation crystal defects from atomistic simulation data

    International Nuclear Information System (INIS)

    We describe a novel method for extracting dislocation lines from atomistic simulation data in a fully automated way. The dislocation extraction algorithm (DXA) generates a geometric description of dislocation lines contained in an arbitrary crystalline model structure. Burgers vectors are determined reliably, and the extracted dislocation network fulfills the Burgers vector conservation rule at each node. All remaining crystal defects (grain boundaries, surfaces, etc), which cannot be represented by one-dimensional dislocation lines, are output as triangulated surfaces. This geometric representation is ideal for visualization of complex defect structures, even if they are not related to dislocation activity. In contrast to the recently proposed on-the-fly dislocation detection algorithm (ODDA) Stukowski (2010 Modelling Simul. Mater. Sci. Eng. 18 015012) the new method is extremely robust. While the ODDA was designed for a computationally efficient on-the-fly analysis, the DXA method enables a detailed analysis of dislocation lines even in highly distorted crystal regions, as they occur, for instance, close to grain boundaries or in dense dislocation networks

  16. Rotational relaxation in ortho-terphenyl: using atomistic simulations to bridge theory and experiment.

    Science.gov (United States)

    Eastwood, Michael P; Chitra, Tarun; Jumper, John M; Palmo, Kim; Pan, Albert C; Shaw, David E

    2013-10-24

    Understanding the nature of the glass transition--the dramatic slowing of dynamics and eventual emergence of a disordered solid from a cooling liquid--is a fundamental challenge in physical science. A central characteristic of glass-forming liquids is a non-exponential main relaxation process. The extent of deviation from exponential relaxation typically becomes more pronounced on cooling. Theories that predict a growth of spatially heterogeneous dynamics as temperature is lowered can explain these observations. In apparent contradiction to these theories, however, some experiments suggest that certain substances--notably including the intensely studied molecular glass-former ortho-terphenyl (OTP)--have a main relaxation process whose shape is essentially temperature independent, even though other observables predicted to be correlated with the degree of dynamical heterogeneity are temperature dependent. Here we report the first simulations based on an atomistic model of OTP that reach equilibrium at temperatures well into the supercooled regime. We first show that the results of these simulations are in reasonable quantitative agreement with experimental data for several basic properties over a wide range of temperatures. We then focus on rotational relaxation, finding nearly exponential behavior at high temperatures with clearly increasing deviations as temperature is lowered. The much weaker temperature dependence observed in light-scattering experiments also emerges from the same simulation data when we calculate correlation functions similar to those probed experimentally; this highlights the diversity of temperature dependencies that can be obtained with different probes. Further analysis suggests that the temperature insensitivity observed in the light-scattering experiments stems from the dependence of these measurements on internal as well as rotational molecular motion. Within the temperature range of our OTP simulations, our results strongly suggest that

  17. Direct numerical simulation of transitional flow in a staggered tube bundle

    Science.gov (United States)

    Linton, D.; Thornber, B.

    2016-02-01

    A series of Direct Numerical Simulations (DNS) of the flow through a staggered tube bundle has been performed over the range 1030 ≤ Rem ≤ 5572 to capture the flow transition that occurs at the matrix transition point of Rem ≈ 3000. The matrix transition is the point at which a second frequency becomes prominent in tube bundles. To date, this is the highest published Reynolds number at which a DNS has been performed on cross-flow over a tube bundle. This study describes the flow behaviour in terms of: the mean flow field, Strouhal numbers, vortex shedding, 3-D flow features, and turbulence properties. These results support the hypothesis that the transition in the vortex shedding behaviour at Rem ≈ 3000 is similar to that which occurs in single cylinder flow at the equivalent Reynolds number. The visualisations presented also demonstrate the nature of the shedding mechanisms before and after the matrix transition point.

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

    Science.gov (United States)

    Sen, Fatih Gurcag

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

  19. 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. PMID:19824035

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

    OpenAIRE

    NEOPHYTOU, Neophytos; Paul, Abhijeet; Lundstrom, Mark S.; Klimeck, Gerhard

    2007-01-01

    As device sizes shrink towards the nanoscale, CMOS development investigates alternative structures and devices. Existing CMOS devices will evolve from planar to 3D non-planar devices at nanometer sizes. These devices will operate under strong confinement and strain, regimes where atomistic effects are important. This work investigates atomistic effects in the transport properties of nanowire devices by using a nearest-neighbor tight binding model (sp3s*d5-SO) for electronic structure calculat...

  1. 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.

  2. 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.

  3. Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

    Science.gov (United States)

    Pan, Xiaoliang; Schwartz, Steven

    2015-03-01

    It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

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

    International Nuclear Information System (INIS)

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

  5. The concept of double bundle ACL simulation with a single bundle patellar tendon graft. A cadaveric feasibility study

    OpenAIRE

    Jacobi Matthias; Magnussen Robert A; Villa Vincent; Demey Guillaume; Neyret Philippe

    2012-01-01

    Abstract Background There is significant interest in the restoration of the double-bundle anatomy of the native ACL when performing ACL reconstruction. Possible techniques include those utilizing two separate grafts with independent tunnels and those that attempt to mimic this anatomy with a single graft and fewer tunnels. Many of the latter techniques require specific instrumentation and are technically challenging. We demonstrate that the double-bundle anatomy of the native ACL can theoreti...

  6. 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

  7. Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension.

    Science.gov (United States)

    Muddana, Hari S; Gullapalli, Ramachandra R; Manias, Evangelos; Butler, Peter J

    2011-01-28

    Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from -2.6 mN m(-1) to 15.9 mN m(-1). Simulations showed that the bilayer thickness decreased linearly with tension consistent with volume-incompressibility, and this thinning was facilitated by a significant increase in acyl chain interdigitation at the bilayer midplane and spreading of the acyl chains. Tension caused a significant drop in the bilayer's peak electrostatic potential, which correlated with the strong reordering of water and lipid dipoles. For the low tension regime, the DPPC lateral diffusion coefficient increased with increasing tension in accordance with free-area theory. For larger tensions, free area theory broke down due to tension-induced changes in molecular shape and friction. Simulated DiI rotational and lateral diffusion coefficients were lower than those of DPPC but increased with tension in a manner similar to DPPC. Direct correlation of membrane order and viscosity near the DiI chromophore, which was just under the DPPC headgroup, indicated that measured DiI fluorescence lifetime, which is reported to decrease with decreasing lipid order, is likely to be a good reporter of tension-induced decreases in lipid headgroup viscosity. Together, these results offer new molecular-level insights into membrane tension-related mechanotransduction and into the utility of DiI in characterizing tension-induced changes in lipid packing. PMID:21152516

  8. 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.

  9. Numerical simulation of the flow in a tight lattice SFR rod-bundle with grid spacers

    International Nuclear Information System (INIS)

    The accurate prediction of the flow in rod bundles is crucial for both the design and the safe operation of nuclear reactor systems. However the geometry complexity and the non-uniformity of the flow introduce peculiar features that can be reproduced only with three-dimensional CFD. In fact, even in bare rod bundles, i.e., bundles that do not contain any spacing device, the structure of the flow is inherently complex, due to the presence of a large-scale instability. Moreover, experimental analysis has clearly shown that when reducing the pitch-to-diameter ratio (P/D) the turbulence field in rod bundles deviates significantly from that in a circular tube. For extremely tight configurations the existence of large-scale coherent structures has been shown, which is responsible for the high inter-sub-channel heat and momentum exchange. While there is a fairly extensive literature on the presence of these structures in bare rod-bundles and simplified geometries, there are no available studies of their presence in geometry containing grid spacers or wires. A series of fully transient simulations of turbulence have been performed for an infinite tight triangular lattice (typical of current SFR designs) with and without a grid spacer. The simulations have been performed using Large Eddy Simulation (LES) with the spectral element code Nek5000 and unsteady Reynolds Averaged Navier-Stokes (URANS) for P/D=1.08. Several structure recognition techniques and statistical methods have been applied in order to investigate the flow field and the three-dimensional pattern of the coherent structures. The results prove that, for the configuration studied, coherent structures are indeed present and contribute significantly to the flow dynamics. (author)

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2014-02-21

    One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level. PMID:24559357

  12. 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

  13. Numerical simulation of supercritical water flow and heat transfer in 4-rod bundle

    International Nuclear Information System (INIS)

    The investigation on the thermal-hydraulic behavior in SCWR fuel bundles is a very significant content of SCWR research. However, there is still a lack of understanding to predict the flow heat transfer behavior of supercritical fluid. In this paper, the heat transfer behavior of supercritical fluid in 4-rod bundle with spacer was numerically simulated. The effect of grid structure on the flow and heat transfer was discussed particularly. The numerical simulation using the SSG turbulent model gives a reasonable prediction compared with the experimental results. The calculation results show that the spacer significantly changes the velocity profile in the downstream, and enhances turbulent mixing and heat transfer. Consequently, the rod wall temperature appears more uniform in the circumferential direction and the peak wall temperature spot also shifts. (authors)

  14. Development of neural network simulating power distribution of a BWR fuel bundle

    International Nuclear Information System (INIS)

    A neural network model is developed to simulate the precise nuclear physics analysis program code for quick scoping survey calculations. The relation between enrichment and local power distribution of BWR fuel bundles was learned using two layers neural network (ENET). A new model is to introduce burnable neutron absorber (Gadolinia), added to several fuel rods to decrease initial reactivity of fresh bundle. The 2nd stages three layers neural network (GNET) is added on the 1st stage network ENET. GNET studies the local distribution difference caused by Gadolinia. Using this method, it becomes possible to survey of the gradients of sigmoid functions and back propagation constants with reasonable time. Using 99 learning patterns of zero burnup, good error convergence curve is obtained after many trials. This neural network model is able to simulate no learned cases fairly as well as the learned cases. Computer time of this neural network model is about 100 times faster than a precise analysis model. (author)

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

    International Nuclear Information System (INIS)

    suggest several improvements to these methods. We used atomistic simulation to calculate the mixing enthalpy along two solid solutions binaries of interest in low-temperature petrology. Results are in agreement with observations in natural systems and confirm the importance of hydration in clay minerals stability. (author)

  16. Atomistic Simulations of Mass and Thermal Transport in Oxide Nuclear Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Anders D. [Los Alamos National Laboratory; Uberuaga, Blas P. [Los Alamos National Laboratory; Du, Shiyu [Los Alamos National Laboratory; Liu, Xiang-Yang [Los Alamos National Laboratory; Nerikar, Pankaj [IBM; Stanek, Christopher R. [Los Alamos National Laboratory; Tonks, Michael [Idaho National Laboratory; Millet, Paul [Idaho National Laboratory; Biner, Bulent [Idaho National Laboratory

    2012-06-04

    boundaries derived from separate atomistic calculations, we simulate Xe redistribution for a few simple microstructures using finite element methods (FEM), as implemented in the MOOSE framework from Idaho National Laboratory. Thermal transport together with the power distribution determines the temperature distribution in the fuel rod and it is thus one of the most influential properties on nuclear fuel performance. The fuel thermal conductivity changes as function of time due to microstructure evolution (e.g. fission gas redistribution) and compositional changes. Using molecular dynamics simulations we have studied the impact of different types of grain boundaries and fission gas bubbles on UO{sub 2} thermal conductivity.

  17. Propagation velocity profile in a cross-section of a cardiac muscle bundle from PSpice simulation

    Directory of Open Access Journals (Sweden)

    Sperelakis Nicholas

    2006-08-01

    Full Text Available Abstract Background The effect of depth on propagation velocity within a bundle of cardiac muscle fibers is likely to be an important factor in the genesis of some heart arrhythmias. Model and methods The velocity profile of simulated action potentials propagated down a bundle of parallel cardiac muscle fibers was examined in a cross-section of the bundle using a PSpice model. The model (20 × 10 consisted of 20 chains in parallel, each chain being 10 cells in length. All 20 chains were stimulated simultaneously at the left end of the bundle using rectangular current pulses (0.25 nA, 0.25 ms duration applied intracellularly. The simulated bundle was symmetrical at the top and bottom (including two grounds, and voltage markers were placed intracellularly only in cells 1, 5 and 10 of each chain to limit the total number of traces to 60. All electrical parameters were standard values; the variables were (1 the number of longitudinal gap-junction (G-j channels (0, 1, 10, 100, (2 the longitudinal resistance between the parallel chains (Rol2 (reflecting the closeness of the packing of the chains, and (3 the bundle termination resistance at the two ends of the bundle (RBT. The standard values for Rol2 and RBT were 200 KΩ. Results The velocity profile was bell-shaped when there was 0 or only 1 gj-channel. With standard Rol2 and RBT values, the velocity at the surface of the bundle (θ1 and θ20 was more than double (2.15 × that at the core of the bundle (θ10, θ11. This surface:core ratio of velocities was dependent on the values of Rol2 and RBT. When Rol2 was lowered 10-fold, θ1 increased slightly and θ2decreased slightly. When there were 100 gj-channels, the velocity profile was flat, i.e. the velocity at the core was about the same as that at the surface. Both velocities were more than 10-fold higher than in the absence of gj-channels. Varying Rol2 and RBT had almost no effect. When there were 10 gj-channels, the cross-sectional velocity profile

  18. CFD simulations on two-phase distribution in rod bundles with grid spacers

    International Nuclear Information System (INIS)

    Considering the bubble coalescence and break-up, the CFD simulations for air/water two-phase flow in 3 × 3 rod bundles with grid spacers have been performed with MUSIG model. The simulation is sensitive with the bubble diameter size but not with the inlet void fraction. The small diameter bubbles are the main effect of void fraction distribution nearby the downstream of the space grid, while the large diameter bubbles are main effect of void fraction distribution at the farther downstream of the space grid. Considering the effect of inlet air-water flow quality, geometry and pressure on bubble max diameter, this paper gives a relation for simulating the bubble with maximum diameter based on which is dealt with numerical simulation for rod bundles with grid spacers is set, and the advice of simulation method and model setting is given. The calculation results show that the shape and peak of void fraction distribution accord well with the experiment, and this simulation method can predict rationally the distribution of two phase flow in complicated channels. (authors)

  19. Automated Algorithms for Quantum-Level Accuracy in Atomistic Simulations: LDRD Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Aidan P.; Schultz, Peter A.; Crozier, Paul; Moore, Stan Gerald; Swiler, Laura Painton; Stephens, John Adam; Trott, Christian Robert; Foiles, Stephen M.; Tucker, Garritt J. (Drexel University)

    2014-09-01

    This report summarizes the result of LDRD project 12-0395, titled %22Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations.%22 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

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

    CERN Document Server

    Cashman, Derek J; Bhatt, Divesh; Zuckerman, Daniel M

    2009-01-01

    The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale interdomain movements that contribute to the receptor's mechanism of action, as well as smaller scale motions, using two different computational methods. We employ extremely fast, "semi-atomistic" Library-Based Monte Carlo (LBMC) simulations, which include all backbone atoms but "implicit" side chains. Our results were compared with previous experiments and an all-atom Langevin dynamics simulation. Both LBMC and Langevin dynamics simulations were performed using both the apo and glucose-bound form of the protein, with LBMC exhibiting significantly larger fluctuations. The LBMC simulations are also in general agreement with the disulfide trapping experiments of Careaga & Falke (JMB, 1992; Biophys. J., 1992), which indicate that distant residues in the crystal structure (i...

  1. Atomistic Simulation of shock induced dislocation dynamics and evolution of different plasticity mechanisms in Single Crystal Copper

    Science.gov (United States)

    Neogi, Anupam; Mitra, Nilanjan

    Deformation and observation of different types of plasticity mechanisms of FCC metals (e.g. Copper) under shock loading of various intensities has been investigated by several groups of researchers around the globe through different types of experiments and/or atomistic simulations. However, there still exists lacuna in this well researched area. In this study the temporal details of dislocation dynamics are provided. Simulations also demonstrate different types of temporal evolution of different loops observed for single crystal Cu under different intensities of shock loading. Observance of formation of twins and their temporal evolution at higher intensities of shock loading are also demonstrated as part of this study. Comparisons of these NEMD simulations using EAM potential are discussed with regards to different experimental and simulation studies in literature.

  2. Simulation of cross-flow-induced vibration of tube bundle by surface vorticity method

    Institute of Scientific and Technical Information of China (English)

    Fenghao WANG; Gedong JIANG; Jong Zhang Lin

    2008-01-01

    A fluid-structure interaction model based on Surface Vorticity Method (SVM) was used to study flow-induced vibrations of tube bundles in medium space ratio. The flow-induced vibrations of four tubes in a rotated square and a staggered tube bundle in three-row and five-column arrangements were simulated in the high sub-critical Reynolds number (Re) range. The results on fluid forces, tube responses and vorticity maps were pre-sented. The vorticity maps of the four rotated-square tubes changed dramatically when the rigid tubes were replaced by the flexible tubes. From the vorticity maps and vibration responses of the staggered tube bundle of different structural parameters, it was found that with the decrease of tube natural frequency, the maximal vibration response moved from the third row to the first. The results also showed that when more flexible tubes are used, the flow pattern changed drastically and the fluid-structure interaction imposed a dominant impact on the flow.

  3. Large eddy simulation of cross flow over in line and staggered tube bundles

    International Nuclear Information System (INIS)

    This paper investigates numerically the turbulent flow characteristics in two tube bundle arrangements. More specifically, the steady approaching cross-flow over an in-line tube bundle at Regap = 3,400 is studied with the Large Eddy Simulation (LES) technique using both the standard Smagorinsky model and a dynamic model without test filtering. The second arrangement is that of a staggered tube bundle at Regap = 8,600 which is also studied using the standard Smagorinsky model. The LES results for the mean velocity compare favourably with the LDA measurements of Konstantinidis et al (2000) for the in-line tube array. However, the predicted stream-wise r.m.s velocity increases faster along the stream-wise direction in the flow lane region compared to the experiments. A single mode of alternate vortex shedding with a constant Strouhal number (0.145) is predicted. The LES calculation of the turbulent cross-flow over the staggered tube array gives excellent agreement with the experiments of Balabani and Yianneskis (1996). Two distinct vortex shedding Strouhal numbers (0.37 and 0.49, St = f D/ubulk) are found behind the first row and the second row in agreement with Weaver et al (1993). The size of the recirculation bubble zones is also correctly predicted. The stream-wise r.m.s velocity in the downstream region is more accurately predicted compared to the in-line arrangement due to smaller dependence on the inlet turbulence level. (authors)

  4. Spectral element code development for incompressible flow simulations In the subchannel of a fuel rod bundle

    International Nuclear Information System (INIS)

    Two decades ago spectral element methods were developed in order to unite the the geometrical flexibility of finite element methods and the spectral convergence property of spectral methods. A code based on spectral element methods is a promising candidate to simulate turbulent incompressible fluid flow in arbitrary geometry. The aim of this work is to develop an accurate Navier-Stokes solver which is capable of simulate turbulent incompressible fluid flow in an arbitrary complex geometry. We present the concept of the spectral element methods and the algorithm used to solve Navier-Stokes equations. The design and implementation issues of a parallel spectral element code able to simulate fluid flows in arbitrary geometry are also discussed. Some preliminary results of flow simulations of in a subchannel of fuel rod bundle are presented (Authors)

  5. Simulation of propagation in a bundle of skeletal muscle fibers: Modulation effects of passive fibers

    DEFF Research Database (Denmark)

    Henneberg, Kaj-åge; F.A., Roberge

    1997-01-01

    Computer simulations are used to study passive fiber modulation of propagation in a tightly packed bundle of frog skeletal muscle fibers (uniform fiber radius of 50 mu m). With T = 20 degrees C and a uniform nominal interstitial cleft width (d) over bar = 0.35 mu m, about 92% of the active fiber...... rate of rise of the action potential upstroke (V-max) from 512 to 503 V/s. Increasing the phase angle of the passive fiber membrane impedence (Z(m)) increases the phase delay between I-ma and I-ep, thereby increasing phi(epp) which in turn slows down propagation and increases V-max....

  6. 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

  7. Large Scale 3-D Dislocation Dynamics and Atomistic Simulations of Flow and Strain-Hardening Behavior of Metallic Micropillars

    Science.gov (United States)

    Rao, Satish

    2015-03-01

    Experimental studies show strong strengthening effects for micrometer-scale FCC as well as two-phase superalloy crystals, even at high initial dislocation densities. This talk shows results from large-scale 3-D discrete dislocation simulations (DDS) used to explicitly model the deformation behavior of FCC Ni (flow stress and strain-hardening) as well as superalloy microcrystals for diameters ranging from 1 - 20 microns. The work shows that two size-sensitive athermal hardening processes, beyond forest and precipitation hardening, are sufficient to develop the dimensional scaling of the flow stress, stochastic stress variation, flow intermittency and, high initial strain-hardening rates, similar to experimental observations for various materials. In addition, 3D dislocation dynamics simulations are used to investigate strain-hardening characteristics and dislocation microstructure evolution with strain in large 20 micron size Ni microcrystals (bulk-like) under three different loading axes: 111, 001 and 110. Three different multi-slip loading axes, , and , are explored for shear strains of ~0.03 and final dislocation densities of ~1013/m2. The orientation dependence of initial strain hardening rates and dislocation microstructure evolution with strain are discussed. The simulated strain hardening results are compared with experimental data under similar loading conditions from bulk single-crystal Ni. Finally, atomistic simulation results on the operation of single arm sources in Ni bipillars with a large angle grain boundary is discussed. The atomistic simulation results are compared with experimental mechanical behavior data on Cu bipillars with a similar large angle grain boundary. This work was supported by AFOSR (Dr. David Stargel), and by a grant of computer time from the DOD High Performance Computing Modernization Program, at the Aeronautical Systems Center/Major Shared Resource Center.

  8. A hybrid molecular dynamics/atomic-scale finite element method for quasi-static atomistic simulations at finite temperature

    CERN Document Server

    Xu, Ran

    2013-01-01

    In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some temperature effects are embedded in static AFEM simulation by applying the virtual and equivalent thermal disturbance forces extracted from MD. Alternatively performing MD and AFEM can quickly obtain a series of thermodynamic equilibrium configurations such that a quasi-static process is modeled. Moreover, a stirring-accelerated MD/AFEM fast relaxation approach is proposed, in which the atomic forces and velocities are randomly exchanged to artificially accelerate the "slow processes" such as mechanical wave propagation and thermal diffusion. The efficiency of the proposed methods is demonstrated by numerical examples on single wall carbon nanotubes.

  9. 3 × 3 rod bundle investigations, CFD single-phase numerical simulations

    International Nuclear Information System (INIS)

    Highlights: • CFD simulations of the flow around a 3 × 3 rod bundle were conducted. • Single-phase calculations performed as pre-investigation of future boiling applications. • The influence of the geometry details (inlet vessel, grid spacers) was investigated. • Turbulent patterns of these flows were analyzed (secondary flows, vortices, flow asymmetries). - Abstract: The work here presented has been performed in the framework of a research project aimed to investigate two-phase (boiling) flows in pressurized water reactors (PWR). CFD investigations of a rod bundle have been conducted while a new experimental facility (ROFEX) was constructed in Helmholtz Zentrum Dresden-Rossendorf (HZDR) for the generation of quality validation data. The apparatus consists of a 3 × 3 rod bundle inside a Plexiglas vertical pipe. The results summarized in this paper are considered as a pre-investigation, being the final goal to be able to predict accurately boiling water flows under high pressure around rods. For this purpose, three steps were defined: analysis of single-phase flows in such geometry, analysis of the multiphase flow when using a refrigerant as a working fluid and, finally, the analysis of a multiphase flow using water. The single-phase approach allows gaining experience regarding the turbulence behaviour of the flow, while the multiphase investigation of the refrigerant simplifies the experimental conditions since it is possible to get boiling situations at lower pressure level. At the moment of writing this paper, the authors were focused on the first step (single-phase flows at low pressure), since this not only made possible to better understand the turbulence in that geometry, but it also resulted in valuable feedback to the experimentalists on improving the construction of the facility. In parallel, HZDR researchers have been developing a new tomography measurement technique to measure gas content in multiphase flows

  10. 3 × 3 rod bundle investigations, CFD single-phase numerical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Lifante, C., E-mail: Conxita.Lifante@ansys.com [ANSYS Germany GmbH, Staudenfeldweg 12, Otterfing D-83624 (Germany); Krull, B., E-mail: Benjamin.Krull@ansys.com [ANSYS Germany GmbH, Staudenfeldweg 12, Otterfing D-83624 (Germany); Frank, Th., E-mail: Thomas.Frank@ansys.com [ANSYS Germany GmbH, Staudenfeldweg 12, Otterfing D-83624 (Germany); Franz, R., E-mail: r.franz@hzdr.de [Experimentelle Thermofluiddynamik, Helmholtz Zentrum Dresden-Rossendorf, POB 510 119, Dresden D-01314 (Germany); Hampel, U., E-mail: u.hampel@hzdr.de [Experimentelle Thermofluiddynamik, Helmholtz Zentrum Dresden-Rossendorf, POB 510 119, Dresden D-01314 (Germany)

    2014-11-15

    Highlights: • CFD simulations of the flow around a 3 × 3 rod bundle were conducted. • Single-phase calculations performed as pre-investigation of future boiling applications. • The influence of the geometry details (inlet vessel, grid spacers) was investigated. • Turbulent patterns of these flows were analyzed (secondary flows, vortices, flow asymmetries). - Abstract: The work here presented has been performed in the framework of a research project aimed to investigate two-phase (boiling) flows in pressurized water reactors (PWR). CFD investigations of a rod bundle have been conducted while a new experimental facility (ROFEX) was constructed in Helmholtz Zentrum Dresden-Rossendorf (HZDR) for the generation of quality validation data. The apparatus consists of a 3 × 3 rod bundle inside a Plexiglas vertical pipe. The results summarized in this paper are considered as a pre-investigation, being the final goal to be able to predict accurately boiling water flows under high pressure around rods. For this purpose, three steps were defined: analysis of single-phase flows in such geometry, analysis of the multiphase flow when using a refrigerant as a working fluid and, finally, the analysis of a multiphase flow using water. The single-phase approach allows gaining experience regarding the turbulence behaviour of the flow, while the multiphase investigation of the refrigerant simplifies the experimental conditions since it is possible to get boiling situations at lower pressure level. At the moment of writing this paper, the authors were focused on the first step (single-phase flows at low pressure), since this not only made possible to better understand the turbulence in that geometry, but it also resulted in valuable feedback to the experimentalists on improving the construction of the facility. In parallel, HZDR researchers have been developing a new tomography measurement technique to measure gas content in multiphase flows.

  11. Numerical visualization of boiling two-phase flow behavior in fuel bundles at simulated earthquake condition

    International Nuclear Information System (INIS)

    In order to evaluate an influence of earthquake acceleration to the boiling two-phase flow behavior in nuclear reactors, numerical simulations were performed under the simulated earthquake condition. The two-phase flow analysis code, ACE-3D, was modified as the influence of the earth quake acceleration can calculate. To check out if the modification is adequate, a series of calculations were carried out and the following summaries were derived; 1) the void fraction in the fuel bundle receives the influence of the earthquake, 2) the liquid-phase in the two-phase flow moves in the same direction as the direction of oscillation due to the inputted earthquake acceleration, and 3) due to the density difference in comparison with the liquid phase, the gas phase of that moves in the direction opposite to the oscillating direction. This study enabled visualized evaluation of the boiling two-phase flow behavior in the nuclear reactors at the earthquake condition. (author)

  12. 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.

  13. Numerical method for simulation of fluid flow and heat transfer in geometrically disturbed rod bundles

    International Nuclear Information System (INIS)

    This paper describes briefly the computational algorithm that includes procedures to obtain finite-difference form of governing convection-diffusion equations, to generate an orthogonal mesh system for complex regions and to solve the finite-difference equation system, and several results of numerical simulation in comparison with experiment. The Reynolds and energy conservation equations for steady-state fully developed turbulent incompressible flows are discretized by the Efficient Finite Difference (EFD) scheme. Here secondary flow components are neglected. In the averaged energy conservation equation, anisotropic turbulent conductivity coefficients are employed based on the axial velocity distribution. An orthogonal mesh generation system has been developed that allows us to model the rod bundle geometry by assembling elementary mesh components generated for every typical sub-domain inside the flow channels. This procedure has been made efficient with a help of object-oriented programming techniques. By solving the derived equations on the boundary-fitted coordinates, good comparisons between calculation and measurement are presented in general for detailed distributions of the local shear stress, axial velocity and wall temperature in a hexagonal rod bundle in the presence of a dislocated rod. Discussion is also made on a discrepancy of the calculated wall shear stress from the experimental data near the narrowest gap position in this 'geometrically disturbed' region. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Judith C. [University of Pittsburgh

    2015-01-09

    The purpose of this grant is to develop the multi-scale theoretical methods to describe the nanoscale oxidation of metal thin films, as the PI (Yang) extensive previous experience in the experimental elucidation of the initial stages of Cu oxidation by primarily in situ transmission electron microscopy methods. Through the use and development of computational tools at varying length (and time) scales, from atomistic quantum mechanical calculation, force field mesoscale simulations, to large scale Kinetic Monte Carlo (KMC) modeling, the fundamental underpinings of the initial stages of Cu oxidation have been elucidated. The development of computational modeling tools allows for accelerated materials discovery. The theoretical tools developed from this program impact a wide range of technologies that depend on surface reactions, including corrosion, catalysis, and nanomaterials fabrication.

  15. Particle-based simulation of melt freezing behavior in pin bundle

    International Nuclear Information System (INIS)

    Relocation and freezing of disrupted core materials are among the important thermal-hydraulic phenomena in core disruptive accidents of a liquid-metal-cooled reactor. In the present study, fully Lagrangian CFD simulations were performed to understand local meso-scale freezing and penetration behavior of melt flowing into narrow channel geometry. An available series of fundamental experiments for melt freezing behavior was analyzed by a 3D particle-based simulation code using the finite volume particle (FVP) method. In the experiments, simulant melts of molten metal and its mixture with solid particles have been injected into a seven-pin bundle made of stainless steel. The simulation results were compared with the observed characteristics of melt penetration and freezing, which arc represented by penetration length as well as geometrical shape of the frozen melt forming blockage due to adhesion on pin surface. The present particle-based simulation based on the FVP method demonstrates practical applicability of its methodology to clarify of local melt relocation and freezing behavior in narrow flow channels. (author)

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

    Directory of Open Access Journals (Sweden)

    Giuseppina Raffaini

    2015-12-01

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

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

    Science.gov (United States)

    Raffaini, Giuseppina; Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

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

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

    Science.gov (United States)

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

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

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

    Science.gov (United States)

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

    2010-07-15

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

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

    CERN Document Server

    Fyta, Maria; Kaxiras, Efthimios; Succi, Sauro

    2007-01-01

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

  1. Modeling of Temperature Dependence of Magnetization in TbFe Films — An Atomistic Spin Simulation Study

    Science.gov (United States)

    Jiao, Xiankai; Zhang, Zongzhi; Liu, Yaowen

    2016-04-01

    In this paper, we performed spin simulations at atomistic level to study the temperature dependent properties of perpendicularly magnetized TbFe thin films. The crystallographically amorphous feature of TbFe ferrimagnetic alloys is modeled by using a lattice system with disordered site occupation of rare earth (RE) and transition metal (TM) spins. The simulated Curie temperature (TC) is consistent well with the mean-field approximation theory. With the increase of Tb concentration, the TC decreases almost linearly, whereas the magnetization compensation temperature (TM) increases gradually until the TC value is reached. The inter-sublattice exchange coupling strength JTM-RE between the RE and TM atoms can significantly affect TM, but has less impact on TC. With the increase of Tb concentration, the TbFe sample of high JTM-RE exhibits a much faster increase in TM than the sample with low JTM-RE. Moreover, we have tested the simulation code to model the laser pulse induced ultrafast nonequilibrium spin dynamics. As an example, the femto-second pulse laser induced demagnetization and recovery process is clearly reproduced. These features are in a good agreement with the experiments, indicating that the simulation model can capture the basic physics in describing the high temperature dependent magnetic property as well as the ultrafast spin dynamics.

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

    International Nuclear Information System (INIS)

    We report a Monte Carlo simulation study of the molten Fe-C-S system with the aim of developing a theoretical understanding of the influence of sulphur during decarburization reactions in Fe-C alloys. Focussing specifically on the role played by free surfaces, computer simulations were based on the hexagonal atomistic model of Fe-C-S system using isotropic atomic interaction parameters; free surfaces were characterized by a missing layer of atoms. Three geometrical configurations, namely a liquid bath, a prismatic block and a spherical droplet, were investigated. Simulations were carried out as a function of melt carbon and sulphur concentration, temperatures and surface/volume ratios of the simulation cell. Sulphur atoms were found to preferentially concentrate in the top few layers, with the second layer showing the highest amounts of sulphur; very little sulphur was observed in the bulk liquid. This trend was observed in all three simulation configurations over a wide carbon/sulphur concentration range and temperatures. Significant levels of iron were observed in the top surface layer. The influence of free surfaces on atomic concentration profiles was found to be a strong function of the surface/volume ratio. The surface segregation of S was more pronounced for small exposed surfaces and was much smaller for liquids with large exposed surfaces. The presence of surface-active sulphur resulted in a major re-distribution of carbon. Carbon tended to concentrate deeper in the bulk, with the surface region being severely depleted of carbon. In addition to several new findings and a better understanding of liquid surfaces, these simulations have helped overcome major limitations of Sain and Belton's model. Key experimental results on decarburization have been explained within the framework of our simulations. These simulation results have significant implications for surface decarburization reactions and carbon-boil phenomena in smelting technologies.

  3. 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.

  4. Insights on the atomistic origin of X and W photoluminescence lines in c-Si from ab initio simulations

    International Nuclear Information System (INIS)

    We have used atomistic simulations to identify and characterize interstitial defect cluster configurations candidate for W and X photoluminescence centers in crystalline Si. The configurational landscape of small self-interstitial defect clusters has been explored through nanosecond annealing and implantation recoil simulations using classical molecular dynamics. Among the large collection of defect configurations obtained, we have selected those defects with the trigonal symmetry of the W center, and the tetrahedral and tetragonal symmetry of the X center. These defect configurations have been characterized using ab initio simulations in terms of their donor levels, their local vibrational modes, the defect induced modifications of the electronic band structure, and the transition amplitudes at band edges. We have found that the so-called I 3-V is the most likely candidate for the W PL center. It has a donor level and local vibrational modes in better agreement with experiments, a lower formation energy, and stronger transition amplitudes than the so-called I 3-I, which was previously proposed as the W center. With respect to defect candidates for the X PL center, our calculations have shown that none of the analyzed defect candidates match all of the experimental characteristics of the X center. Although the Arai tetra-interstitial configuration previously proposed as the X center cannot be excluded, the other defect candidates for the X center found, I 3-C and I 3-X, cannot be discarded either. (paper)

  5. Room Temperature Deformation Mechanisms of Alumina Particles Observed from In Situ Micro-compression and Atomistic Simulations

    Science.gov (United States)

    Sarobol, Pylin; Chandross, Michael; Carroll, Jay D.; Mook, William M.; Bufford, Daniel C.; Boyce, Brad L.; Hattar, Khalid; Kotula, Paul G.; Hall, Aaron C.

    2016-01-01

    Aerosol deposition (AD) is a solid-state deposition technology that has been developed to fabricate ceramic coatings nominally at room temperature. Sub-micron ceramic particles accelerated by pressurized gas impact, deform, and consolidate on substrates under vacuum. Ceramic particle consolidation in AD coatings is highly dependent on particle deformation and bonding; these behaviors are not well understood. In this work, atomistic simulations and in situ micro-compressions in the scanning electron microscope, and the transmission electron microscope (TEM) were utilized to investigate fundamental mechanisms responsible for plastic deformation/fracture of particles under applied compression. Results showed that highly defective micron-sized alumina particles, initially containing numerous dislocations or a grain boundary, exhibited no observable shape change before fracture/fragmentation. Simulations and experimental results indicated that particles containing a grain boundary only accommodate low strain energy per unit volume before crack nucleation and propagation. In contrast, nearly defect-free, sub-micron, single crystal alumina particles exhibited plastic deformation and fracture without fragmentation. Dislocation nucleation/motion, significant plastic deformation, and shape change were observed. Simulation and TEM in situ micro-compression results indicated that nearly defect-free particles accommodate high strain energy per unit volume associated with dislocation plasticity before fracture. The identified deformation mechanisms provide insight into feedstock design for AD.

  6. Bundled procurement

    OpenAIRE

    Chen, Yongmin; Li, Jianpei

    2015-01-01

    When procuring multiple products from competing firms, a buyer may choose separate purchase, pure bundling, or mixed bundling. We show that pure bundling will generate higher buyer surplus than both separate purchase and mixed bundling, provided that trade for each good is likely to be efficient. Pure bundling is superior because it intensifies the competition between firms by reducing their cost asymmetry. Mixed bundling is inferior because it allows firms to coordinate to ...

  7. Atomistic Origin of Brittle Failure of Boron Carbide from Large-Scale Reactive Dynamics Simulations: Suggestions toward Improved Ductility

    Science.gov (United States)

    An, Qi; Goddard, William A.

    2015-09-01

    Ceramics are strong, but their low fracture toughness prevents extended engineering applications. In particular, boron carbide (B4C ), the third hardest material in nature, has not been incorporated into many commercial applications because it exhibits anomalous failure when subjected to hypervelocity impact. To determine the atomistic origin of this brittle failure, we performed large-scale (˜200 000 atoms /cell ) reactive-molecular-dynamics simulations of shear deformations of B4C , using the quantum-mechanics-derived reactive force field simulation. We examined the (0001 )/⟨10 1 ¯ 0 ⟩ slip system related to deformation twinning and the (01 1 ¯ 1 ¯ )/⟨1 ¯ 101 ⟩ slip system related to amorphous band formation. We find that brittle failure in B4C arises from formation of higher density amorphous bands due to fracture of the icosahedra, a unique feature of these boron based materials. This leads to negative pressure and cavitation resulting in crack opening. Thus, to design ductile materials based on B4C we propose alloying aimed at promoting shear relaxation through intericosahedral slip that avoids icosahedral fracture.

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

    International Nuclear Information System (INIS)

    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

  9. Temperature escalation in PWR fuel rod simulator bundles due to the zircaloy/steam reaction: Test ESBU-1

    International Nuclear Information System (INIS)

    This report describes the test conduct and results of the bundle test ESBU-1. The test objective was the investigation of temperature escalation of zircaloy clad fuel rods. The investigation of the temperature escalation is part of a program of out-of-pile experiments, performed within the framework of the PNS Several Fuel Damage Program. The bundle was composed of a 3x3 array of fuel rod simulators surrounded by a zircaloy shroud which was insulated with a ZrO2 fiber ceramic wrap. The fuel rod simulators comprised a tungsten heater, UO2 annular pellets, and zircaloy cladding over a 0.4 m heated length. A steam flow of 1 g/s was inlet to the bundle. The most pronounced temperature escalation was found on the central rod. The initial heatup rate of 20C/s at 11000C increased to approximately 60C/s. The maximum temperature reached was 22500C. The following fast temperature decrease was caused by runoff of molten zircaloy. Molten zircaloy swept down the thin cladding oxide layer formed during heatup. The melt dissolved the surface of the UO2 pellets and refroze as a coherent lump in the lower part of the bundle. The remaining pellets fragmented during cooldown and formed a powdery layer on the refrozen lump. The lump was sectioned posttest at several elevations: Dissolution of UO2 by the molten zircaloy, interaction between the melt and previously oxidized zircaloy, and oxidation of the melt had occurred. (orig.)

  10. Nontrivial correlation length distinguishes melt from glass in a large-scale atomistic non-equilibrium simulation of a glass transition

    Science.gov (United States)

    Mandadapu, Kranthi; Hudson, Alexander; Chandler, David

    2015-03-01

    Dynamical facilitation theory predicts the emergence of a non-trivial correlation length from the cooling process that transforms the reversible melt to the irreversible glass. A decrease in cooling rate produces an increase in correlation length, and an increase in correlation length coincides with an increase in stability and aging rate of the glass. Here, we present results from a large-scale non-equilibrium numerical simulation that provide the first demonstration of the emergent nonequilbrium correlation length for an atomistic model. The study also tests the ability of the theory to predict the value of the nonequilibrium length and its corresponding glass transition temperature in terms of material properties and cooling protocols. Nontrivial correlation length distinguishes melt from glass in a large-scale atomistic non-equilibrium simulation of a glass transition

  11. Does Fe(2+) in olivine-based interstellar grains play any role in the formation of H2? Atomistic insights from DFT periodic simulations.

    Science.gov (United States)

    Navarro-Ruiz, J; Ugliengo, P; Sodupe, M; Rimola, A

    2016-05-25

    Using periodic DFT-D2 methods, atomistic simulations of interstellar H adsorption and H2 formation on a (010) Fe-containing olivine surface are presented. At variance with the (010) Mg2SiO4 surface and key to these processes are the large Fe/H interaction energies, suggesting that olivine surfaces are good reservoirs of H atoms for subsequent recombination to form H2. PMID:27103407

  12. 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.

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

    International Nuclear Information System (INIS)

    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

  14. Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains.

    Science.gov (United States)

    Chugunov, Anton O; Volynsky, Pavel E; Krylov, Nikolay A; Nolde, Dmitry E; Efremov, Roman G

    2016-01-01

    Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed "iris-like" symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity. PMID:27612191

  15. 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.

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

    Science.gov (United States)

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

    2016-05-01

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

  17. Cobra-IE Evaluation by Simulation of the NUPEC BWR Full-Size Fine-Mesh Bundle Test (BFBT)

    Energy Technology Data Exchange (ETDEWEB)

    Burns, C. J. and Aumiler, D. L.

    2006-04-26

    The COBRA-IE computer code is a thermal-hydraulic subchannel analysis program capable of simulating phenomena present in both PWRs and BWRs. As part of ongoing COBRA-IE assessment efforts, the code has been evaluated against experimental data from the NUPEC BWR Full-Size Fine-Mesh Bundle Tests (BFBT). The BFBT experiments utilized an 8 x 8 rod bundle to simulate BWR operating conditions and power profiles, providing an excellent database for investigation of the capabilities of the code. Benchmarks performed included steady-state and transient void distribution, single-phase and two-phase pressure drop, and steady-state and transient critical power measurements. COBRA-IE effectively captured the trends seen in the experimental data with acceptable prediction error. Future sensitivity studies are planned to investigate the effects of enabling and/or modifying optional code models dealing with void drift, turbulent mixing, rewetting, and CHF.

  18. Cobra-IE Evaluation by Simulation of the NUPEC BWR Full-Size Fine-Mesh Bundle Test (BFBT)

    International Nuclear Information System (INIS)

    The COBRA-IE computer code is a thermal-hydraulic subchannel analysis program capable of simulating phenomena present in both PWRs and BWRs. As part of ongoing COBRA-IE assessment efforts, the code has been evaluated against experimental data from the NUPEC BWR Full-Size Fine-Mesh Bundle Tests (BFBT). The BFBT experiments utilized an 8 x 8 rod bundle to simulate BWR operating conditions and power profiles, providing an excellent database for investigation of the capabilities of the code. Benchmarks performed included steady-state and transient void distribution, single-phase and two-phase pressure drop, and steady-state and transient critical power measurements. COBRA-IE effectively captured the trends seen in the experimental data with acceptable prediction error. Future sensitivity studies are planned to investigate the effects of enabling and/or modifying optional code models dealing with void drift, turbulent mixing, rewetting, and CHF

  19. Atomistic simulations of electrolyte solutions and hydrogels with explicit solvent models

    CERN Document Server

    Walter, Jonathan; Reiser, Steffen; Horsch, Martin; Vrabec, Jadran; Hasse, Hans

    2011-01-01

    Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the development and optimization of molecular force fields and models, a large number of simulation runs have to be evaluated to obtain the sensitivity of the target properties with respect to the model parameters. The present work discusses force field development for electrolytes regarding thermodynamic properties of their aqueous solutions. Furthermore, simulations are conducted for the volume transition of hydrogels in the presence of electrolytes. It is shown that the properties of these complex systems can be captured by molecular simulation.

  20. Atomistic simulations of the implantation of low energy boron and nitrogen ions into graphene

    OpenAIRE

    Åhlgren, E. H.; Kotakoski, J.; Krasheninnikov, A. V.

    2011-01-01

    By combining classical molecular dynamics simulations and density functional theory total energy calculations, we study the possibility of doping graphene with B/N atoms using low-energy ion irradiation. Our simulations show that the optimum irradiation energy is 50 eV with substitution probabilities of 55% for N and 40% for B. We further estimate probabilities for different defect configurations to appear under B/N ion irradiation. We analyze the processes responsible for defect production a...

  1. Atomistic simulation and virtual diffraction characterization of stable and metastable alumina surfaces

    International Nuclear Information System (INIS)

    The structures of select alumina surfaces are studied using molecular statics and molecular dynamics simulations and are characterized using virtual diffraction methods. First, bulk alumina simulations are performed to validate the transferability of the ReaxFF potential to model different alumina phases. Bulk alumina simulations accurately predict α-Al2O3 as the lowest energy crystalline phase; however, they unexpectedly predict an even lower-energy amorphous phase. At 0 K, virtual X-ray diffraction patterns of the bulk crystalline phases and select alumina surfaces are validated by experimental studies. Molecular statics simulations of select alumina surfaces are consistent with prior first-principles studies. However, molecular dynamics simulations show that many surfaces experience significant reconstructions at temperatures below what is expected from experiments. It is believed that premature surface reconstructions are biased by the predicted lower-energy amorphous phase and occur due to the extra degrees of freedom allowed by the free surfaces as well as the available thermal energy during dynamics. Discrete peaks appearing in virtual selected-area electron diffraction patterns indicate that the reconstructions are not fully amorphous due to lattice constraints imposed by the internal bulk structure. Bulk and surface energies are tabulated for each simulation to be used in future predictive mesoscale models of polymorphic alumina

  2. Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations.

    Science.gov (United States)

    Papachristos, Kostas; Muench, Stephen P; Paci, Emanuele

    2016-09-01

    Rotary ATPases are involved in numerous physiological processes, with the three distinct types (F/A/V-ATPases) sharing functional properties and structural features. The basic mechanism involves the counter rotation of two motors, a soluble ATP hydrolyzing/synthesizing domain and a membrane-embedded ion pump connected through a central rotor axle and a stator complex. Within the A/V-ATPase family conformational flexibility of the EG stators has been shown to accommodate catalytic cycling and is considered to be important to function. For the A-ATPase three EG structures have been reported, thought to represent conformational states of the stator during different stages of rotary catalysis. Here we use long, detailed atomistic simulations to show that those structures are conformers explored through thermal fluctuations, but do not represent highly populated states of the EG stator in solution. We show that the coiled coil tail domain has a high persistence length (∼100 nm), but retains the ability to adapt to different conformational states through the presence of two hinge regions. Moreover, the stator network of the related V-ATPase has been suggested to adapt to subunit interactions in the collar region in addition to the nucleotide occupancy of the catalytic domain. The MD simulations reported here, reinforce this observation showing that the EG stators have enough flexibility to adapt to significantly different structural re-arrangements and accommodate structural changes in the catalytic domain whilst resisting the large torque generated by catalytic cycling. These results are important to understand the role the stators play in the rotary-ATPase mechanism. Proteins 2016; 84:1203-1212. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:27177595

  3. Effects of alpha decays on nuclear waste glasses, simulation through atomistic models

    International Nuclear Information System (INIS)

    In a simplified (SiO2, B2O3, Na2O3, Al2O3, ZrO2) nuclear glass we have simulated, by Molecular Dynamics simulations, the effects of displacement cascades created by the slowing-down of the recoil nucleus. The methodology employed to construct and validate the used Molecular Dynamics model representing the basis matrix of the 'light-water' French nuclear glass (R77) and the manner which are simulated atomic displacements are described. Although the energies given to recoil nucleus were relatively low (≤ 1/10 of actual energies) the study has yielded a number of interesting results. Notably we have: - identified the main mechanisms responsible for the depolymerization of the network; - observed, at the atomic level, the kinetic of the structure evolution; - detailed the behavior and displacement mechanisms of every atomic species during the cascade sequences; - made a link with the experimentation through the calculation of some physical properties. (authors)

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

    DEFF Research Database (Denmark)

    Vegge, T.; Rasmussen, T.; Leffers, T.; Pedersen, O.B.; Jacobsen, K.W.

    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-band path technique. We find low barriers and effective masses for the conservative motion along the dislocations of elementary jogs on both ordinary {111}[110] and non-octahedral {110}[110] slip systems. The jogs are found to be constricted and therefore effectively act as pre-existing constrictions; the...

  5. Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential

    Science.gov (United States)

    Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

    2015-12-01

    To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are

  6. Numerical Simulation of Boiling Two-Phase Flow in Tight-Lattice Rod Bundle by 3-Dimensional Two-Fluid Model Code ACE-3D

    Science.gov (United States)

    Yoshida, Hiroyuki; Misawa, Takeharu; Takase, Kazuyuki

    Two-fluid model can simulate two-phase flow by computational cost less than detailed two-phase flow simulation method such as interface tracking method or particle interaction method. Therefore, two-fluid model is useful for thermal hydraulic analysis in large-scale domain such as a rod bundle. Japan Atomic Energy Agency (JAEA) develops three dimensional two-fluid model analysis code ACE-3D that adopts boundary fitted coordinate system in order to simulate complex shape flow channel. In this paper, boiling two-phase flow analysis in a tight-lattice rod bundle was performed by ACE-3D code. The parallel computation using 126 CPUs was applied to this analysis. In the results, the void fraction, which distributes in outermost region of rod bundle, is lower than that in center region of rod bundle. The tendency of void fraction distribution agreed with the measurement results by neutron radiography qualitatively. To evaluate effects of two-phase flow model used in ACE-3D code, numerical simulation of boiling two-phase in tight-lattice rod bundle with no lift force model was also performed. From the comparison of calculated results, it was concluded that the effects of lift force model were not so large for overall void fraction distribution of tight-lattice rod bundle. However, the lift force model is important for local void fraction distribution of fuel bundles.

  7. Numerical simulation of boiling two-phase flow in tight-lattice rod bundle by 3-dimensional two-fluid model code ACE-3D

    International Nuclear Information System (INIS)

    Two-fluid model can simulate two-phase flow by computational cost less than detailed two-phase flow simulation method such as interface tracking method or particle interaction method. Therefore, two-fluid model is useful for thermal hydraulic analysis in large-scale domain such as a rod bundle. Japan Atomic Energy Agency (JAEA) develops three dimensional two-fluid model analysis code ACE-3D that adopts boundary fitted coordinate system in order to simulate complex shape flow channel. In this paper, boiling two-phase flow analysis in a tight-lattice rod bundle was performed by ACE-3D code. The parallel computation using 126 CPUs was applied to this analysis. In the results, the void fraction, which distributes in outermost region of rod bundle, is lower than that in center region of rod bundle. The tendency of void fraction distribution agreed with the measurement results by neutron radiography qualitatively. To evaluate effects of two-phase flow model used in ACE-3D code, numerical simulation of boiling two-phase in tight-lattice rod bundle with no lift force model was also performed. From the comparison of calculated results, it was concluded that the effects of lift force model were not so large for overall void fraction distribution of tight-lattice rod bundle. However, the lift force model is important for local void fraction distribution of fuel bundles. (author)

  8. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

    Czech Academy of Sciences Publication Activity Database

    Krepl, Miroslav; Havrila, Marek; Stadlbauer, Petr; Banáš, P.; Otyepka, M.; Pasulka, J.; Stefl, R.; Šponer, Jiří

    2015-01-01

    Roč. 11, č. 3 (2015), s. 1220-1243. ISSN 1549-9618 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * PARTICLE MESH EWALD * MECHANICS FORCE-FIELDS Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014

  9. Atomistic Simulations of Fluid Flow through Graphene Channels and Carbon Nanotubes

    DEFF Research Database (Denmark)

    Zambrano, Harvey A.; Walther, Jens Honore; Oyarzua, Elton E.;

    2015-01-01

    fields, electro-osmosis and thermal gradients are evaluated. We conduct a detailed analysis of the transport efficiency of each system to impose similar volumetric flow rates. From the simulations, we extract density and velocity profiles to study the liquid structure, wall slippage and flow enhancement...

  10. Atomistic simulation of Cu-Ta thin film deposition and other phenomena

    NARCIS (Netherlands)

    Klaver, T.P.C.

    2004-01-01

    Tantalum (Ta) is a metal with good properties to act as a diffusion barrier material in computer chips, where it should prevent the mixing of Cu into Si and SiO. The deposition of thin Cu films onto various Ta substrates has been studied through molecular dynamics simulations, using either empirical

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

    Science.gov (United States)

    Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice; Tildesley, Dominic J

    2015-10-13

    The long-range correction to the surface tension can amount to up to 55% of the calculated value of the surface tension for cutoffs in the range of 2.1-6.4 σ. The calculation of the long-range corrections to the surface tension and to the configurational energy in two-phase systems remains an active area of research. In this work, we compare the long-range corrections methods proposed by Guo and Lu ( J. Chem. Phys. 1997 , 106 , 3688 - 3695 ) and Janeček ( J. Phys. Chem. B 2006 , 110 , 6264 - 6269 ) for the calculation of the surface tension and of the coexisting densities in Monte Carlo simulations of the truncated Lennard-Jones potential and the truncated and shifted Lennard-Jones potential models. These methods require an estimate of the long-range correction at each step in the Monte Carlo simulation. We apply the full version of the Guo and Lu method, which involves the calculation of a double integral that contains a series of density differences, and we compare these results with the simplified version of the method which is routinely used in two-phase simulations. We conclude that the cutoff dependencies of the surface tension and coexisting densities are identical for the full versions of Guo and Lu and Janeček methods. We show that it is possible to avoid applying the long-range correction at every step by using the truncated Lennard-Jones potential with a cutoff rc ≥ 5 σ. The long-range correction can then be applied at the end of the simulation. The limiting factor in the accurate calculation of this final correction is an accurate estimate of the coexisting densities. Link-cell simulations performed using a cutoff rc = 5.5 σ require twice as much computing time as those with a more typical cutoff of rc = 3.0 σ. The application of the Janeček correction increases the running time of the simulation by less than 10%, and it can be profitably applied with the shorter cutoff. PMID:26574249

  12. Octadecahedral and dodecahedral iron nanoparticles: An atomistic simulation on stability and shape evolutions

    Science.gov (United States)

    Wu, Yu-Ning; Huang, Rao; Zeng, Xiang-Ming; Wen, Yu-Hua

    2016-02-01

    Fe nanoparticles have attracted great interest due to their potent magnetic and catalytic properties which strongly depend on the structures and morphologies. In this article, molecular dynamic simulations were employed to investigate structural and thermal stabilities of body-centered cubic Fe nanoparticles with octadecahedral, dodecahedral and spherical shapes. Size-dependent structural stability was firstly examined. Subsequently, computer simulations on the heating process of octadecahedral Fe nanoparticle discovered that {100} facets premelt earlier than {110} ones. As a result, the dodecahedral nanoparticle enclosed by {110} facets exhibited a better thermal stability than the octadecahedral one terminated by both {110} and {100} facets. Nevertheless, it was found that the octadecahedron presented a better shape stability than the dodecahedron by monitoring the shape factor and statistical radius during continuous heating. This study provides a significant insight not only into the experimental preparation of polyhedral Fe nanoparticles but also into their utilization in high-temperature environments.

  13. Atomistic simulations of the tensile and melting behavior of silicon nanowires

    Institute of Scientific and Technical Information of China (English)

    Jing Yuhang; Meng Qingyuan; Zhao Wei

    2009-01-01

    Molecular dynamics simulations with Stillinger-Weber potential are used to study the tensile and melting behavior of single-crystalline silicon nanowires (SiNWs). The tensile tests show that the tensile behavior of the SiNWs is strongly dependent on the simulation temperature, the strain rate, and the diameter of the nanowires.For a given diameter, the critical load significantly decreases as the temperature increases and also as the strain rate decreases. Additionally, the critical load increases as the diameter increases. Moreover, the melting tests demonstrate that both melting temperature and melting heat of the SiNWs decrease with decreasing diameter and length, due to the increase in surface energy. The melting process of SiNWs with increasing temperature is also investigated.

  14. Atomistic understanding of cation exchange in PbS nanocrystals using simulations with pseudoligands

    Science.gov (United States)

    Fan, Zhaochuan; Lin, Li-Chiang; Buijs, Wim; Vlugt, Thijs J. H.; van Huis, Marijn A.

    2016-05-01

    Cation exchange is a powerful tool for the synthesis of nanostructures such as core-shell nanocrystals, however, the underlying mechanism is poorly understood. Interactions of cations with ligands and solvent molecules are systematically ignored in simulations. Here, we introduce the concept of pseudoligands to incorporate cation-ligand-solvent interactions in molecular dynamics. This leads to excellent agreement with experimental data on cation exchange of PbS nanocrystals, whereby Pb ions are partially replaced by Cd ions from solution. The temperature and the ligand-type control the exchange rate and equilibrium composition of cations in the nanocrystal. Our simulations reveal that Pb ions are kicked out by exchanged Cd interstitials and migrate through interstitial sites, aided by local relaxations at core-shell interfaces and point defects. We also predict that high-pressure conditions facilitate strongly enhanced cation exchange reactions at elevated temperatures. Our approach is easily extendable to other semiconductor compounds and to other families of nanocrystals.

  15. Stearic acid spin labels in lipid bilayers: insight through atomistic simulations.

    Science.gov (United States)

    Stimson, Lorna; Dong, Lei; Karttunen, Mikko; Wisniewska, Anna; Dutka, Małgorzata; Róg, Tomasz

    2007-11-01

    Spin-labeled stearic acid species are commonly used for electron paramagnetic resonance (EPR) studies of cell membranes to investigate phase transitions, fluidity, and other physical properties. In this paper, we use large-scale molecular dynamics simulations to investigate the position and behavior of nitroxide spin labels attached to stearic acid molecules in dipalmitoylphosphatidylcholine (DPPC) bilayers. The results of these studies are potentially very important for the interpretation of EPR spectra, which rely on assumptions about the position of the label in the membrane. Additionally, we investigate the effect of chirality and ionization of the carboxyl group of the label. For a non-ionized species, we observe that spin-label molecules are even able to make flip-flop transitions between the leaflets of the bilayer. Such transitions have been previously observed only in very rare cases in molecular simulations. PMID:17929861

  16. Stretching and breaking of monolayer MoS2—an atomistic simulation

    Science.gov (United States)

    Lorenz, Tommy; Joswig, Jan-Ole; Seifert, Gotthard

    2014-06-01

    We report on the simulation of the nanoindentation process of monolayer MoS2 using molecular-dynamics simulations and a density-functional based tight-binding method. A circular sheet of MoS2 with clamped boundaries was indented by a slowly moved tip, which deformed and finally pierced the layer. We found the Young’s modulus of monolayer MoS2 to be 262 GPa, which is in good agreement with experimental observations. Furthermore, the energetic and structural behavior during the indentation process was analyzed. Elasticity theory supplies the necessary equations to explain the experiment. Thereby, the nature of the linear term in the force-deflection relation is discussed.

  17. Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations.

    Science.gov (United States)

    Carballo-Pacheco, Martín; Ismail, Ahmed E; Strodel, Birgit

    2015-07-30

    Amyloids are associated with diseases, including Alzheimer's, as well as functional roles such as storage of peptide hormones. It is still unclear what differences exist between aberrant and functional amyloids. However, it is known that soluble oligomers formed during amyloid aggregation are more toxic than the final fibrils. Here, we perform molecular dynamics simulations to study the aggregation of the amyloid-β peptide Aβ25-35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Although the three peptides have similar primary sequences, tachykinin peptides, in contrast to Aβ25-35, form nontoxic amyloids. Our simulations reveal that the charge of the C-terminus is essential to controlling the aggregation process. In particular, when the kassinin C-terminus is not amidated, the aggregation kinetics decreases considerably. In addition, we observe that the monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations. PMID:26130191

  18. Atomistic simulation of sorption in model pores with reduced spatial periodicity

    International Nuclear Information System (INIS)

    Grand Canonical Monte Carlo (GCMC) was used to study the sorption thermodynamics of carbon dioxide in model graphite slit-like pores and nanotubes by means of the Ewald technique, suitably adapted for the computation of long range (electrostatic) interactions of sorbates confined in pore systems exhibiting reduced periodicity in space. The computed thereby micropore size distributions extracted via mathematical elaboration of the simulation results with respect to real graphitic materials, reproduced successfully the experimentally measured isotherms of carbon dioxide in these materials at various temperatures. In the case of nanotubes, a direct Coulomb summation over a large number of periodic images proved to be a sufficient approximation leading to excellent agreement between the simulated and measured isotherms

  19. Atomistic simulations of epitaxial recrystallization in 4H-SiC along the [0001] direction

    International Nuclear Information System (INIS)

    Molecular dynamics methods have been employed to study epitaxial recrystallization and the amorphous-to-crystalline (a-c) transition in 4H-SiC along the [0001] direction, with simulation times of up to a few hundred nanoseconds and at temperatures of 1500 and 2000K. The results are compared with those simulated previously along the [1-bar21-bar0] and [1-bar010] directions to investigate the anisotropies of recrystallization processes. The recovery of bond defects at the interfaces is an important process driving the initial epitaxial recrystallization of the amorphous layers. The amorphous layers with the a-c interface normal along the [0001] direction can be completely recrystallized at 2000K, but the recrystallized region contains dislocation loops. The temperature required for complete recrystallization is in good agreement with those observed experimentally

  20. Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations

    CERN Document Server

    Yu, Jin

    2015-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We keep away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while address only statistical physics modeling approach and all-atom molecular dynamics simulation approach. We organize this review around our own modeling and simulation practices on a single-subunit T7 RNA poly...

  1. Simulations of resonant Raman response in bundles of semiconductor carbon nanotubes

    Science.gov (United States)

    Roslyak, Oleksiy; Piryatinski, Andrei; Doorn, Stephen; Haroz, Erik; Telg, Hagen; Duque, Juan; Crochet, Jared; Simpson, J. R.; Hight Walker, A. R.; LANL Collaboration; Fordham Collaboration; NIST Collaboration

    This work is motivated by an experimental study of resonant Raman spectroscopy under E22 excitation, which shows a new, sharp feature associated with bundling in (6,5) semiconductor carbon nanotubes. In order to provide an insight into the experimental data, we model Raman excitation spectra using our modified discrete dipole approximation (DDA) method. The calculations account for the exciton states polarized along and across the nanotube axis that are characterized by a small energy splitting. Strong polarization of the nanotubes forming the bundle results in the exciton state mixing whose spectroscopic signatures such as peaks positions, line widths, and depolarization ratio are calculated and compared to the experiment. Furthermore, the effects of the energy and structural disorder, as well as structural defects within the bundle are also examined and compared with the experimental data.

  2. Atomistic simulation of ion solvation in water explains surface preference of halides

    OpenAIRE

    Caleman, C.; Hub, J. S.; van Maaren, P.; van der Spoel, D

    2011-01-01

    Water is a demanding partner. It strongly attracts ions, yet some halide anions—chloride, bromide, and iodide—are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl-, Br-, and I- have shallow minima near the surface. We demons...

  3. Atomistic simulations of electrochemical metallization cells: mechanisms of ultra-fast resistance switching in nanoscale devices

    Science.gov (United States)

    Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

    2016-07-01

    We describe a new method that enables reactive molecular dynamics (MD) simulations of electrochemical processes and apply it to study electrochemical metallization cells (ECMs). The model, called EChemDID, extends the charge equilibration method to capture the effect of external electrochemical potential on partial atomic charges and describes its equilibration over connected metallic structures, on-the-fly, during the MD simulation. We use EChemDID to simulate resistance switching in nanoscale ECMs; these devices consist of an electroactive metal separated from an inactive electrode by an insulator and can be reversibly switched to a low-resistance state by the electrochemical formation of a conducting filament between electrodes. Our structures use Cu as the active electrode and SiO2 as the dielectric and have dimensions at the foreseen limit of scalability of the technology, with a dielectric thickness of approximately 1 nm. We explore the effect of device geometry on switching timescales and find that nanowires with an electroactive shell, where ions migrate towards a smaller inactive electrode core, result in faster switching than planar devices. We observe significant device-to-device variability in switching timescales and intermittent switching for these nanoscale devices. To characterize the evolution in the electronic structure of the dielectric as dissolved metallic ions switch the device, we perform density functional theory calculations on structures obtained from an EChemDID MD simulation. These results confirm the appearance of states around the Fermi energy as the metallic filament bridges the electrodes and show that the metallic ions and not defects in the dielectric contribute to the majority of those states.

  4. Large-Scale Atomistic Simulations of Environmental Effects on the Formation and Properties of Molecular Junctions

    OpenAIRE

    French, William R.; Iacovella, Christopher R.; Cummings, Peter T.

    2012-01-01

    Using an updated simulation tool, we examine molecular junctions comprised of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and inter-electrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multi-molecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high de...

  5. Atomistic simulations of electrochemical metallization cells: mechanisms of ultra-fast resistance switching in nanoscale devices.

    Science.gov (United States)

    Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

    2016-08-01

    We describe a new method that enables reactive molecular dynamics (MD) simulations of electrochemical processes and apply it to study electrochemical metallization cells (ECMs). The model, called EChemDID, extends the charge equilibration method to capture the effect of external electrochemical potential on partial atomic charges and describes its equilibration over connected metallic structures, on-the-fly, during the MD simulation. We use EChemDID to simulate resistance switching in nanoscale ECMs; these devices consist of an electroactive metal separated from an inactive electrode by an insulator and can be reversibly switched to a low-resistance state by the electrochemical formation of a conducting filament between electrodes. Our structures use Cu as the active electrode and SiO2 as the dielectric and have dimensions at the foreseen limit of scalability of the technology, with a dielectric thickness of approximately 1 nm. We explore the effect of device geometry on switching timescales and find that nanowires with an electroactive shell, where ions migrate towards a smaller inactive electrode core, result in faster switching than planar devices. We observe significant device-to-device variability in switching timescales and intermittent switching for these nanoscale devices. To characterize the evolution in the electronic structure of the dielectric as dissolved metallic ions switch the device, we perform density functional theory calculations on structures obtained from an EChemDID MD simulation. These results confirm the appearance of states around the Fermi energy as the metallic filament bridges the electrodes and show that the metallic ions and not defects in the dielectric contribute to the majority of those states. PMID:27218609

  6. Carbon nanotubes as masks against ion irradiation: An insight from atomistic simulations

    International Nuclear Information System (INIS)

    Recent experiments show that carbon nanotubes can be used as masks against ion irradiation to make metallic nanowires of a few nanometers in width. In order to ascertain the limitations of this technique, we use molecular dynamics and simulate ion irradiation of multiwalled nanotubes. We derive an equation which for a given nanowire material allows one to estimate the theoretical limit on the minimum width of the wire which can be made using this technique

  7. Understanding Sodium Channel Function and Modulation Using Atomistic Simulations of Bacterial Channel Structures.

    Science.gov (United States)

    Boiteux, C; Allen, T W

    2016-01-01

    Sodium channels are chief proteins involved in electrical signaling in the nervous system, enabling critical functions like heartbeat and brain activity. New high-resolution X-ray structures for bacterial sodium channels have created an opportunity to see how these proteins operate at the molecular level. An important challenge to overcome is establishing relationships between the structures and functions of mammalian and bacterial channels. Bacterial sodium channels are known to exhibit the main structural features of their mammalian counterparts, as well as several key functional characteristics, including selective ion conduction, voltage-dependent gating, pore-based inactivation and modulation by local anesthetic, antiarrhythmic and antiepileptic drugs. Simulations have begun to shed light on each of these features in the past few years. Despite deviations in selectivity signatures for bacterial and mammalian channels, simulations have uncovered the nature of the multiion conduction mechanism associated with Na(+) binding to a high-field strength site established by charged glutamate side chains. Simulations demonstrated a surprising level of flexibility of the protein, showing that these side chains are active participants in the permeation process. They have also uncovered changes in protein structure, leading to asymmetrical collapses of the activation gate that have been proposed to correspond to inactivated structures. These observations offer the potential to examine the mechanisms of state-dependent drug activity, focusing on pore-blocking and pore-based slow inactivation in bacterial channels, without the complexities of inactivation on multiple timescales seen in eukaryotic channels. Simulations have provided molecular views of the interactions of drugs, consistent with sites predicted in mammalian channels, as well as a wealth of other sites as potential new drug targets. In this chapter, we survey the new insights into sodium channel function that

  8. Atomistic simulation in powder technology: from growth control and dispersion stabilization to segregation at doped interfaces

    OpenAIRE

    Aschauer, Ulrich

    2008-01-01

    Despite many years of intensive research there still remain many unresolved questions in powder and ceramic technology. A majority of these issues are linked to interfacial phenomena of atomic scale origin, which makes their experimental investigation very difficult due to limitations in the spatial resolution of the available analysis techniques. Computer simulations at the atomic scale provide with the advent of more and more advanced methods and increasing computer power an ever more power...

  9. Atomistic spin model simulation of magnetic reversal modes near the Curie point

    OpenAIRE

    Barker, Joe; Evans, Richard Francis L.; Chantrell, Roy W.; Hinzke, Denise; Nowak, Ulrich

    2010-01-01

    The so-called linear reversal mode is demonstrated in spin model simulations of the high anisotropy material L10 FePt. Reversal of the magnetization is found to readily occur in the linear regime despite an energy barrier (KV/kBT) that would conventionally ensure stability on this timescale. The timescale for the reversal is also established with a comparison to the Landau Lifshitz Bloch equation showing good agreement.

  10. Atomistic simulation study of the shear-band deformation mechanism in Mg-Cu metallic glasses

    DEFF Research Database (Denmark)

    Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel

    2006-01-01

    We have simulated plastic deformation of a model Mg-Cu metallic glass in order to study shear banding. In uniaxial tension, we find a necking instability occurs rather than shear banding. We can force the latter to occur by deforming in plane strain, forbidding the change of length in one...... of the transverse directions. Furthermore, in most of the simulations a notch is used to initiate shear bands, which lie at a 45 degrees angle to the tensile loading direction. The shear bands are characterized by the Falk and Langer local measure of plastic deformation D-min(2), averaged here over volumes...... containing many atoms. The D-min(2) profile has a peak whose width is around 10 nm; this width is largely independent of the strain rate. Most of the simulations were, at least nominally, at 100 K, about T-g/3 for this system. The development of the shear bands takes a few tens of ps, once plastic flow has...

  11. Accelerating atomistic simulations through self-learning bond-boost hyperdynamics

    Energy Technology Data Exchange (ETDEWEB)

    Perez, Danny [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory

    2008-01-01

    By altering the potential energy landscape on which molecular dynamics are carried out, the hyperdynamics method of Voter enables one to significantly accelerate the simulation state-to-state dynamics of physical systems. While very powerful, successful application of the method entails solving the subtle problem of the parametrization of the so-called bias potential. In this study, we first clarify the constraints that must be obeyed by the bias potential and demonstrate that fast sampling of the biased landscape is key to the obtention of proper kinetics. We then propose an approach by which the bond boost potential of Miron and Fichthorn can be safely parametrized based on data acquired in the course of a molecular dynamics simulation. Finally, we introduce a procedure, the Self-Learning Bond Boost method, in which the parametrization is step efficiently carried out on-the-fly for each new state that is visited during the simulation by safely ramping up the strength of the bias potential up to its optimal value. The stability and accuracy of the method are demonstrated.

  12. Mechanism of crack healing at room temperature revealed by atomistic simulations

    International Nuclear Information System (INIS)

    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

  13. Thermodynamic interpretation of reactive processes in Ni–Al nanolayers from atomistic simulations

    International Nuclear Information System (INIS)

    Metals that can form intermetallic compounds by exothermic reactions constitute a class of reactive materials with multiple applications. Ni–Al laminates of thin alternating layers are being considered as model nanometric metallic multilayers for studying various reaction processes. However, the reaction kinetics at short timescales after mixing are not entirely understood. In this work, we calculate the free energies of Ni–Al alloys as a function of composition and temperature for different solid phases using thermodynamic integration based on state-of-the-art interatomic potentials. We use this information to interpret molecular dynamics (MD) simulations of bilayer systems at 800 K and zero pressure, both in isothermal and isenthalpic conditions. We find that a disordered phase always forms upon mixing as a precursor to a more stable nano crystalline B2 phase. We construe the reactions observed in terms of thermodynamic trajectories governed by the state variables computed. Simulated times of up to 30 ns were achieved, which provides a window to phenomena not previously observed in MD simulations. Our results provide insight into the early experimental reaction timescales and suggest that the path (segregated reactants) → (disordered phase) → (B2 structure) is always realized irrespective of the imposed boundary conditions. (paper)

  14. Lattice Boltzmann simulation on liquid flow and mass transport in a bioreactor with cylinder bundle for hydrogen production

    Science.gov (United States)

    Liao, Qiang; Yang, Yan-Xia; Zhu, Xun; Wang, Hong; Ding, Yu-Dong

    2015-06-01

    The lattice Boltzmann method is adopted to simulate hydrodynamics and mass transfer accompanying with biochemical reaction in a channel with cylinder bundle, which is the scenario of biohydrogen production by photosynthetic bacteria in the biofilm attached on the surface of cylinder bundle in photobioreactor. The effects of cylinder spacing, Reynolds number and cylinder arrangement are investigated. The numerical results reveal that highest glucose concentration and the lowest hydrogen concentration are obtained at the front of the first row cylinders for all cases. The staggered arrangement leads to an increment in average drag coefficient, Sherwood number and consumption efficiency of substrate under a given condition, and the increment in Sherwood number reaches up to 30 %, while that in drag coefficient is around 1 %, moreover, the increment in consumption efficiency reaches the maximum value of 12 %. The results indicate that the staggered arrangement is beneficial to the mass transfer and biochemical reaction.

  15. Explicit core-follow simulations for a CANDU 6 reactor fuelled with recovered-uranium CANFLEX bundles

    International Nuclear Information System (INIS)

    Recovered uranium (RU) is a by-product of many light-water reactor (LWR) fuel recycling programs. After fission products and plutonium (Pu) have been removed from spent LWR fuel, RU is left. A fissile content in the RU of 0.9 to 1.0% makes it impossible for reuse in an LWR without re-enrichment, but CANDU reactors have a sufficiently high neutron economy to use RU as fuel. Explicit core-follow simulations were run to analyse the viability of RU as a fuel for existing CANDU 6 cores. The core follow was performed with RFSP, using WIMS-AECL lattice properties. During the core follow, channel powers and bundle powers were tracked to determine the operating envelope for RU in a CANFLEX bundle. The results show that RU fits the operating criteria of a generic CANDU 6 core and is a viable fuel option in CANDU reactors. (author)

  16. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations

    Science.gov (United States)

    Jin, Yu

    2016-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We stay away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while addressing statistical physics modeling approaches along with all-atom molecular dynamics simulation studies. We organize this review around our own modeling and simulation practices on a single subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases as well. For multi-subunit RNA polymerases that have been actively studied in recent years, we leave systematical reviews of the simulation achievements to latest computational chemistry surveys, while covering only representative studies published very recently, including our own work modeling structure-based elongation kinetic of yeast RNA polymerase II. In the end, we briefly go through physical modeling on elongation pauses and backtracking activities of the multi-subunit RNAPs. We emphasize on the fluctuation and control mechanisms of the polymerase actions, highlight the non-equilibrium nature of the operation system, and try to build some perspectives toward understanding the polymerase impacts from the single molecule level to a genome-wide scale. Project supported by the National Natural Science Foundation (Grant No. 11275022).

  17. Atomistic simulations of anionic Au-144(SR)(60) nanoparticles interacting with asymmetric model lipid membranes

    DEFF Research Database (Denmark)

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

    2014-01-01

    whose lipid composition and transmembrane distribution are to a large extent consistent with real plasma membranes of eukaryotic cells. To this end, we use a model system which comprises two cellular compartments, extracellular and cytosolic, divided by two asymmetric lipid bilayers. The simulations...... water phase due to Coulomb repulsion that arises from negatively charged phosphatidylserine lipids interacting with AuNP-. A number of structural and dynamical features resulting from these basic phenomena are discussed. We close the article with a brief discussion of potential implications. (C) 2014...

  18. Atomistic simulations of the effect of helium clusters on grain boundary mobility in iron

    Science.gov (United States)

    Wicaksono, A. T.; Militzer, M.; Sinclair, C. W.

    2015-08-01

    A series of molecular dynamics simulations was performed in this work to investigate the kinetic interaction between helium clusters and grain boundaries in iron. Helium cluster formation and size distributions were found to be markedly different in the bulk compared to the region of a stationary boundary. Upon reaching a steady-state cluster distribution, the spatial fluctuation of cluster-enriched boundaries was analyzed to determine the grain boundary mobility using the random walk method. Segregated clusters reduced the boundary mobility, the drag effect of clusters increasing as the bulk solute concentration increases. The drag effect was further rationalized by employing Cahn's solute drag model using the effective binding energy of He clusters and the grain boundary diffusivity of a single He atom, their magnitudes having been determined from the segregation level and from monitoring the trajectory of a solute atom in the investigated grain boundaries, respectively. The model is found to provide a satisfactory explanation of the simulation results in the zero velocity limit.

  19. Atomistic simulations of nanowelding of single-crystal and amorphous gold nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Cheng-Da, E-mail: nanowu@cycu.edu.tw [Department of Mechanical Engineering, Chung Yuan Christian University, 200, Chung Pei Rd., Chung Li City, Taoyuan County 32023, Taiwan (China); Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net; Wu, Chung-Chin, E-mail: 1100303179@kuas.edu.tw [Department of Mechanical Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 807, Taiwan (China)

    2015-01-07

    The mechanism and quality of the welding of single-crystal (SC) and amorphous gold nanowires (NWs) with head-to-head contact are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. The results are discussed in terms of atomic trajectories, slip vectors, stress, and radial distribution function. Simulation results show that the alignment for the amorphous NWs during welding is easier than that for the SC NWs due to the former's relatively stable geometry. A few dislocations nucleate and propagate on the (111) close-packed plane (slip plane) inside the SC NWs during the welding and stretching processes. During welding, an incomplete jointing area first forms through the interactions of the van der Waals attractive force, and the jointing area increases with increasing extent of contact between the two NWs. A crystallization transition region forms in the jointing area for the welding of SC-amorphous or amorphous-SC NWs. With increasing interference, an amorphous gold NW shortens more than does a SC gold NW due to the former's relatively poor strength. The pressure required for welding decreases with increasing temperature.

  20. Defects and threshold displacement energies in SrTiO3 perovskite using atomistic computer simulations

    International Nuclear Information System (INIS)

    The mode and energy of simple defect incorporation in SrTiO3 (vacancies and interstitials) is quantified using computer simulation techniques with an empirical partial charge model of interatomic forces, as well as using density functional theory calculations. Oxygen and strontium interstitials form split-interstitial configurations whereas titanium interstitials occupy channel positions. Defect migration energies and paths are also considered; interstitials are more mobile than vacancies, with a low predicted oxygen interstitial migration energy of around 0.3 eV. We also calculate the threshold displacement energy (Ed) for each atom type in SrTiO3 perovskite using molecular dynamics simulations, by introducing a primary knock-on atom with a range of energies (20-250 eV) in principal crystallographic directions at 300 K. We find that all atom types are most easily displaced via direct replacement sequences on their own sublattices, which are extensive for Sr atoms due to focusson processes acting along channels. The weighted average threshold displacement energies (for use in TRIM-type calculations) are 50 eV for oxygen, 70 eV for strontium and 140 eV for titanium atoms. These computed energies for O and Sr are comparable to experimentally-derived values in perovskites, whereas the Ed for Ti is much higher; it is expected that the value reported here is more accurate due to experimental difficulties in distinguishing different types of defects

  1. Atomistic simulation of the structural, thermodynamic, and elastic properties of Li2TiO3

    International Nuclear Information System (INIS)

    Lithium-based ceramics, such as lithium metatitanate, have been proposed for adoption in the breeder blanket region of a fusion reactor. In this article, we report a combination of empirical and density functional theory (DFT) simulations employing 'on-the-fly' pseudopotentials for Li2TiO3. The smoothing parameters of the plane-wave pseudopotentials were optimized to ensure an appropriate level of precision for determination of structural, thermodynamic, and elastic properties. As the elastic properties of lithium metatitanate are not well-known, the efficacy of the DFT simulations employing the new pseudopotentials was explored using Li2O and TiO2 where experimental data are available. These pseudopotentials are then used to investigate the three intermediate temperature Phases of Li2TiO3 (i.e., C2/c, C2/m, and P3112). Finally we examine the elastic properties of Li2TiO3 using both DFT and an empirical potential model and find it to be, irrespective of space group, more resistant to deformation than other promising ceramic breeder materials. (authors)

  2. Accelerated path integral methods for atomistic simulations at ultra-low temperatures.

    Science.gov (United States)

    Uhl, Felix; Marx, Dominik; Ceriotti, Michele

    2016-08-01

    Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated path integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH5 (+). We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH4 to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state. PMID:27497533

  3. Wettability alteration properties of fluorinated silica nanoparticles in liquid-loaded pores: An atomistic simulation

    Science.gov (United States)

    Sepehrinia, Kazem; Mohammadi, Aliasghar

    2016-05-01

    Control over the wettability of reservoir rocks is of crucial importance for enhancing oil and gas recovery. In order to develop chemicals for controlling the wettability of reservoir rocks, we present a study of functionalized silica nanoparticles as candidates for wettability alteration and improved gas recovery applications. In this paper, properties of fluorinated silica nanoparticles were investigated in water or decane-loaded pores of mineral silica using molecular dynamics simulation. Trifluoromethyl groups as water and oil repellents were placed on the nanoparticles. Simulating a pore in the presence of trapped water or decane molecules leads to liquid bridging for both of the liquids. Adsorption of nanoparticles on the pore wall reduces the density of liquid molecules adjacent to the wall. The density of liquid molecules around the nanoparticles decreases significantly with increasing the number of trifluoromethyl groups on the nanoparticles' surfaces. An increased hydrophobicity of the pore wall was observed in the presence of adsorbed fluorinated silica nanoparticles. Also, it is observed that increasing the number of the trifluoromethyl groups results in weakening of liquid bridges. Moreover, the free energy of adsorption on mineral surface was evaluated to be more favorable than that of aggregation of nanoparticles, which suggests nanoparticles adsorb preferably on mineral surface.

  4. Atomistic simulations of aromatic polyurea and polyamide for capacitive energy storage

    Science.gov (United States)

    Dong, Rui; Ranjan, V.; Buongiorno Nardelli, Marco; Bernholc, J.

    2015-07-01

    Materials for capacitive energy storage with high energy density and low loss are desired in many fields. We investigate several polymers with urea and amide functional groups using density functional theory and classical molecular dynamics simulations. For aromatic polyurea (APU) and para-aramid (PA), we find several nearly energetically degenerate ordered structures, while meta-aromatic polyurea (mAPU) tends to be rotationally disordered along the polymer chains. Simulated annealing of APU and PA structures results in the formation of hydrogen-bonded sheets, highlighting the importance of dipole-dipole interactions. In contrast, hydrogen bonding does not play a significant role in mAPU, hence the propensity to disorder. We find that the disordered structures with misaligned chains have significantly larger dielectric constants, due to significant increase in the free volume, which leads to easier reorientation of dipolar groups in the presence of an electric field. Large segment motion is still not allowed below the glass transition temperature, which explains the experimentally observed very low loss at high field and elevated temperature. However, the degree of disorder needs to be controlled, because highly entangled structures diminish the free dipoles and decrease permittivity. Among the considered materials, mAPU is the most promising dielectric for capacitive energy storage, but the concept of increasing permittivity while maintaining low loss through disorder-induced free volume increase is generally applicable and provides an alternative pathway for the design of high-performance dielectrics for capacitive energy storage.

  5. 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.

  6. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev

    2014-05-01

    Full Text Available Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1–100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

  7. Atomistic understanding of cation exchange in PbS nanocrystals using simulations with pseudoligands

    Science.gov (United States)

    Fan, Zhaochuan; Lin, Li-Chiang; Buijs, Wim; Vlugt, Thijs J. H.; van Huis, Marijn A.

    2016-01-01

    Cation exchange is a powerful tool for the synthesis of nanostructures such as core–shell nanocrystals, however, the underlying mechanism is poorly understood. Interactions of cations with ligands and solvent molecules are systematically ignored in simulations. Here, we introduce the concept of pseudoligands to incorporate cation-ligand-solvent interactions in molecular dynamics. This leads to excellent agreement with experimental data on cation exchange of PbS nanocrystals, whereby Pb ions are partially replaced by Cd ions from solution. The temperature and the ligand-type control the exchange rate and equilibrium composition of cations in the nanocrystal. Our simulations reveal that Pb ions are kicked out by exchanged Cd interstitials and migrate through interstitial sites, aided by local relaxations at core–shell interfaces and point defects. We also predict that high-pressure conditions facilitate strongly enhanced cation exchange reactions at elevated temperatures. Our approach is easily extendable to other semiconductor compounds and to other families of nanocrystals. PMID:27160371

  8. Accelerated path integral methods for atomistic simulations at ultra-low temperatures

    Science.gov (United States)

    Uhl, Felix; Marx, Dominik; Ceriotti, Michele

    2016-08-01

    Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated path integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH5+. We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH4 to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.

  9. Atomistic simulation of separation of hydrogen and hydrocarbons in carbon nano tubes

    International Nuclear Information System (INIS)

    Full Text:As an important research direction in nano-science and nano-technology, carbon nano tubes have aroused great interest: due to their unique structure and stability. We are studying the transport and separation of hydrogen and hydrocarbons mixtures, which is of considerable research interest in the chemical and pharmaceutical industries. Computational methods, such as molecular Dynamics or Monte Carlo simulation, have been widely applied to determine the nature of the diffusion of molecules inside carbon nano tubes. Transport phenomena in carbon nano tubes depend on the pore size, the pore network structure, the molecule dimensions, the temperature of the gas mixture and the interaction bets-Fen the transported mixture and the tube. The solid tube is modeled using the Brenner (Bond-Order) potential energy which can model intermolecular chemical bonding in a variety of small hydrocarbons as well as graphite. I will present a molecular dynamics simulation of diffusion of methane molecules inside carbon nano tube, and find obtain the apparent diffusivity values

  10. Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential.

    Science.gov (United States)

    Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

    2016-01-14

    To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results. PMID:26658834

  11. Large-Scale Reactive Atomistic Simulation of Shock-induced Initiation Processes in Energetic Materials

    Science.gov (United States)

    Thompson, Aidan

    2013-06-01

    Initiation in energetic materials is fundamentally dependent on the interaction between a host of complex chemical and mechanical processes, occurring on scales ranging from intramolecular vibrations through molecular crystal plasticity up to hydrodynamic phenomena at the mesoscale. A variety of methods (e.g. quantum electronic structure methods (QM), non-reactive classical molecular dynamics (MD), mesoscopic continuum mechanics) exist to study processes occurring on each of these scales in isolation, but cannot describe how these processes interact with each other. In contrast, the ReaxFF reactive force field, implemented in the LAMMPS parallel MD code, allows us to routinely perform multimillion-atom reactive MD simulations of shock-induced initiation in a variety of energetic materials. This is done either by explicitly driving a shock-wave through the structure (NEMD) or by imposing thermodynamic constraints on the collective dynamics of the simulation cell e.g. using the Multiscale Shock Technique (MSST). These MD simulations allow us to directly observe how energy is transferred from the shockwave into other processes, including intramolecular vibrational modes, plastic deformation of the crystal, and hydrodynamic jetting at interfaces. These processes in turn cause thermal excitation of chemical bonds leading to initial chemical reactions, and ultimately to exothermic formation of product species. Results will be presented on the application of this approach to several important energetic materials, including pentaerythritol tetranitrate (PETN) and ammonium nitrate/fuel oil (ANFO). In both cases, we validate the ReaxFF parameterizations against QM and experimental data. For PETN, we observe initiation occurring via different chemical pathways, depending on the shock direction. For PETN containing spherical voids, we observe enhanced sensitivity due to jetting, void collapse, and hotspot formation, with sensitivity increasing with void size. For ANFO, we

  12. Atomistic simulations of tungsten surface evolution under low-energy neon implantation

    Science.gov (United States)

    Backman, Marie; Hammond, Karl D.; Sefta, Faiza; Wirth, Brian D.

    2016-04-01

    Tungsten is a candidate material for the divertor of fusion reactors, where it will be subject to a high flux of particles coming from the fusion plasma as well as a significant heat load. Under helium plasma exposure in fusion-reactor-like conditions, a nanostructured morphology is known to form on the tungsten surface in certain temperature and incident energy ranges, although the formation mechanism is not fully established. A recent experimental study (Yajima et al 2013 Plasma Sci. Technol. 15 282-6) using neon or argon exposure did not produce similar nanostructure. This article presents molecular dynamics simulations of neon implantation in tungsten aimed at investigating the surface evolution and elucidating the role of noble gas mass in fuzz formation. In contrast to helium, neon impacts can sputter both tungsten and previously implanted neon atoms. The shorter range of neon ions, along with sputtering, limit the formation of large bubbles and likely prevents nanostructure formation.

  13. The configurations of nanoalloy by impact deposition: atomistic simulation on Ni–Al system

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jianfeng, E-mail: hnjftang@aliyun.com [Hunan Agricultural University, Department of Applied Physics (China); Yang, Jianyu, E-mail: hnieyjy@aliyun.com [Hunan Institute of Engineering (China)

    2013-11-15

    The use of energetic particles can change the growth mode and provide control of nanoalloy morphology and properties. The impact deposition of Ni (or Al) on the truncated octahedral nanoparticle of Al (or Ni) is studied. The embedded atom method is used for the description of the interatomic interactions in combination with molecular dynamics method for the growth simulation. Three configurations of Ni–Al nanoparticle are obtained depending on incident energy and deposition sequence. A perfect core–shell nanoparticle with Ni-core/Al-shell is obtained as Al atoms are deposited over Ni nanoparticle. For the deposition of Ni atoms on Al nanoparticle, an onion-like nanoparticle at smaller incident energy, and a configuration with Al-shell and alloyed Ni–Al core at larger incident energy are observed, respectively. The formation energies show that the latter is energetically favorable.

  14. Si-coated single-walled carbon nanotubes under axial loads: An atomistic simulation study

    International Nuclear Information System (INIS)

    The mechanical properties of the Si-coated imperfect (5, 5) single-walled carbon nanotube (SWCNT), the imperfect (5, 5) SWCNT and several perfect armchair SWCNTs under axial loads were investigated using molecular dynamics simulation. The interactions between atoms were modeled using the empirical Tersoff potential and the Tersoff-Brenner potential coupled with the Lennard-Jones potential. We get Young's modulus of the defective (5, 5) nanotube with and without the Si coating under axial tension 1107.92 and 1076.02 GPa, respectively. The results also show that the structure failure of the Si-coated imperfect (5, 5) SWCNT under axial compression occurs at a slightly higher strain than for the perfect (5, 5) SWCNT. Therefore, we can confirm the protective effect of Si as a coating material for defective SWCNTs. We also obtain the critical buckling strains of perfect SWCNTs

  15. Structure Based Modeling of Small Molecules Binding to the TLR7 by Atomistic Level Simulations

    Directory of Open Access Journals (Sweden)

    Francesco Gentile

    2015-05-01

    Full Text Available Toll-Like Receptors (TLR are a large family of proteins involved in the immune system response. Both the activation and the inhibition of these receptors can have positive effects on several diseases, including viral pathologies and cancer, therefore prompting the development of new compounds. In order to provide new indications for the design of Toll-Like Receptor 7 (TLR7-targeting drugs, the mechanism of interaction between the TLR7 and two important classes of agonists (imidazoquinoline and adenine derivatives was investigated through docking and Molecular Dynamics simulations. To perform the computational analysis, a new model for the dimeric form of the receptors was necessary and therefore created. Qualitative and quantitative differences between agonists and inactive compounds were determined. The in silico results were compared with previous experimental observations and employed to define the ligand binding mechanism of TLR7.

  16. Force-field derivation and atomistic simulation of HMX–TATB–graphite mixture explosives

    International Nuclear Information System (INIS)

    We have studied the interfaces between octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and graphite, where the former is a sensitive explosive, the middle one is an insensitive explosive and the latter is a desensitizer. The force-field across the interfaces is obtained by ab initio calculation and least-squares optimization. We use this force-field to simulate the breaking and deformation processes of the HMX–TATB–graphite interface and polycrystal systems. The breaking, coating and plasticizing properties are discussed. A set of mechanical parameters for the mixture explosives is obtained. (paper)

  17. Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations

    Science.gov (United States)

    Kreis, K.; Fogarty, A. C.; Kremer, K.; Potestio, R.

    2015-09-01

    In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One of the main advantages of such approaches is the computational efficiency gained in the coarse-grained region. In this respect the best coarse-grained system to employ in the low resolution region would be the ideal gas, making intermolecular force calculations in the coarse-grained subdomain redundant. In this case, however, a smooth coupling is challenging due to the high energetic imbalance between typical liquids and a system of non-interacting particles. In the present work, we investigate this approach, using as a test case the most biologically relevant fluid, water. We demonstrate that a successful coupling of water to the ideal gas can be achieved with current adaptive resolution methods, and discuss the issues that remain to be addressed.

  18. Atomistic simulations of displacement cascades in Y{sub 2}O{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Dholakia, Manan, E-mail: manan@igcar.gov.in [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu (India); Chandra, Sharat [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu (India); Valsakumar, M.C. [School of Engineering Sciences and Technology, University of Hyderabad, Hyderabad 500 046 (India); Mathi Jaya, S. [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu (India)

    2014-11-15

    Graphical abstract: (a) The averaged distortion index and the Y–O bond length of the Y{sub 2}O{sub 3} octahedra as a function of the simulation time for 5 keV PKA. (b) Shows the nearest neighbourhood of one of the Y ions as a function of simulation time, showing the destruction and the recovery of the YO{sub 6} octahedron during the cascade corresponding to 5 keV Y PKA. - Highlights: • Qualitative difference in displacement cascades exists for Y and O PKA. • Nearest neighbour correlation between Y and O ions exists even at cascade peak. • Cascade core in Y{sub 2}O{sub 3} does not undergo melting. • Topological connectivity of YO{sub 6} polyhedra plays important role in stability of Y{sub 2}O{sub 3}. - Abstract: We study the characteristics of displacement cascades in single crystal Y{sub 2}O{sub 3} using classical molecular dynamics. There are two possible ways to generate the cascades in yttria, using either the Y or the O atoms as the primary knock-on (PKA) atom. It is shown that there is a qualitative difference in the characteristics of the cascades obtained in these two cases. Even though the crystal is seen to be in a highly disordered state in the cascade volume, as seen from the plots of radial distribution function, the correlation between the Y and O atoms is not completely lost. This facilitates a quick recovery of the system during the annealing phase. Topological connectivity of the YO{sub 6} polyhedral units plays an important role in imparting stability to the Y{sub 2}O{sub 3} crystal. These characteristics of the cascades can help explain the stability of the yttria nanoparticles when they are dispersed in oxide dispersion strengthened steels.

  19. Large-scale simulations on thermal-hydraulics in fuel bundles of advanced nuclear reactors (Annual Report of the Earth Simulator Center, Dec 2008, 2007 issue)

    International Nuclear Information System (INIS)

    In order to predict the water-vapor two-phase flow dynamics in a fuel bundle of an advanced light-water reactor, large-scale numerical simulations were performed using a highly parallel-vector supercomputer, the earth simulator. Although conventional analysis methods such as subchannel codes and system analysis codes need composition equations based on the experimental data, it is difficult to obtain high prediction accuracy when experimental data to obtain the composition equations. Then, the present large-scale direct simulation method of water-vapor two-phase flow was proposed. The void fraction distribution in a fuel bundle under boiling heat transfer condition was analyzed and the bubble dynamics around the fuel rod surface were predicted quantitatively. (author)

  20. Atomistic simulations of the effect of reactor-relevant parameters on be sputtering

    International Nuclear Information System (INIS)

    Beryllium (Be) is the main plasma-facing material in the present day fusion reactor JET as well as in the upcoming ITER. Thus, the Be erosion plays a key role in predicting the life-time and viability of the reactors. In this work, Be surface erosion and morphology changes due to deuterium (D) irradiation are studied by using molecular dynamics simulations, varying key parameters such as particle flux, surface temperature and impact energy. At low temperatures, the main molecular species among the sputtered particles is BeD due to a low D surface concentration, as the incoming D projectiles cluster beneath the surface. At higher temperatures, the D surface concentration increases and larger species (BeD2, BeD3) dominate the molecular erosion, lowering the BeD to Be ratio. When approaching the Be melting point, D desorbs from the surface, increasing the fraction of Be eroded as BeD. The larger molecules will dissociate as soon as entering the edge plasma, with only a minor contribution to the BeD formation. These findings correlate well with observations at JET. The effect of the incoming D flux on the results is negligible

  1. The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations.

    Science.gov (United States)

    Rog, Tomasz; Koivuniemi, Artturi

    2016-01-01

    Given the importance of plasmalogens in cellular membranes and neurodegenerative diseases, a better understanding of how plasmalogens affect the lipid membrane properties is needed. Here we carried out molecular dynamics simulations to study a lipid membrane comprised of ethanolamine plasmalogens (PE-plasmalogens). We compared the results to the PE-diacyl counterpart and palmitoyl-oleyl-phosphatidylcholine (POPC) bilayers. Results show that PE-plasmalogens form more compressed, thicker, and rigid lipid bilayers in comparison with the PE-diacyl and POPC membranes. The results also point out that the vinyl-ether linkage increases the ordering of sn-1 chain substantially and the ordering of the sn-2 chain to a minor extent. Further, the vinyl-ether linkage changes the orientation of the lipid head group, but it does not cause changes in the head group and glycerol backbone tilt angles with respect to the bilayer normal. The vinyl-ether linkage also packs the proximal regions of the sn-1 and sn-2 chains more closely together which also decreases the distance between the rest of the sn-1 and sn-2 chains. PMID:26522077

  2. Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.

    Science.gov (United States)

    Zerze, Gül H; Best, Robert B; Mittal, Jeetain

    2015-11-19

    We use all-atom molecular simulation with explicit solvent to study the properties of selected intrinsically disordered proteins and unfolded states of foldable proteins, which include chain dimensions and shape, secondary structure propensity, solvent accessible surface area, and contact formation. We find that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. In particular, unfolded globular proteins tend to be more collapsed under the same conditions than charged disordered sequences of the same length. However, inclusion of explicit solvent in addition naturally captures temperature-dependent solvation effects, which results in an initial collapse of the chains as temperature is increased, in qualitative agreement with experiment. There is a universal origin to the collapse, revealed in the change of hydration of individual residues as a function of temperature: namely, that the initial collapse is driven by unfavorable solvation free energy of individual residues, which in turn has a strong temperature dependence. We also observe that in unfolded globular proteins, increased temperature also initially favors formation of native-like (rather than non-native-like) structure. Our results help to establish how sequence encodes the degree of intrinsic disorder or order as well as its response to changes in environmental conditions. PMID:26498157

  3. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N. [Qatar Environment and Energy Research Institute (QEERI), Hamad Ben Khalifa University (HBKU), Qatar Foundation, P.O. Box 5825, Doha (Qatar); Harrabi, K. [Department of Physics, King Fahd University of Petroleum and Minerals, 31261 Dhahran (Saudi Arabia); Mehmood, U.; Hussein, I. A. [Department of Chemical Engineering, King Fahd University of Petroleum and Minerals, 31261 Dharan (Saudi Arabia); Peeters, F. M. [Departement Fysica, Universiteit Antwerpen, Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Zhang, J. [Department of Materials and London Centre for Nanotechnology, Imperial College London, SW7 2AZ London (United Kingdom); McLachlan, M. A. [Department of Materials and Centre for Plastic Electronics, Imperial College London, SW7 2AZ London (United Kingdom)

    2015-07-14

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.

  4. Atomistic simulation of the point defects in TaW ordered alloy

    Indian Academy of Sciences (India)

    Zhong-Liang Lin; Jian-Min Zhang; Yan Zhang; Vincent Ji

    2011-01-01

    Combining molecular dynamics (MD) simulation with modified analytic embeddedatom method (MAEAM), the formation, migration and activation energies of the point defects for six-kind migration mechanisms in B2-type TaW alloy have been investigated. The results showed that the anti-site defects TaW and WTa were easier to form than Ta and W vacancies owing to their lower formation energies. Comparing the migration and activation energies needed for six-kind migration mechanisms of a Ta (or W) vacancy, we found that one nearest-neighbour jump (1NNJ) was the most favourable because of its lowest migration and activation energies, but it would lead to a disorder in the alloy. One next-nearest-neighbour jump (1NNNJ) and one third-nearest-neighbour jump (1TNNJ) could maintain the ordered property of the alloy but required higher migration and activation energies. So the 1NNNJ and 1TNNJ should be replaced by straight [100] six nearestneighbor cyclic jumps (S[100]6NNCJ) (especially) or bent [100] six nearest-neighbour cyclic jumps (B[100]6NNCJ) and [110] six nearest-neighbor cyclic jumps ([110]6NNCJ), respectively.

  5. Atomistic simulation of martensite-austenite phase transition in nanoscale nickel-titanium crystals

    Science.gov (United States)

    Kexel, Christian; Schramm, Stefan; Solov'yov, Andrey V.

    2015-09-01

    Shape-memory (SM) alloys can, after initial inelastic deformation, reconstruct their pristine lattice structure upon heating. The underlying phenomenon is the structural solid-solid phase transition from low-temperature lower-symmetry martensite to the high-temperature higher-symmetry austenite. Conventional nickel-titanium (NiTi) with near-equiatomic concentration already possesses an eminent importance for many applications, whereas the nanostructured equivalent can exhibit yet enhanced thermomechanical properties. However, no plausible microscopic theory of the SM effect in NiTi exists, especially for nanoscale systems. We investigate the thermally induced martensite-austenite phase transition in free equiatomic nanocrystals, comprising up to approximately 40 000 atoms, by means of molecular-dynamics simulations (MD) using a classical Gupta-type many-body scheme. Thereby we complement and extend a previously published study [D. Mutter, P. Nielaba, Eur. Phys. J. B 84, 109 (2011)]. The structural transition, revealing features of a first-order phase transition, is demonstrated. It is contrasted with the melting phase transition, a quantum solid model and bulk experimental findings. Moreover, a nucleation-growth process is observed as well as the irreversibility of the transition upon cooling.

  6. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    International Nuclear Information System (INIS)

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C60 fullerene. As a typical example, we consider [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C60 and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C60 is an order of magnitude larger than the one for PCBM

  7. Effects of Zr doping on the surface energy and surface structure of UO2: Atomistic simulations

    International Nuclear Information System (INIS)

    A shell-core model is applied to investigate the effects of Zr doping on the surface energies and surface structures of the three low Miller index surfaces in UO2 using the molecular dynamics (MD) technique. The surface energies and atomic structures of the Zr-doped and undoped UO2 (1 0 0), (1 1 0) and (1 1 1) surfaces are compared. Simulation results indicate that (i) the surface energy of (U1−yZry)O2 depend on the crystallographic orientation, as well as of undoped UO2. The (1 0 0) surface exhibits the highest surface energy, followed by the (1 1 0) surface, and the (1 1 1) surface; (ii) Zr doping will significantly increase the surface energy of UO2 by approximately 20% on (1 0 0) surface, 10% on (1 1 0) surface and 15% on (1 1 1) surface with the ZrO2 contents ranging from 0 to 12.5 mol%, respectively; (iii) the surface energies of the three low Miller index surfaces decrease with increasing temperature both in undoped UO2 and in (U1−yZry)O2; (iv) the addition of Zr induces a severe distortion of the (U1−yZry)O2 surface structure, and the outermost top layer exhibits the strongest rumpling; (v) the considerable reconstructions can be observed in the two top layers of Zr-doped and undoped UO2 surfaces when the temperature is elevated to 900–1500 K

  8. Microchemical effects in irradiated Fe–Cr alloys as revealed by atomistic simulation

    International Nuclear Information System (INIS)

    Neutron irradiation produces evolving nanostructural defects in materials, that affect their macroscopic properties. Defect production and evolution is expected to be influenced by the chemical composition of the material. In turn, the accumulation of defects in the material results in microchemical changes, which may induce further changes in macroscopic properties. In this work we review the results of recent atomic-level simulations conducted in Fe–Cr alloys, as model materials for high-Cr ferritic–martensitic steels, to address the following questions: 1. Is the primary damage produced in displacement cascades influenced by the Cr content? If so, how? 2. Does Cr change the stability of radiation-produced defects? 3. Is the diffusivity of cascade-produced defects changed by Cr content? 4. How do Cr atoms redistribute under irradiation inside the material under the action of thermodynamic driving forces and radiation-defect fluxes? It is found that the presence of Cr does not influence the type of damage created by displacement cascades, as compared to pure Fe, while cascades do contribute to redistributing Cr, in the same direction as thermodynamic driving forces. The presence of Cr does change the stability of point-defects: the effect is weak in the case of vacancies, stronger in the case of self-interstitials. In the latter case, Cr increases the stability of self-interstitial clusters, especially those so small to be invisible to the electron microscope. Cr reduces also significantly the diffusivity of self-interstitials and their clusters, in a way that depends in a non-monotonic way on Cr content, as well as on cluster size and temperature; however, the effect is negligible on the mobility of self-interstitial clusters large enough to become visible dislocation loops. Finally, Cr-rich precipitate formation is favoured in the tensile region of edge dislocations, while it appears not to be influenced by screw dislocations; prismatic dislocation loops

  9. Microchemical effects in irradiated Fe–Cr alloys as revealed by atomistic simulation

    Energy Technology Data Exchange (ETDEWEB)

    Malerba, L., E-mail: lmalerba@sckcen.be [Structural Materials Modelling and Microstructure Unit, SMA/NMS, Studiecentrum voor Kernenergie, Centre d’Etudes de l’Energie Nucléaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Bonny, G.; Terentyev, D. [Structural Materials Modelling and Microstructure Unit, SMA/NMS, Studiecentrum voor Kernenergie, Centre d’Etudes de l’Energie Nucléaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Zhurkin, E.E. [Experimental Nuclear Physics Department, K-89, Faculty of Physics and Mechanics, Saint-Petersburg State Polytechnical University, 29 Polytekhnicheskaya Str., 195251 St. Petersburg (Russian Federation); Hou, M. [Physique des Solides Irradiés et des Nanostructures CP234, Faculté des Sciences, Université Libre de Bruxelles, Bd du Triomphe, B-1050 Bruxelles (Belgium); Vörtler, K.; Nordlund, K. [Association EURATOM-Tekes, Department of Physics, P.O. Box 43, FI-00014, University of Helsinki (Finland)

    2013-11-15

    Neutron irradiation produces evolving nanostructural defects in materials, that affect their macroscopic properties. Defect production and evolution is expected to be influenced by the chemical composition of the material. In turn, the accumulation of defects in the material results in microchemical changes, which may induce further changes in macroscopic properties. In this work we review the results of recent atomic-level simulations conducted in Fe–Cr alloys, as model materials for high-Cr ferritic–martensitic steels, to address the following questions: 1. Is the primary damage produced in displacement cascades influenced by the Cr content? If so, how? 2. Does Cr change the stability of radiation-produced defects? 3. Is the diffusivity of cascade-produced defects changed by Cr content? 4. How do Cr atoms redistribute under irradiation inside the material under the action of thermodynamic driving forces and radiation-defect fluxes? It is found that the presence of Cr does not influence the type of damage created by displacement cascades, as compared to pure Fe, while cascades do contribute to redistributing Cr, in the same direction as thermodynamic driving forces. The presence of Cr does change the stability of point-defects: the effect is weak in the case of vacancies, stronger in the case of self-interstitials. In the latter case, Cr increases the stability of self-interstitial clusters, especially those so small to be invisible to the electron microscope. Cr reduces also significantly the diffusivity of self-interstitials and their clusters, in a way that depends in a non-monotonic way on Cr content, as well as on cluster size and temperature; however, the effect is negligible on the mobility of self-interstitial clusters large enough to become visible dislocation loops. Finally, Cr-rich precipitate formation is favoured in the tensile region of edge dislocations, while it appears not to be influenced by screw dislocations; prismatic dislocation loops

  10. Application of X-ray absorption spectroscopy and molecular dynamics simulation to study the atomistic solvation structure of tetraglyme:KSCN electrolytes

    International Nuclear Information System (INIS)

    The atomistic solvation structure of tetraglyme:KSCN (TET:KSCN) electrolytes with various K+:ether oxygen (M:O) ratio were studied by a combination of molecular dynamic (MD) simulation and Extended X-Ray Absorption Fine Structure (EXAFS) called “MD-EXAFS” method. This method gives useful information at the atomistic scale including the average distance between atom pair around the probed ion (R0) and Coordination Number (N). MD simulation results suggest that K+ ions are mostly coordinated to ether oxygen and the conformation around C–C bond prefer the gauche state and TET becomes more compact shape. K+ ions are also coordinated to thiocyanate (SCN−) anion at both nitrogen and sulfur atoms due to strong electron delocalization over three atoms in SCN− (S, C and N). A comparison between MD-EXAFS with the experimental spectra gives an overall good agreement for both frequency and amplitude of the oscillations. - Graphical abstract: A snapshot from MD simulation of TET:KSCN complex that represent the solvation structure of K+ ion by TET oxygens and SCN− anion. The most probable case is the solvation by 1 TET chain with 3 oxygen atoms and 2 SCN− anion. - Highlights: • This work combines MD simulation and XAS to study polymer electrolytes. • Doping KSCN can slightly induce the conformational change of TET chain. • Both polymer and anions are included in first solvation shell of cation

  11. 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

    Cytochrome (cyt) bc(1) complex, which is an integral part of the respiratory chain and related energy-conserving systems, has two quinone-binding cavities (Q(o)- and Q(i)-sites), where the substrate participates in electron and proton transfer. Due to its complexity, many of the mechanistic details...... 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...

  12. Numerical simulation of fluid flow and heat transfer of supercritical fluids in fuel bundles

    International Nuclear Information System (INIS)

    A supercritical water-cooled reactor (SCWR) was proposed as a kind of generation IV reactor in order to improve the efficiency of nuclear reactors. Although investigations on the thermal-hydraulic behavior in SCWR have attracted much attention, there is still a lack of CFD study on the heat transfer of supercritical water in fuel channels. In order to understand the thermal-hydraulic behavior of supercritical fluids in nuclear reactors, the local fluid flow and heat transfer of supercritical water in a 37-element fuel bundle has been studied numerically in this work. Results show that secondary flow appears and the cladding surface temperature (CST) is very nonuniform in the fuel bundle. The maximum cladding surface temperature (MaxCST), which is an important design parameter for SCWR, can be predicted and analyzed using the CFD method. Due to a very large circumferential temperature gradient in cladding surfaces of the fuel bundle, the precise cladding temperature distributions using the CFD method is highly recommended. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    PI: Yang, Judith C., Mechanical Eng. & Materials Science, University of Pittsburgh; Co-PI: McGaughey, Alan, Mechanical Eng., Carnegie Mellon University; Sinnott, Susan and Phillpot, Simon, Materials Science & Eng., University of Florida

    2007-09-30

    , and calculations of these values are part of the ongoing effort with University of Florida (UF) and proposed activity with Carnegie Mellon University (CMU). Brief highlights of our progress to date are summarized below: - Development of TFOx-2D, a versatile kinetic Monte Carlo code that can simulate atomistic transport, nucleation and growth, and includes potential gradients to simulate medium-range substrate mediated effects (e.g., strain). - Systematic study of TFOx-2D input parameters to reveal a variety of nano-structures that resemble those seen experimentally. - Parallelization of the Streitz-Mintmire potential and Rappe-Goddard approach for determining dynamic charge transfer at a metal-oxide interface, which is the critical step required for molecular dynamic simulations of oxygen-metal interactions. - Benchmark calculations of Cu and Cu2O physical properties to determine the most accurate electronic structure approach. - Demonstration of the greater universality of the Tersoff-Tromp elastic strain relief model of nano-rod formation to a gas-surface reaction. Hence, we have established the ground work for a truly comprehensive and multi-scale theoretical tool that can simulate any gas-surface reaction, including oxidation, from the atomic level to the mesoscale, from first principles. The direct comparison between these simulations and in situ experiments of metal nano-oxidation will lead to new knowledge of this important surface reaction.

  14. Measurement of Quasi-periodic Oscillating Flow Motion in Simulated Dual-cooled Annular Fuel Bundle

    International Nuclear Information System (INIS)

    In order to increase a significant amount of reactor power in OPR1000, KAERI (Korea Atomic Energy Research Institute) has been developing a dual-cooled annular fuel. The dual-cooled annular fuel is simultaneously cooled by the water flow through the inner and the outer channels. KAERI proposed the 12x12 dual-cooled annular fuel array which was designed to be structurally compatible with the 16x16 cylindrical solid fuel array by maintaining the same array size and the guide tubes in the same locations, as shown in Fig. 1. In such a case, due to larger outer diameter of dual-cooled annular fuel than conventional solid fuel, a P/D (Pitch-to-Diameter ratio) of dual cooled annular fuel assembly becomes smaller than that of cylindrical solid fuel. A change in P/D of fuel bundle can cause a difference in the flow mixing phenomena between the dual-cooled annular and conventional cylindrical solid fuel assemblies. In this study, the rod bundle flow motion appearing in a small P/D case is investigated preliminarily using PIV (Particle Image Velocimetry) for dual-cooled annular fuel application

  15. Confinement-dependent friction in peptide bundles.

    Science.gov (United States)

    Erbaş, Aykut; Netz, Roland R

    2013-03-19

    Friction within globular proteins or between adhering macromolecules crucially determines the kinetics of protein folding, the formation, and the relaxation of self-assembled molecular systems. One fundamental question is how these friction effects depend on the local environment and in particular on the presence of water. In this model study, we use fully atomistic MD simulations with explicit water to obtain friction forces as a single polyglycine peptide chain is pulled out of a bundle of k adhering parallel polyglycine peptide chains. The whole system is periodically replicated along the peptide axes, so a stationary state at prescribed mean sliding velocity V is achieved. The aggregation number is varied between k = 2 (two peptide chains adhering to each other with plenty of water present at the adhesion sites) and k = 7 (one peptide chain pulled out from a close-packed cylindrical array of six neighboring peptide chains with no water inside the bundle). The friction coefficient per hydrogen bond, extrapolated to the viscous limit of vanishing pulling velocity V → 0, exhibits an increase by five orders of magnitude when going from k = 2 to k = 7. This dramatic confinement-induced friction enhancement we argue to be due to a combination of water depletion and increased hydrogen-bond cooperativity. PMID:23528088

  16. Heat transfer to liquid metals in a hexagonal rod bundle with grid spacers: Experimental and simulation results

    International Nuclear Information System (INIS)

    Highlights: • Forced-convective flow of LBE along rod bundles is studied. • A 19-rod bundle with three gird spacers is studied experimentally. • Pre-test and post-test analyses support the experiment, with good agreement. • Advanced models are developed and tested for this geometry. - Abstract: Thermal-hydraulics is a key scientific subject to be investigated for the development of innovative reactor systems. For applications using liquid metals as coolants this task is particularly challenging due to their very low Prandtl number (Pr), preventing the application of common analogies between the turbulent transport of momentum and heat. Thus specific models and validation data with low-Pr fluids are required for representing safety-related thermal-hydraulic scenarios, such as heat transfer in fuel assemblies. Aiming to achieve a better understanding of these flow scenarios, in the European FP7 cooperation project THINS (2010–2014) this subject is investigated at three complementary levels. An experimental campaign consisting of an electrically heated 19-pin hexagonal rod bundle cooled by lead-bismuth eutectic (LBE) is carried out at typical reactor conditions in terms of operating temperature, power density and velocity. Both pre- and post-test analyses using existing numerical tools are performed for evaluating the differential pressure and heat transfer characteristics of the test section. Moreover, advanced turbulence models and numerical techniques are developed and applied to this geometry. Overall, the goals of this project are achieved. The experiments show good degree of repeatability and provide reliable validation data. For intermediate flow rates a good agreement is observed with the results of the heat transfer simulations, based on a constant turbulent Prandtl number. Two advanced approaches for representing the turbulent heat transport considering look-up tables and a four-equation model are successfully tested and overcome the limitations of

  17. CTF/STAR-CD off-line coupling for simulation of crossflow caused by mixing vane spacers in rod bundles

    International Nuclear Information System (INIS)

    Understanding the impact of the spacer grids on the reactor core thermal-hydraulics involves experimental mockup tests, numerical simulations, and development of reliable empirical or semi-empirical models. The state-of-the-art in modeling spacer effects on the thermal-hydraulic performance of the flow in Light Water Reactor (LWR) rod bundles employs numerical experiments by means of Computational Fluid Dynamics (CFD) calculations. The capabilities of the CFD codes are usually being validated against mock-up tests. Once validated, the CFD predictions can be used for improvement and development of more sophisticated models of the subchannel codes. Because of the involved computational cost, CFD codes can not be yet efficiently utilized for full bundle predictions, while advanced subchannel codes are a powerful tool for LWR safety and design analyses. Subchannel analyses are used for whole LWR core evaluations with relatively short CPU times and reasonable computer resources. The objectives of the presented work were to develop, implement, and qualify an innovative spacer grid model utilizing the Computational Fluid Dynamics within a framework of an efficient subchannel analysis tool. A methodology was developed for off-line coupling between the CFD code STAR-CD and the subchannel code CTF. The developed coupling scheme is flexible in axial mesh overlays. It was developed to be easily adapted to any pair of a CFD and a subchannel code. Separate modeling of the spacer grid effects on the diffusive and on the convective processes was implemented and successfully validated against experimental data. (author)

  18. 3D 'atomistic' simulations of dopant induced variability in nanoscale implant free In0.75Ga0.25As MOSFETs

    Science.gov (United States)

    Seoane, N.; Aldegunde, M.; García-Loureiro, A.; Valin, R.; Kalna, K.

    2012-03-01

    A detailed simulation study of the impact of quantum effects on random dopant induced fluctuations in a 15 nm gate length, implant free In0.75Ga0.25As MOSFET is carried out using parallel 3D finite-element drift-diffusion (DD) device simulations and a mesh with atomistic resolution. The DD device simulations are calibrated against finite element heterostructure ensemble Monte Carlo simulations. Three figures of merit for the off-state have been investigated: threshold voltage, off-current, and sub-threshold slope. Quantum confinement effects are taken into account through the density gradient approximation meticulously calibrating carrier density in the channel against 1D Poisson-Schrödinger solutions. We have shown that the net result of including quantum effects, while considering statistical dopant fluctuations, is a decrease in both threshold voltage fluctuations and threshold voltage shift. These results show the opposite trend generally seen in bulk Si MOSFETs simulated using 3D quantum corrected DD simulations with random discrete dopants in the channel region.

  19. 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.

  20. Numerical simulation of multidimensional two-phase boiling flow in rod bundles

    International Nuclear Information System (INIS)

    The present paper describes an approach to model two-phase boiling flow in a nuclear rod bundles with multidimensional treatment of the phenomena. The model is based on the two-fluid approach, and is treating 5 different flow fields. The fields are used to describe the two-phase flow structure, which can consist of continuous liquid phase, continuous gas phase, dispersed liquid phase (drops), dispersed gas phase (bubbles) and liquid film. A distinction is made between the continuous liquid phase and the liquid film, since the latter one is described by a quasi 2D field, whereas all other fields are considered in fully 3D space. The governing equations are solved with the CFX code, a widely used and accepted Computational Fluid Dynamics solver developed at AEA Technology, UK. The system of the governing equations is completed with closure relationships to describe interfacial mass, momentum and energy transfer. The droplets diffusion and deposition on the liquid film in annular flow are modelled with the Lagrangian frame of reference. The model is applied for prediction of multidimensional distribution of void fraction in bubbly flow with subcooled boiling heat transfer, and also for prediction of void fraction and liquid film thickness in annular boiling flow. The calculations are compared with measured data and a good agreement is obtained. (author)

  1. CANFLEX fuel bundle impact test

    International Nuclear Information System (INIS)

    This document outlines the test results for the impact test of the CANFLEX fuel bundle. Impact test is performed to determine and verify the amount of general bundle shape distortion and defect of the pressure tube that may occur during refuelling. The test specification requires that the fuel bundles and the pressure tube retain their integrities after the impact test under the conservative conditions (10 stationary bundles with 31kg/s flow rate) considering the pressure tube creep. The refuelling simulator operating with pneumatic force and simulated shield plug were fabricated and the velocity/displacement transducer and the high speed camera were also used in this test. The characteristics of the moving bundle (velocity, displacement, impacting force) were measured and analyzed with the impact sensor and the high speed camera system. The important test procedures and measurement results were discussed as follows. 1) Test bundle measurements and the pressure tube inspections 2) Simulated shield plug, outlet flange installation and bundle loading 3) refuelling simulator, inlet flange installation and sensors, high speed camera installation 4) Perform the impact test with operating the refuelling simulator and measure the dynamic characteristics 5) Inspections of the fuel bundles and the pressure tube. (author). 8 refs., 23 tabs., 13 figs

  2. CANFLEX fuel bundle impact test

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Seok Kyu; Chung, C. H.; Park, J. S.; Hong, S. D.; Kim, B. D.

    1997-08-01

    This document outlines the test results for the impact test of the CANFLEX fuel bundle. Impact test is performed to determine and verify the amount of general bundle shape distortion and defect of the pressure tube that may occur during refuelling. The test specification requires that the fuel bundles and the pressure tube retain their integrities after the impact test under the conservative conditions (10 stationary bundles with 31kg/s flow rate) considering the pressure tube creep. The refuelling simulator operating with pneumatic force and simulated shield plug were fabricated and the velocity/displacement transducer and the high speed camera were also used in this test. The characteristics of the moving bundle (velocity, displacement, impacting force) were measured and analyzed with the impact sensor and the high speed camera system. The important test procedures and measurement results were discussed as follows. 1) Test bundle measurements and the pressure tube inspections 2) Simulated shield plug, outlet flange installation and bundle loading 3) refuelling simulator, inlet flange installation and sensors, high speed camera installation 4) Perform the impact test with operating the refuelling simulator and measure the dynamic characteristics 5) Inspections of the fuel bundles and the pressure tube. (author). 8 refs., 23 tabs., 13 figs.

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

    Science.gov (United States)

    Raffaini, Giuseppina; Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

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

    Science.gov (United States)

    Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Summary Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

  5. CFD simulation of turbulent flow in a rod bundle with spacer grids (MATIS-H) using STAR-CCM+

    Energy Technology Data Exchange (ETDEWEB)

    Cinosi, N., E-mail: n.cinosi@imperial.ac.uk; Walker, S.P.; Bluck, M.J.; Issa, R.

    2014-11-15

    Highlights: • CDF simulation of turbulent flow generated by a typical PWR spacer grid. • Benchmarking against the MATIS-H experiments run at KAERI in Daejeon, Korea. • Deployment of various steady RANS models to compute the turbulence. • Sensitivity analysis of hardware components. - Abstract: This paper presents the CFD simulation of the turbulent flow generated by a model PWR spacer grid within a rod bundle. The investigation was part of the MATIS-H benchmark exercise, organized by the OECD-NEA, with measurements performed at the KAERI facilities in Daejeon, Korea. The study employed the CD-Adapco code Star-CCM+. An initial sensitivity study was conducted to attempt to assess the importance to the overall flow of components such as the outlet plenum and the end support grid; these were shown to be able to be safely neglected, but the tapered end portion of the rods was found to be significant, and this was incorporated in the model analyzed. A RANS model using any of K-epsilon, K-omega and Reynolds-stress turbulence models was found to be adequate for the prediction of mean velocity profiles, but they all three underestimate the time-averaged turbulent velocity components. Vorticity seems to be better predicted, although the measured values of vorticity are only presented via colored contour plots, making quantitative comparison rather difficult. Circulation, calculated via an integral for each channel, seems to be well predicted by all three models.

  6. Evidence for faster etching at the mask-substrate interface: atomistic simulation of complex cavities at the micron-/submicron-scale by the continuous cellular automaton

    Science.gov (United States)

    Gosálvez, M. A.; Ferrando, N.; Fedoryshyn, Y.; Leuthold, J.; McPeak, K. M.

    2016-04-01

    We combine experiments and simulations to study the acceleration of anisotropic etching of crystalline silicon at the mask-substrate interface, as a function of the coordination number of the substrate atoms located at the junction between obtuse-angled {1 1 1} facets and the mask layer. Atomistic simulations based on the use of the continuous cellular automaton (CCA) conclude that the interface atoms react faster with the etchant, thus initiating a step flow process that results in increased etch rates for the obtuse facets. By generating a wide range of complex cavities on high-index silicon wafers with a single-side, single-step etching, the comparison of the experimental and simulated results strongly indicates that the CCA method is suitable for accurately describing not only the development of micron-scaled structures but also, for the first time, the formation of submicron shapes. The study also describes the acceleration of obtuse facets formed through double-side etching, obtaining results in good agreement with previous experiments.

  7. Large Eddy Simulation of turbulent flow in wire wrapped fuel pin bundles cooled by sodium

    International Nuclear Information System (INIS)

    The objective of the study is to understand the thermal hydraulics in a core sub-assembly with liquid sodium as coolant by performing detailed numerical simulations. The passage for the coolant flow between the fuel rods is maintained by thin wires wrapped around the rods. The contact point between the fuel pin and the spacer wire is the region of creation of hot spots and a cyclic variation of temperature in hot spots can adversely affect the mechanical properties of the clad due to the phenomena like thermal stripping. The current status quo provides two different models to perform the numerical simulations, namely Reynolds Averaged Navier-Stokes (RANS) and Large Eddy Simulation (LES). The two models differ in the extent of modelling used to close the Navier-Stokes equations. LES is a filtered approach where the large scale of motions are explicitly resolved while the small scale motions are modelled whereas RANS is a time averaging approach where all scale of motions are modelled. Thus LES involves less modelling as compared to RANS and so the results are comparatively more accurate. An attempt has been made to use the LES model. The simulations have been performed using the code Trio-U (developed by CEA). The turbulent statistics of the flow and thermal quantities are calculated. Finally the goal is to obtain the frequency of temperature oscillations at the region of hot spots near the spacer wire. (authors)

  8. Simulation of hemp fibre bundle and cores using discrete element method

    Energy Technology Data Exchange (ETDEWEB)

    Al-Amin Sadek, M.; Chen, Y. [Manitoba Univ., Winnipeg, MB (Canada). Dept. of Biosystems Engineering; Lague, C. [Ottawa Univ., Ottawa, ON (Canada). Faculty of Engineering; Landry, H. [Prairie Agricultural Machinery Inst., Humboldt, SK (Canada); Peng, Q. [Manitoba Univ., Winnipeg, MB (Canada). Dept. of Mechanical and Manufacturing Engineering; Zhong, W. [Manitoba Univ., Winnipeg, MB (Canada). Dept. of Textile Sciences

    2010-07-01

    The mechanical behaviour of hemp fibre and core must be well understood in order to obtain high-grade hemp fibre that is currently in high demand for various industrial applications. Modelling by discrete element method can simulate the mechanical behaviour of such materials. A commercial discrete element software called Particle Flow Code was used in this study. In particular, the 3-dimension (PFC3D) was used to simulate hemp fibre and core. Since the basic PFC3D particles are spherical, the individual virtual hemp fibres were defined as strings of balls held together by PFC3D parallel bonds. The study showed that the virtual fibre is flexible and can bend and break by forces. This reflects the characteristics of hemp fibre. Using the clump logic of PFC3D, the virtual hemp core was defined as a rigid and unbreakable body, which reflect the characteristics of the core. The virtual fibre and core were defined with several microproperties, some of which were previously calibrated. The PFC3D bond properties were calibrated in this study. They included normal and shear stiffness; pb{sub k}n and pb{sub k}s; normal and shear strength; and bond disk radius, R of the virtual fibre. The calibration started with developing a PFC3D model to simulate fibre tensile test. The microproperties of virtual fibre and core were calibrated by running the PFC3D model. Literature data from fibre tensile tests was compared with simulation results.

  9. Large eddy simulation of new subgrid scale model for three-dimensional bundle flows

    International Nuclear Information System (INIS)

    Having led to increased inefficiencies and power plant shutdowns fluid flow induced vibrations within heat exchangers are of great concern due to tube fretting-wear or fatigue failures. Historically, scaling law and measurement accuracy problems were encountered for experimental analysis at considerable effort and expense. However, supercomputers and accurate numerical methods have provided reliable results and substantial decrease in cost. In this investigation Large Eddy Simulation has been successfully used to simulate turbulent flow by the numeric solution of the incompressible, isothermal, single phase Navier-Stokes equations. The eddy viscosity model and a new subgrid scale model have been utilized to model the smaller eddies in the flow domain. A triangular array flow field was considered and numerical simulations were performed in two- and three-dimensional fields, and were compared to experimental findings. Results show good agreement of the numerical findings to that of the experimental, and solutions obtained with the new subgrid scale model represent better energy dissipation for the smaller eddies. (author)

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

    International Nuclear Information System (INIS)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rao, S.I., E-mail: satish.rao@wpafb.af.mil [UES Inc., 4401 Dayton-Xenia Road, Dayton, OH 45432-1894 (United States); Dimiduk, D.M. [Air Force Research Laboratory, Materials and Manufacturing Directorate, AFRL/MLLM Wright-Patterson AFB, OH 45433-7817 (United States); El-Awady, J.A. [UTC, Dayton, OH 45432 (United States); Parthasarathy, T.A. [UES Inc., 4401 Dayton-Xenia Road, Dayton, OH 45432-1894 (United States); Uchic, M.D.; Woodward, C. [Air Force Research Laboratory, Materials and Manufacturing Directorate, AFRL/MLLM Wright-Patterson AFB, OH 45433-7817 (United States)

    2010-10-15

    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({radical}(3)d/b)]{sup 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.

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

    Science.gov (United States)

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

    2012-03-01

    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 PbTiO3 and tetragonal Pb(Zr,Ti)O3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed.

  13. Benchmark of SIMULATE5 thermal hydraulics against the Frigg and NUPEC full bundle test experiments

    International Nuclear Information System (INIS)

    SIMULATE5 is Studsvik Scandpower's next generation nodal code. The core portion of the thermal hydraulic models of PWR and BWRs are treated as essentially identical, with each assembly having an active channel and a number of parallel water channels. In addition, the BWR assembly may be divided into four radial sub-assemblies. For natural circulation reactors, the BWR thermal hydraulic model is capable of modeling an entire vessel loop: core, chimney, upper plenum, standpipes, steam separators, downcomer, recirculation pumps, and lower plenum. This paper presents results of the validation of the BWR thermal hydraulic model against: (1) pressure drop data measured in the Frigg and NUPEC test facilities; (2) void fraction distribution measured in the Frigg and NUPEC loops; (3) quarter-assembly void fraction measured in the NUPEC experiments and (4) natural and forced circulation flow measurements in the Frigg loop. (author)

  14. Unsteady Reynolds Averaged Navier-Stokes and Large Eddy Simulations of Flows across Staggered Tube Bundle for a VHTR Lower Plenum Design

    International Nuclear Information System (INIS)

    In this work, behavior of unsteady and oscillating flow through a typical tube bundle array are analyzed by unsteady computations: 2D unsteady Reynolds averaged Navier-Stokes (URANS) and 3D Large Eddy Simulation (LES) and the results are compared with existing experimental data. In order to confirm appropriateness and limitations of CFD applications in the Korean VHTR design, two types of unsteady computations are performed such as 2D unsteady Reynolds averaged Navier-Stokes (URANS) and 3D Large Eddy Simulation (LES) for the existing tube bundle array. The velocity component profiles are compared with the experimental data and it is concluded that the URANS with the standard k-ω model is reasonably appropriate for cost-effective VHTR lower plenum analysis. Nevertheless, if more accurate results are needed, the LES-Smagorinsky computation is recommended considering limitations in the time averaged RANS in capturing small eddies

  15. Numerical simulations of void fractions in air-water tests with a 4 x 4 rod bundle under stagnant water conditions

    International Nuclear Information System (INIS)

    After termination of natural circulation during hypothetical accidents in light water reactors, vapor generated by decay heat forms two-phase flow in stagnant coolant liquid and rises in a reactor core. In these conditions, void fractions in the reactor core affect the two-phase mixture level and cooling of fuel rods. In this study, numerical simulations were carried out for a 4 x 4 rod bundle which was a mock-up of the PWR core by using the computational fluid dynamics (CFD) software, FLUENT 6.3.26. Simulated void fractions showed a similar trend to air-water data but were about 0.10 higher than measured void fractions at large air volumetric fluxes. Over-prediction of void fractions might be due to severe flooding at the upper end of the bundle. (author)

  16. Bundling biodiversity

    OpenAIRE

    Heal, Geoffrey

    2002-01-01

    Biodiversity provides essential services to human societies. Many of these services are provided as public goods, so that they will typically be underprovided both by market mechanisms (because of the impossibility of excluding non-payers from using the services) and by government-run systems (because of the free rider problem). I suggest here that in some cases the public goods provided by biodiversity conservation can be bundled with private goods and their value to consumers captured in th...

  17. Simulation of the VVER-Type bundle experiment QUENCH-12 with ATHLET-CD

    International Nuclear Information System (INIS)

    To ensure the coolability of an overheated core, reflood of the uncovered fuel elements is an essential accident management measure to terminate a severe accident transient in Light Water Reactors (LWR) and therefore to avoid further core degradation. From analysis of the TMI-2 accident it is known that an enhanced oxidation of the zircaloy cladding may occur before the water succeeds in cooling the fuel rods. This oxidation process results in a sharp temperature increase, hydrogen generation and can finally after fuel rod cladding failure lead to fission product release. For further development and validation of the program ATHLET-CD, post-test calculations of experiments creating a reflood scenario in a controlled and defined environment are used. One of these experiments is QUNECH-12 in which Zr1%Nb (E 110) fuel rod claddings are used. Typically, fuel rods of VVER reactors are made from this material. In this work, the QUENCH-12 experiment and its conduct will be presented followed by explanations of the modeling in ATHLET-CD version 2.2A. Results of ATHLET-CD simulating the test will be discussed in order to validate the code's ability to adequately calculate phenomena like hydrogen production and melt oxidation during reflooding of uncovered fuel rods of E 110. (orig.)

  18. Simulation of the VVER-Type bundle experiment QUENCH-12 with ATHLET-CD

    Energy Technology Data Exchange (ETDEWEB)

    Bratfisch, Christian; Hoffmann, Mathias; Koch, Marco K. [Bochum Univ. (Germany). Chair of Energy Systems and Energy Economics (LEE)

    2012-11-01

    To ensure the coolability of an overheated core, reflood of the uncovered fuel elements is an essential accident management measure to terminate a severe accident transient in Light Water Reactors (LWR) and therefore to avoid further core degradation. From analysis of the TMI-2 accident it is known that an enhanced oxidation of the zircaloy cladding may occur before the water succeeds in cooling the fuel rods. This oxidation process results in a sharp temperature increase, hydrogen generation and can finally after fuel rod cladding failure lead to fission product release. For further development and validation of the program ATHLET-CD, post-test calculations of experiments creating a reflood scenario in a controlled and defined environment are used. One of these experiments is QUNECH-12 in which Zr1%Nb (E 110) fuel rod claddings are used. Typically, fuel rods of VVER reactors are made from this material. In this work, the QUENCH-12 experiment and its conduct will be presented followed by explanations of the modeling in ATHLET-CD version 2.2A. Results of ATHLET-CD simulating the test will be discussed in order to validate the code's ability to adequately calculate phenomena like hydrogen production and melt oxidation during reflooding of uncovered fuel rods of E 110. (orig.)

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

    International Nuclear Information System (INIS)

    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.

  20. The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)

    Science.gov (United States)

    Bruno, Agostino; Scrima, Mario; Novellino, Ettore; D'Errico, Gerardino; D'Ursi, Anna Maria; Limongelli, Vittorio

    2015-03-01

    Glycoproteins are often recognized as not-self molecules by antibodies triggering the onset of severe autoimmune diseases such as Multiple Sclerosis (MS). Thus, the development of antigen-mimicking biomarkers represents an attractive strategy for an early diagnosis of the disease. An example is the synthetic glycopeptide CSF114(Glc), which was designed and tested as MS biomarker and whose clinical application was limited by its reduced ability to detect autoantibodies in MS patients. In the attempt to improve the efficacy of CSF114(Glc), we have characterized all the events leading to the final binding of the biomarker to the autoantibody using atomistic simulations, ESR and NMR experiments. The glycosydic moiety plays a primary role in the whole process. In particular, in an environment mimicking that used in the clinical tests the glycopeptide assumes a α-helix structure that is functional for the interaction with the antibody. In this conformation CSF114(Glc) binds the monoclonal antibody mAb8-18C5 similarly to the myelin oligodendrocyte glycoprotein MOG, which is a known MS auto-antigen, thus explaining its diagnostic activity. Our study offers new molecular bases to design more effective biomarkers and provides a most valid protocol to investigate other systems where the environment effect is determinant for the biological activity.

  1. Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provide a general way that is accessible to other metals in laser heating.

  2. Numerical simulation of cross-flow in tube-bundles to model flow circulation of the moderator in CANDU-6

    International Nuclear Information System (INIS)

    The knowledge of external wall temperature distributions around calandria tubes is a major concern during normal and off-normal operating conditions of CANDU power reactors. To this aim, the use of Computational Fluid Dynamics (CFD) techniques to model moderator local flow velocities and temperatures can largely help in performing nuclear safety analyses. However, present numerical codes applied for this purpose makes use of the well known porous media approach. This method necessitates a previous knowledge of distributed hydraulic resistances that must be obtained from appropriate scaled experiments. Within this framework, this paper presents a set of 2D CFD simulations of incompressible cross-flows along in-line and staggered tube bundles. The numerical results are validated against experimental data obtained from the open literature. Calculations are performed using FLUENT-6 code. The Reynolds-Average Navier Stokes (RANS) equations are used in conjunction with several turbulence models and both the SIMPLE (Semi-Implicit Pressure Linked Equation) as well as the coupled pressure-based algorithm. In general, it is observed that two-equation turbulence models are able to reproduce mean velocities. Even though reasonably good predictions of flow distributions along staggered tube set-ups are obtained, the predictions of the pressure drop along in-line tubes are in general not satisfactory. In most cases, the coupled pressure-based algorithm seems to perform better but requires longer computation time. In general, the standard κ-ε is superior to others κ-ε models. The κ-ω model behaves better for fairly well developed flows. (author)

  3. Large-scale atomistic simulations of nanostructured materials based on divide-and-conquer density functional theory

    Science.gov (United States)

    Shimojo, F.; Ohmura, S.; Nakano, A.; Kalia, R. K.; Vashishta, P.

    2011-05-01

    A linear-scaling algorithm based on a divide-and-conquer (DC) scheme is designed to perform large-scale molecular-dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). This scheme is applied to the thermite reaction at an Al/Fe2O3 interface. It is found that mass diffusion and reaction rate at the interface are enhanced by a concerted metal-oxygen flip mechanism. Preliminary simulations are carried out for an aluminum particle in water based on the conventional DFT, as a target system for large-scale DC-DFT simulations. A pair of Lewis acid and base sites on the aluminum surface preferentially catalyzes hydrogen production in a low activation-barrier mechanism found in the simulations

  4. Large-scale atomistic simulations of nanostructured materials based on divide-and-conquer density functional theory

    Directory of Open Access Journals (Sweden)

    Vashishta P.

    2011-05-01

    Full Text Available A linear-scaling algorithm based on a divide-and-conquer (DC scheme is designed to perform large-scale molecular-dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT. This scheme is applied to the thermite reaction at an Al/Fe2O3 interface. It is found that mass diffusion and reaction rate at the interface are enhanced by a concerted metal-oxygen flip mechanism. Preliminary simulations are carried out for an aluminum particle in water based on the conventional DFT, as a target system for large-scale DC-DFT simulations. A pair of Lewis acid and base sites on the aluminum surface preferentially catalyzes hydrogen production in a low activation-barrier mechanism found in the simulations

  5. Dynamics of flagellar bundling

    Science.gov (United States)

    Janssen, Pieter; Graham, Michael

    2010-11-01

    Flagella are long thin appendages of microscopic organisms used for propulsion in low-Reynolds environments. For E. coli the flagella are driven by a molecular motor, which rotates the flagella in a counter-clockwise motion (CCM). When in a forward swimming motion, all flagella bundle up. If a motor reverses rotation direction, the flagella unbundle and the cell makes a tumbling motion. When all motors turn in the same CC direction again, the flagella bundle up, and forward swimming continues. To investigate the bundling, we consider two flexible helices next to each other, as well as several flagella attached to a spherical body. Each helix is modeled as several prolate spheroids connected at the tips by springs. For hydrodynamic interactions, we consider the flagella to made up of point forces, while the finite size of the body is incorporated via Fax'en's laws. We show that synchronization occurs quickly relative to the bundling process. For flagella next to each other, the initial deflection is generated by rotlet interactions generated by the rotating helices. At longer times, simulations show the flagella only wrap once around each other, but only for flagella that are closer than about 4 helix radii. Finally, we show a run-and-tumble motion of the body with attached flagella.

  6. Numerical simulation, statistical and hybrid turbulence modelling in a tube bundle under crossflow at high Reynolds number in the context of fluid-structure interaction

    International Nuclear Information System (INIS)

    The prediction of fluid-elastic instabilities that develop in a tube bundle is of major importance for the design of modern heat exchangers in nuclear reactors, to prevent accidents associated with such instabilities. The fluid-elastic instabilities, or flutter, cause material fatigue, shocks between beams and damage to the solid walls. These issues are very complex for scientific applications involving the nuclear industry. This work is a collaboration between EDF, CEA and IMFT. It aims to improve the numerical simulation of the fluid-structure interaction in the tube bundle, in particular in the range of critical parameters contribute to the onset of damping negative system and the fluid-elastic instability. (author)

  7. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

    International Nuclear Information System (INIS)

    Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (ATOPLS). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the ATOPLS PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (ATCHARMM) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, ATOPLS PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA)3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret CG and

  8. 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

    helical segment brought about an interesting view that the flexible loop observed in our work can be a common structural element in these types of proteins. In the same spirit we close the article by discussing the role of salt bridges in the formation of three-dimensional structures of membrane proteins...... 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...

  9. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

    DEFF Research Database (Denmark)

    Kaszuba, K.; Postila, P. A.; Cramariuc, O.;

    2013-01-01

    -molecular interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...... verified by running a 200-ns MD simulation encompassing the entire cyt bc(1) complex embedded in a lipid bilayer and solvated with explicit water. The results indicate that these meticulously derived parameters are ready for running extensive MD simulations encompassing all biologically relevant stages of...

  10. Large-scale atomistic simulations of nanostructured materials based on divide-and-conquer density functional theory

    OpenAIRE

    Vashishta P.; Kalia R. K.; Shimojo F.; Ohmura S.; Nakano A.

    2011-01-01

    A linear-scaling algorithm based on a divide-and-conquer (DC) scheme is designed to perform large-scale molecular-dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). This scheme is applied to the thermite reaction at an Al/Fe2O3 interface. It is found that mass diffusion and reaction rate at the interface are enhanced by a concerted metal-oxygen flip mechanism. Preliminary simulations are carried out for ...

  11. Atomistic simulation of tantalum nanoindentation: Effects of indenter diameter, penetration velocity, and interatomic potentials on defect mechanisms and evolution

    International Nuclear Information System (INIS)

    Nanoindentation simulations are a helpful complement to experiments. There is a dearth of nanoindentation simulations for bcc metals, partly due to the lack of computationally efficient and reliable interatomic potentials at large strains. We carry out indentation simulations for bcc tantalum using three different interatomic potentials and present the defect mechanisms responsible for the creation and expansion of the plastic deformation zone: twins are initially formed, giving rise to shear loop expansion and the formation of sequential prismatic loops. The calculated elastic constants as function of pressure as well as stacking fault energy surfaces explain the significant differences found in the defect structures generated for the three potentials investigated in this study. The simulations enable the quantification of total dislocation length and twinning fraction. The indenter velocity is varied and, as expected, the penetration depth for the first pop-in (defect emission) event shows a strain rate sensitivity m in the range of 0.037–0.055. The effect of indenter diameter on the first pop-in is discussed. A new intrinsic length-scale model is presented based on the profile of the residual indentation and geometrically necessary dislocation theory

  12. Atomistic simulation of tantalum nanoindentation: Effects of indenter diameter, penetration velocity, and interatomic potentials on defect mechanisms and evolution

    Energy Technology Data Exchange (ETDEWEB)

    Ruestes, C.J., E-mail: cjruestes@hotmail.com [Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States); Facultad de Ciencias Exactas y Naturales, Univ. Nac. de Cuyo, Mendoza 5500 (Argentina); CONICET, Mendoza 5500 (Argentina); Stukowski, A. [Technische Universität Darmstadt, Darmstadt 64287 (Germany); Tang, Y. [Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072 (China); Tramontina, D.R. [Facultad de Ciencias Exactas y Naturales, Univ. Nac. de Cuyo, Mendoza 5500 (Argentina); Erhart, P. [Chalmers University of Technology, Department of Applied Physics, Gothenburg 41296 (Sweden); Remington, B.A. [Lawrence Livermore National Lab, Livermore, CA 94550 (United States); Urbassek, H.M. [Physics Department and Research Center OPTIMAS, University of Kaiserslautern, Kaiserslautern 67663 (Germany); Meyers, M.A. [Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States); Bringa, E.M. [Facultad de Ciencias Exactas y Naturales, Univ. Nac. de Cuyo, Mendoza 5500 (Argentina); CONICET, Mendoza 5500 (Argentina)

    2014-09-08

    Nanoindentation simulations are a helpful complement to experiments. There is a dearth of nanoindentation simulations for bcc metals, partly due to the lack of computationally efficient and reliable interatomic potentials at large strains. We carry out indentation simulations for bcc tantalum using three different interatomic potentials and present the defect mechanisms responsible for the creation and expansion of the plastic deformation zone: twins are initially formed, giving rise to shear loop expansion and the formation of sequential prismatic loops. The calculated elastic constants as function of pressure as well as stacking fault energy surfaces explain the significant differences found in the defect structures generated for the three potentials investigated in this study. The simulations enable the quantification of total dislocation length and twinning fraction. The indenter velocity is varied and, as expected, the penetration depth for the first pop-in (defect emission) event shows a strain rate sensitivity m in the range of 0.037–0.055. The effect of indenter diameter on the first pop-in is discussed. A new intrinsic length-scale model is presented based on the profile of the residual indentation and geometrically necessary dislocation theory.

  13. Atomistic simulations of grain boundary segregation in nanocrystalline yttria-stabilized zirconia and gadolinia-doped ceria solid oxide electrolytes

    International Nuclear Information System (INIS)

    Hybrid Monte Carlo–molecular dynamics simulations are carried out to study defect distributions near Σ5(3 1 0)/[0 0 1] pure tilt grain boundaries (GBs) in nanocrystalline yttria-stabilized zirconia and gadolinia-doped ceria. The simulations predict equilibrium distributions of dopant cations and oxygen vacancies in the vicinity of the GBs where both materials display considerable amounts of dopant segregation. The predictions are in qualitative agreement with various experimental observations. Further analyses show that the degree of dopant segregation increases with the doping level and applied pressure in both materials. The equilibrium segregation profiles are also strongly influenced by the microscopic structure of the GBs. The high concentration of oxygen vacancies at the GB interface due to lower vacancy formation energies triggers the dopant segregation, and the final segregation profiles are largely determined by the dopant–vacancy interaction

  14. Evaluation of a numeric procedure for flow simulation of a 5X5 PWR rod bundle with a mixing vane spacer

    International Nuclear Information System (INIS)

    The fuel assemblies of the Pressurized Water Reactors (PWR) are constituted of rod bundles arranged in a regular square configuration by spacer grids placed along its length. The presence of the spacer grids promote two antagonist effects on the core: a desirable increase of the local heat transfer downstream the grids and an adverse increase of the pressure drop due the constriction on the coolant flow area. Most spacer grids are designed with mixing vanes which cause a cross and swirl flow between and within the subchannels, enhancing even more the heat transfer performance in the grid vicinity. The improvement of the heat transfer increases the departure from the nucleate boiling ratio, allowing higher operating power in the reactor. Due to these important thermal and fluid dynamic features, experimental and theoretical investigations have been carried out in the past years for the development of spacer grid design. More recently, the Computational Fluid Dynamics (CFD) using three dimensional Reynolds Averaged Navier Stokes (RANS) analysis has been used efficiently for this purpose. Many computational works have been performed, but the appropriate numerical procedure for the flow in rod bundle simulations is not yet a consensus. This work presents results of flow simulations performed with the commercial code CFX 11.0 in a PWR 5x5 rod bundle segment with a split vane spacer grid. The geometrical configuration and flow conditions used in the experimental studies performed by Karoutas et al. were assumed in the simulations. To make the simulation possible with a limited computational capacity and acceptable mesh refinement, the computational domain was divided in 7 subdomains. The subdomains were simulated sequentially applying the outlet results of a previous subdomain as inlet condition for the next. In this study the κ-ε turbulence model was used. The simulations were also compared with those performed by Karoutas et al. in half a subchannel and In et al. in

  15. Fuel bundle

    International Nuclear Information System (INIS)

    This patent describes a method of forming a fuel bundle of a nuclear reactor. The method consists of positioning the fuel rods in the bottom plate, positioning the tie rod in the bottom plate with the key passed through the receptacle to the underside of the bottom plate and, after the tie rod is so positioned, turning the tie rod so that the key is in engagement with the underside of the bottom plate. Thereafter mounting the top plate is mounted in engagement with the fuel rods with the upper end of the tie rod extending through the opening in the top plate and extending above the top plate, and the tie rod is secured to the upper side of sid top plate thus simultaneously securing the key to the underside of the bottom plate

  16. Strain-Rate Dependence of Material Strength: Large-Scale Atomistic Simulations of Defective Cu and Ta Crystals

    Science.gov (United States)

    Abeywardhana, M.; Vasquez, A.; Gaglione, J.; Germann, T. C.; Ravelo, R.

    2015-06-01

    Large-Scale molecular dynamics (MD) simulations are used to model shock wave (SW) and quasi-isentropic compression (QIC) in defective copper and tantalum crystals. The atomic interactions were modeled employing embedded-atom method (EAM) potentials. In the QIC simulations, the MD equations of motion are modified by incorporating a collective strain rate function in the positions and velocities equations, so that the change in internal energy equals the PV work on the system. We examined the deformation mechanisms and material strength for strain rates in the 109-1012 s-1 range For both Cu and Ta defective crystals, we find that the strain rate dependence of the flow stress in this strain rate regime, follows a power law with an exponent close to 0.40. This work was supported by the Air Force Office of Scientific Research under AFOSR Award No. FA9550-12-1-0476. Work at Los Alamos was performed under the auspices of the U.S. Department of Energy (DOE) under Contract No. DE-AC52-06NA25396.

  17. Defects and threshold displacement energies in SrTiO{sub 3} perovskite using atomistic computer simulations

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, B.S. [Australian Nuclear Science and Technology Organisation, Private Mail Bag 1, New Illawarra Road, Menai NSW 2234 (Australia); School of Physics, University of Sydney NSW 2006 (Australia); E-mail: b.thomas@ansto.gov.au; Marks, N.A. [School of Physics, University of Sydney NSW 2006 (Australia); Begg, B.D. [Australian Nuclear Science and Technology Organisation, Private Mail Bag 1, New Illawarra Road, Menai NSW 2234 (Australia)

    2007-01-15

    The mode and energy of simple defect incorporation in SrTiO{sub 3} (vacancies and interstitials) is quantified using computer simulation techniques with an empirical partial charge model of interatomic forces, as well as using density functional theory calculations. Oxygen and strontium interstitials form split-interstitial configurations whereas titanium interstitials occupy channel positions. Defect migration energies and paths are also considered; interstitials are more mobile than vacancies, with a low predicted oxygen interstitial migration energy of around 0.3 eV. We also calculate the threshold displacement energy (E{sub d}) for each atom type in SrTiO{sub 3} perovskite using molecular dynamics simulations, by introducing a primary knock-on atom with a range of energies (20-250 eV) in principal crystallographic directions at 300 K. We find that all atom types are most easily displaced via direct replacement sequences on their own sublattices, which are extensive for Sr atoms due to focusson processes acting along channels. The weighted average threshold displacement energies (for use in TRIM-type calculations) are 50 eV for oxygen, 70 eV for strontium and 140 eV for titanium atoms. These computed energies for O and Sr are comparable to experimentally-derived values in perovskites, whereas the E{sub d} for Ti is much higher; it is expected that the value reported here is more accurate due to experimental difficulties in distinguishing different types of defects.

  18. Influences of Zr, Ce and Ba fission products on the surface properties of UO2: Atomistic simulations

    Science.gov (United States)

    Xiao, Hongxing; Long, Chongsheng; Tian, Xiaofeng; Chen, Hongsheng

    2016-07-01

    Molecular dynamics (MD) simulations with a shell-core model have been carried out to investigate the influences of Zr, Ce and Ba fission products on the surface properties of UO2. Simulation results indicate that (i) the presence of these fission products will change the surface energy of three low-index surfaces in UO2; (ii) the individual addition of Ce has no significant effect on the surface energy, while the individual addition of Ba will dramatically decrease the surface energy of UO2 by approximately 18% on (100) surface, 7% on (110) surface and 9% on (111) surface with the Ba contents ranging from 0 to 12.5 mol% at 300 K, which is obviously contrary to the Zr; (iii) the combined additions of Zr, Ce and Ba fission products will continuously increase the surface energy of UO2 (100), (110) and (111) surfaces; (iv) the structures of the three low-index surfaces in pure UO2 as well as U0.8(Zr, Ce, Ba)0.2O2 are dramatically disturbed after the free relaxation; (v) The nearest O atoms move towards the Zr and Ce atoms center by about 0.21 Å and 0.12 Å but move away from the Ba atom center by about 0.27 Å.

  19. Atomistic molecular dynamics simulations of the structure of symmetric Polyelectrolyte block copolymer micelle in salt-free aqueous solution

    Science.gov (United States)

    Chockalingam, Rajalakshmi; Natarajan, Upendra

    2014-03-01

    The structure of a symmetric polystyrene- b - poly(acrylic acid) (PS- b - PAA) micelle in salt-free aqueous solution as a function of degree-of-neutralization (or ionization, f) of the PAA is studied via explicit-atom-ion MD simulations, for the first time for a polyelectrolyte block copolymer in a polar solvent. Micelle size increases with fin agreement with experimental observations in literature, due to extension of PAA at higher ionization. Pair RDF's with respect to water oxygens show that corona-water interaction becomes stronger with f due to an increase in number density of carboxylate (COO-) groups on the chain. Water-PAA coordination (carboxylate O's) increases with ionization. H-bonding between PAA and water increases with f due to greater extent of corona-water affinity. With increase in f, atom and counter-ion ρ profiles confirm extension of corona blocks and micelle existing in the ``osmotic regime,'' and a decrease in scattering peak intensity, in agreement with neutron scattering experiments and mean-field theory in literature. Inter-chain distance in PS core is found to decrease with ionization. Macromolecular Simulation and Modeling Laboratory, Dept. of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036.

  20. Liquid state DNP at high magnetic fields: Instrumentation, experimental results and atomistic modelling by molecular dynamics simulations

    Science.gov (United States)

    Prisner, Thomas; Denysenkov, Vasyl; Sezer, Deniz

    2016-03-01

    Dynamic nuclear polarization (DNP) at high magnetic fields has recently become one of the major research areas in magnetic resonance spectroscopy and imaging. Whereas much work has been devoted to experiments where the polarization transfer from the electron spin to the nuclear spin is performed in the solid state, only a few examples exist of experiments where the polarization transfer is performed in the liquid state. Here we describe such experiments at a magnetic field of 9.2 T, corresponding to a nuclear Larmor frequency of 400 MHz for proton spins and an excitation frequency of 263 GHz for the electron spins. The technical requirements to perform such experiments are discussed in the context of the double resonance structures that we have implemented. The experimental steps that allowed access to the enhancement factors for proton spins of several organic solvents with nitroxide radicals as polarizing agents are described. A computational scheme for calculating the coupling factors from molecular dynamics (MD) simulations is outlined and used to highlight the limitations of the classical models based on translational and rotational motion that are typically employed to quantify the observed coupling factors. The ability of MD simulations to predict enhancements for a variety of radicals and solvent molecules at any magnetic field strength should prove useful in optimizing experimental conditions for DNP in the liquid state.

  1. Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids

    Science.gov (United States)

    Morrow, Brian H.; Koenig, Peter H.; Shen, Jana K.

    2012-11-01

    Detailed knowledge of the self-assembly and phase behavior of pH-sensitive surfactants has implications in areas such as targeted drug delivery. Here we present a study of the formation of micelle and bilayer from lauric acids using a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with conformational sampling in explicit solvent and the pH-based replica-exchange protocol. We find that at high pH conditions a spherical micelle is formed, while at low pH conditions a bilayer is formed with a considerable degree of interdigitation. The mid-point of the phase transition is in good agreement with experiment. Preliminary investigation also reveals that the effect of counterions and salt screening shifts the transition mid-point and does not change the structure of the surfactant assembly. Based on these data we suggest that CpHMD simulations may be applied to computational design of surfactant-based nano devices in the future.

  2. Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel

    DEFF Research Database (Denmark)

    Bjelkmar, Pär; Niemelä, Perttu S; Vattulainen, Ilpo;

    2009-01-01

    the crystal structure where the hyperpolarization destabilizes S4-lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the......, including up to 120 degrees rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation ( approximately 35 degrees ) of the extracellular end of all S4 segments is present also in a reference 0.5 micros simulation without applied field, which...... indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 3(10) helix contents in S4, starting from the intracellular side. This could support a model for transition from...

  3. 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...... determinant of the excimer/monomer fluorescence ratio. Thus, the results do not support the usage of di-pyr-PC molecules to measure the shape of the lateral pressure profile. We yet discuss how the probes could potentially be exploited to gain qualitative insight of the changes in pressure profile when lipid...... 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...

  4. Assessment of hardening due to dislocation loops in bcc iron: Overview and analysis of atomistic simulations for edge dislocations

    Science.gov (United States)

    Bonny, G.; Terentyev, D.; Elena, J.; Zinovev, A.; Minov, B.; Zhurkin, E. E.

    2016-05-01

    Upon irradiation, iron based steels used for nuclear applications contain dislocation loops of both and ½ type. Both types of loops are known to contribute to the radiation hardening and embrittlement of steels. In the literature many molecular dynamics works studying the interaction of dislocations with dislocation loops are available. Recently, based on such studies, a thermo-mechanical model to threat the dislocation - dislocation loop (DL) interaction within a discrete dislocation dynamics framework was developed for ½ loops. In this work, we make a literature review of the dislocation - DL interaction in bcc iron. We also perform molecular dynamics simulations to derive the stress-energy function for loops. As a result we deliver the function of the activation energy versus activation stress for loops that can be applied in a discrete dislocation dynamics framework.

  5. Investigation of the role of polysaccharide in the dolomite growth at low temperature by using atomistic simulations

    CERN Document Server

    Shen, Zhizhang; Szlufarska, Izabela; Xu, Huifang

    2016-01-01

    Dehydration of water from surface Mg2+ is most likely the rate-limiting step in the dolomite growth at low temperature. Here, we investigate the role of polysaccharide in this step using classical molecular dynamics (MD) calculations. Free energy (potential of mean force, PMF) calculations have been performed for water molecules leaving the first two hydration layers above the dolomite (104) surface under the following three conditions: without catalyst, with monosaccharide (mannose) and with oligosaccharide (three units of mannose). MD simulations reveal that there is no obvious effect of monosaccharide in lowering the dehydration barrier for surface Mg2+. However, we found that there are metastable configurations of oligosaccharide, which can decrease the dehydration barrier of surface Mg2+ by about 0.7-1.1 kcal/mol. In these configurations, the molecule lies relatively flat on the surface and forms a bridge shape. The hydrophobic space near the surface created by the non-polar -CH groups of the oligosaccha...

  6. Reactive atomistic simulations of shock-induced initiation processes in mixtures of ammonium nitrate and fuel oil

    International Nuclear Information System (INIS)

    Ammonium nitrate mixed with fuel oil (ANFO) is a commonly used blasting agent. In this paper we investigated the shock properties of pure ammonium nitrate (AN) and two different mixtures of ammonium nitrate and n-dodecane by characterizing their Hugoniot states. We simulated shock compression of pure AN and ANFO mixtures using the Multi-scale Shock Technique, and observed differences in chemical reaction. We also performed a large-scale explicit sub-threshold shock of AN crystal with a 10 nm void filled with 4.4 wt% of n-dodecane. We observed the formation of hotspots and enhanced reactivity at the interface region between AN and n-dodecane molecules.

  7. Atomistic Simulations of Displacement Cascades in Fused Silica: It is Compared with Different Concentration of H in the Bulk

    International Nuclear Information System (INIS)

    Amorphous Silica is one of candidate materials for both final focusing optics of lasers for NIF and future inertial fusion reactors and diagnostics of the Safety and Control Systems of the ITER machine as well as DEMO magnetic fusion reactors. In operation, these materials will be exposed to high neutron irradiation fluxes and it can result in point defect and vary the optical absorption, that is, degradation of the optical properties. In this paper we present molecular dynamic simulation of displacement cascade due to energetic recoils in amorphous silica without hydrogen atoms and with 1% of hydrogen atoms trying to identify defects formation. We have made a statistics of the different kind of defects at different energy of primary knock-on atoms (PKA). The range of studied PKA energies are from 400 eV to 3.5 keV and it is made to both component of this material Silicon and Oxygen. (authors)

  8. The inhibitory mechanism of a fullerene derivative against amyloid-β peptide aggregation: an atomistic simulation study.

    Science.gov (United States)

    Sun, Yunxiang; Qian, Zhenyu; Wei, Guanghong

    2016-05-14

    Alzheimer's disease (AD) is associated with the pathological self-assembly of amyloid-β (Aβ) peptides into β-sheet enriched fibrillar aggregates. Aβ dimers formed in the initial step of Aβ aggregation were reported to be the smallest toxic species. Inhibiting the formation of β-sheet-rich oligomers and fibrils is considered as the primary therapeutic strategy for AD. Previous studies reported that fullerene derivatives strongly inhibit Aβ fibrillation. However, the underlying inhibitory mechanism remains elusive. As a first step to understand fullerene-modulated full-length Aβ aggregation, we investigated the conformational ensemble of the Aβ1-42 dimer with and without 1,2-(dimethoxymethano)fullerene (DMF) - a more water-soluble fullerene derivative - by performing a 340 ns explicit-solvent replica exchange molecular dynamics simulation. Our simulations show that although disordered states are the most abundant conformations of the Aβ1-42 dimer, conformations containing diverse extended β-hairpins are also populated. The first most-populated β-hairpins involving residues L17-D23 and A30-V36 strongly resemble the engineered β-hairpin which is a building block of toxic Aβ oligomers. We find that the interaction of DMFs with Aβ peptides greatly impedes the formation of such β-hairpins and inter-peptide β-sheets. Binding energy analyses demonstrate that DMF preferentially binds not only to the central hydrophobic motif LVFFA of the Aβ peptide as suggested experimentally, but also to the aromatic residues including F4 and Y10 and the C-terminal hydrophobic region I31-V40. This study reveals a complete picture of the inhibitory mechanism of full-length Aβ1-42 aggregation by fullerenes, providing theoretical insights into the development of drug candidates against AD. PMID:27091578

  9. CFD simulating the transient thermal–hydraulic characteristics in a 17 × 17 bundle for a spent fuel pool under the loss of external cooling system accident

    International Nuclear Information System (INIS)

    Highlights: • A 3-D CFD is adopted to simulate transient behaviors in an SFP under the accident. • This model realistically simulates a 17 × 17 bundle, rid of porous media approach. • The loss of external cooling system accident for an SFP is assumed in this paper. • Thermal–hydraulic characteristics in a bundle are strongly influenced by grids. • The results confirm temperature rising rate used in Maanshan NPP is conservative. - Abstract: This paper develops a three-dimensional (3-D) transient computational fluid dynamics (CFD) model to simulate the thermal–hydraulic characteristics in a fuel bundle located in a spent fuel pool (SFP) under the loss of external cooling system accident. The SFP located in the Maanshan nuclear power plant (NPP) is selected herein. Without adopting the porous media approach usually used in the previous CFD works, this model uses a real-geometry simulation of a 17 × 17 fuel bundle, which can obtain the localized distributions of the flow and heat transfer during the accident. These distribution characteristics include several peaks in the axial distributions of flow, pressure, temperature, and Nusselt number (Nu) near the support grids, the non-uniform distribution of secondary flow, and the non-uniform temperature distribution due to flow mixing between rods, etc. According to the conditions adopted in the Procedure 597.1 (MNPP Plant Procedure 597.1, 2010) for the management of the loss-of-cooling event of the spent fuel pool in the Maanshan NPP, the temperature rising rate predicted by the present model can be equivalent to 1.26 K/h, which is the same order as that of 3.5 K/h in the this procedure. This result also confirms that the temperature rising rate used in the Procedure 597.1 for the Maanshan NPP is conservative. In addition, after the loss of external cooling system, there are about 44 h for the operator to repair the malfunctioning system or provide the alternative water source for the pool inventory to

  10. 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

  11. Investigation of the Role of Polysaccharide in the Dolomite Growth at Low Temperature by Using Atomistic Simulations.

    Science.gov (United States)

    Shen, Zhizhang; Szlufarska, Izabela; Brown, Philip E; Xu, Huifang

    2015-09-29

    Dehydration of water from surface Mg(2+) is most likely the rate-limiting step in the dolomite growth at low temperature. Here, we investigate the role of polysaccharide in this step using classical molecular dynamics (MD) calculations. Free energy (potential of mean force, PMF) calculations have been performed for water molecules leaving the first two hydration layers above the dolomite (104) surface under the following three conditions: without catalyst, with monosaccharide (mannose), and with oligosaccharide (three units of mannose). MD simulations reveal that there is no obvious effect of monosaccharide in lowering the dehydration barrier for surface Mg(2+). However, we found that there are metastable configurations of oligosaccharide, which can decrease the dehydration barrier of surface Mg(2+) by about 0.7-1.1 kcal/mol. In these configurations, the molecule lies relatively flat on the surface and forms a bridge shape. The hydrophobic space near the surface created by the nonpolar -CH groups of the oligosaccharide in the bridge conformation is the reason for the observed reduction of dehydration barrier. PMID:26334253

  12. Point defect evolution in Ni, NiFe and NiCr alloys from atomistic simulations and irradiation experiments

    International Nuclear Information System (INIS)

    Using molecular dynamics simulations, we elucidate irradiation-induced point defect evolution in fcc pure Ni, Ni0.5Fe0.5, and Ni0.8Cr0.2 solid solution alloys. We find that irradiation-induced interstitials form dislocation loops that are of 1/3〈1 1 1〉{1 1 1}-type, consistent with our experimental results. While the loops are formed in all the three materials, the kinetics of formation is considerably slower in NiFe and NiCr than in pure Ni, indicating that defect migration barriers and extended defect formation energies could be higher in the alloys than pure Ni. As a result, while larger size clusters are formed in pure Ni, smaller and more clusters are observed in the alloys. Vacancy diffusion occurs at relatively higher temperatures than interstitials, and their clustering leads to the formation of stacking fault tetrahedra, consistent with our experiments. The results also show that the surviving Frenkel pairs are composition dependent and are largely Ni dominated

  13. Atomistic simulations of ammonium-based protic ionic liquids: steric effects on structure, low frequency vibrational modes and electrical conductivity.

    Science.gov (United States)

    Sunda, Anurag Prakash; Mondal, Anirban; Balasubramanian, Sundaram

    2015-02-14

    Protic ionic liquids (PILs) are of great interest as electrolytes in various energy applications. Molecular dynamics simulations of trialkylammonium (with varying alkyl group such as methyl, ethyl, and n-propyl) triflate PILs are performed to characterize the influence of the alkyl group on the acidic site (N-H) of the ammonium cation. Spatial distribution function of anions over this site on the cation reveals significant influence of the length of alkyl tail on intermolecular structure. Vibrational density of states and normal modes are calculated for bulk liquids to probe atomic displacements in the far infrared region. The observed N-H···O hydrogen bond stretching vibration in 155-165 cm(-1) frequency region agrees well with experiments. Trends in electrical conductivity calculated using Nernst-Einstein and Green-Kubo relation are in qualitative agreement with experiments. The self-diffusion coefficient and the electrical conductivity is highest for N,N-dimethyl-N-ethylammonium triflate ([N112][TfO]) and is lowest for N,N-di-n-propyl-N-methylammonium triflate ([N133][TfO]) IL. PMID:25585541

  14. Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations.

    Science.gov (United States)

    Comitani, Federico; Melis, Claudio; Molteni, Carla

    2015-04-01

    Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand-protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed. PMID:25849909

  15. Atomistic Mechanisms of Chemical Mechanical Polishing of a Cu Surface in Aqueous H2O2: Tight-Binding Quantum Chemical Molecular Dynamics Simulations.

    Science.gov (United States)

    Kawaguchi, Kentaro; Ito, Hiroshi; Kuwahara, Takuya; Higuchi, Yuji; Ozawa, Nobuki; Kubo, Momoji

    2016-05-11

    We applied our original chemical mechanical polishing (CMP) simulator based on the tight-binding quantum chemical molecular dynamics (TB-QCMD) method to clarify the atomistic mechanism of CMP processes on a Cu(111) surface polished with a SiO2 abrasive grain in aqueous H2O2. We reveal that the oxidation of the Cu(111) surface mechanically induced at the friction interface is a key process in CMP. In aqueous H2O2, in the first step, OH groups and O atoms adsorbed on a nascent Cu surface are generated by the chemical reactions of H2O2 molecules. In the second step, at the friction interface between the Cu surface and the abrasive grain, the surface-adsorbed O atom intrudes into the Cu bulk and dissociates the Cu-Cu bonds. The dissociation of the Cu-Cu back-bonds raises a Cu atom from the surface that is mechanically sheared by the abrasive grain. In the third step, the raised Cu atom bound to the surface-adsorbed OH groups is removed from the surface by the generation and desorption of a Cu(OH)2 molecule. In contrast, in pure water, there are no geometrical changes in the Cu surface because the H2O molecules do not react with the Cu surface, and the abrasive grain slides smoothly on the planar Cu surface. The comparison between the CMP simulations in aqueous H2O2 and pure water indicates that the intrusion of a surface-adsorbed O atom into the Cu bulk is the most important process for the efficient polishing of the Cu surface because it induces the dissociation of the Cu-Cu bonds and generates raised Cu atoms that are sheared off by the abrasive grain. Furthermore, density functional theory calculations show that the intrusion of the surface-adsorbed O atoms into the Cu bulk has a high activation energy of 28.2 kcal/mol, which is difficult to overcome at 300 K. Thus, we suggest that the intrusion of surface-adsorbed O atoms into the Cu bulk induced by abrasive grains at the friction interface is a rate-determining step in the Cu CMP process. PMID:27092706

  16. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nishizawa, Manami; Nishizawa, Kazuhisa, E-mail: kazunet@med.teikyo-u.ac.jp [Teikyo University School of Medical Technology, Itabashi, Tokyo (Japan)

    2014-08-21

    Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT{sup OPLS}). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT{sup OPLS} PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT{sup CHARMM}) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT{sup OPLS} PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA){sub 3} peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These

  17. Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.

    Energy Technology Data Exchange (ETDEWEB)

    Prezhdo, Oleg V.

    2012-03-22

    provided a unified atomistic picture of the nature and dynamics of photoexcited states in semiconductor QDs. We also summarized our recent findings about the photoinduced electron dynamics at the chromophore-semiconductor interfaces from a time-domain ab initio perspective. The interface provides the foundation for a new, promising type of solar cell and presents a fundamentally important case study for several fields, including photo-, electro- and analytical chemistries, molecular electronics, and photography. Further, the interface offers a classic example of an interaction between an organic molecular species and an inorganic bulk material. Scientists employ different concepts and terminologies to describe molecular and solid states of matter, and these differences make it difficult to describe the interface with a single model. At the basic atomistic level of description, however, this challenge can be largely overcome. Recent advances in non-adiabatic molecular dynamics and time-domain density functional theory have created a unique opportunity for simulating the ultrafast, photoinduced processes on a computer very similar to the way that they occur in nature. These state-of-the-art theoretical tools offered a comprehensive picture of a variety of electron transfer processes that occur at the interface, including electron injection from the chromophore to the semiconductor, electron relaxation and delocalization inside the semiconductor, back-transfer of the electron to the chromophore and to the electrolyte, and regeneration of the neutral chromophore by the electrolyte. The ab initio time-domain modeling is particularly valuable for understanding these dynamic features of the ultrafast electron transfer processes, which cannot be represented by a simple rate description. We demonstrated using symmetry adapted cluster theory with configuration interaction (SAC-CI) that charging of small PbSe nanocrystals (NCs) greatly modifies their electronic states and optical

  18. Atomistic stimulation of defective oxides

    CERN Document Server

    Minervini, L

    2000-01-01

    defect processes. The predominant intrinsic disorder reaction and the mechanism by which excess oxygen is accommodated are established. Furthermore, the most favourable migration mechanism and pathway for oxygen ions is predicted. Chapters 7 and 8 investigate pyrochlore oxides. These materials are candidates for solid oxide fuel cell components and as actinide host phases. Such applications require a detailed understanding of the defect processes. The defect energies, displayed as contour maps, are able to account for structure stability and, given an appropriate partial charge potential model, to accurately determine the oxygen positional parameter. In particular, the dependence of the positional parameter on intrinsic disorder is predicted. It is demonstrated, by radiation damage experiments, that these results are able to predict the radiation performance of pyrochlore oxides. Atomistic simulation calculations based on energy minimization techniques and classical pair potentials are used to study several i...

  19. NEPTUN-III reflooding and boil-off experiments with an LWHCR fuel rod bundle simulator: experimental results and initial code assessment efforts

    International Nuclear Information System (INIS)

    The NEPTUN test facility at Wuerenlingen has been modified to enable LWHCR-representative reflooding and boil-off experiments to be carried out. Results from a first series of forced feed reflooding tests, simulating cold-leg injection, are presented for a range of values of the parameters flooding rate, rod power and initial temperature. Rewetting of the LWHCR fuel bundle simulator was found to be possible in each case. Analysis of the NEPTUN-III reflooding experiments with RELAP5/MOD2 yield discrepant results and it has been shown, in the context of calculcations of the boil-off experiments, that some LWHCR-specific models and correlations need to be developed. (author)

  20. REBEKA bundle experiments

    International Nuclear Information System (INIS)

    This report is a summary of experimental investigations describing the fuel rod behavior in the refilling and reflooding phase of a loss-of-coolant accident of a PWR. The experiments were performed with 5x5 and 7x7 rod bundles, using indirectly electrically heated fuel rod simulators of full length with original PWR-KWU-geometry, original grid spacers and Zircaloy-4-claddings (Type Biblis B). The fuel rod simulators showed a cosine shaped axial power profile in 7 steps and continuous, respectively. The results describe the influence of the different parameters such as bundle size on the maximum coolant channel blockage, that of the cooling on the size of the circumferential strain of the cladding (azimuthal temperature distribution) a cold control rod guide thimble and the flow direction (axial temperature distribution) on the resulting coolant channel blockage. The rewetting behavior of different fuel rod simulators including ballooned and burst Zircaloy claddings is discussed as well as the influence of thermocouples on the cladding temperature history and the rewetting behavior. All results prove the coolability of a PWR in the case of a LOCA. Therefore, it can be concluded that the ECC-criteria established by licensing authorities can be fulfilled. (orig./HP)

  1. An Angstrom Sized Window on the Origin of Water in the Inner Solar System: Atomistic Simulation of Adsorption of Water on Olivine

    Science.gov (United States)

    Stimpfl, M.; Walker, A. M.; Drake, M. J.; Deymier, P.

    2005-12-01

    Ther'e is no consensus on the origin of water in the inner solar system. One group of theories envisages the delivery of water to the Earth by means of comets and asteroids after the planet acquired about 85% of its mass formation. However, isotopic and geochemical fingerprints seem to indicate that comets and asteroids alone could not have been the principal source of water for the Earth (Morbidelli et al. 2000; Kleine et al. 2002). These discrepancies could be avoided if the Earth acquired its water locally. We explore the role of adsorption onto grains prior to planetary accretion as a possible new mechanism that could bring water to the Earth. Atomistic simulation can be employed to investigate the interaction between volatiles and materials found in the nebula. We have been exploring how water adsorbs on olivine with the goal of understanding the energetic involved in this process. Volatiles (including water) and fine grained dust coexisted in the nebula for millions of years, opening the possibility for these two components to interact. The importance of characterizing the interaction between water gas and the surface of olivine lies in the possibility of explaining the presence of water in the inner solar system due to adsorption of water onto the nebular dust before accretion. Monte Carlo simulation of adsorption onto a flat surface showed that this mechanism can store up to 3 times the Earth's oceans on dust grains in the pre-accretion disk (Stimpfl et al. 2004). This model, however, did not take into account the specific surface interactions between water gas and the crystalline surface, nor did it rigorously investigate the role of porosity. To fill this gap, we are currently performing energy minimization and molecular dynamics simulations of the system water and olivine using the code GULP and DLpOLY, respectively. Bulk olivine is modelled using periodic boundary conditions and a well tested parameterized potential model for the short ranged repulsion

  2. Atomistic spin dynamics and surface magnons

    International Nuclear Information System (INIS)

    Atomistic spin dynamics simulations have evolved to become a powerful and versatile tool for simulating dynamic properties of magnetic materials. It has a wide range of applications, for instance switching of magnetic states in bulk and nano-magnets, dynamics of topological magnets, such as skyrmions and vortices and domain wall motion. In this review, after a brief summary of the existing investigation tools for the study of magnons, we focus on calculations of spin-wave excitations in low-dimensional magnets and the effect of relativistic and temperature effects in such structures. In general, we find a good agreement between our results and the experimental values. For material specific studies, the atomistic spin dynamics is combined with electronic structure calculations within the density functional theory from which the required parameters are calculated, such as magnetic exchange interactions, magnetocrystalline anisotropy, and Dzyaloshinskii–Moriya vectors. (topical review)

  3. Strategic Aspects of Bundling

    International Nuclear Information System (INIS)

    The increase of bundle supply has become widespread in several sectors (for instance in telecommunications and energy fields). This paper review relates strategic aspects of bundling. The main purpose of this paper is to analyze profitability of bundling strategies according to the degree of competition and the characteristics of goods. Moreover, bundling can be used as price discrimination tool, screening device or entry barriers. In monopoly case bundling strategy is efficient to sort consumers in different categories in order to capture a maximum of surplus. However, when competition increases, the profitability on bundling strategies depends on correlation of consumers' reservations values. (author)

  4. Equivariant bundle gerbes

    CERN Document Server

    Murray, Michael K; Stevenson, Danny; Vozzo, Raymond F

    2015-01-01

    We develop the theory of simplicial extensions for bundle gerbes and their characteristic classes. This formalism is used to study descent problems and equivariance for bundle gerbes. We consider in detail two examples: the basic bundle gerbe on a unitary group and a string structure for a principal bundle. We show that the basic bundle gerbe is equivariant for the conjugation action and calculate its characteristic class and that a string structure gives rise to a bundle gerbe which is equivariant for a natural action of the String 2-group.

  5. Effect of shape and thickness of asbestos bundles and fibres on EDS microanalysis: A Monte Carlo simulation

    Science.gov (United States)

    Moro, D.; Valdre, G.

    2016-02-01

    Quantitative microanalysis of tiny asbestos mineral fibres by scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy (SEM-EDS) still represents a complex analytical issue. This complexity arises from the variable fibre shape and small thickness (asbestos bundles and fibres shape and thickness on the detected EDS X-ray intensity was observed. The X-ray intensity trends as a function of fibre thickness showed a non-linear dependence for all the elements and minerals. In general, the X-ray intensities showed a considerable reduction for thicknesses below about 5 μm at 5 keV, 2 μm at 15 keV, and 5 μm at 25 keV. Correction parameters, k-ratios, for the asbestos fibre thickness effect, are reported.

  6. A comparison of finite element and atomistic modelling of fracture

    International Nuclear Information System (INIS)

    Are the cohesive laws of interfaces sufficient for modelling fracture in polycrystals using the cohesive zone model? We examine this question by comparing a fully atomistic simulation of a silicon polycrystal with a finite element simulation with a similar overall geometry. The cohesive laws used in the finite element simulation are measured atomistically. We describe in detail how to convert the output of atomistic grain boundary fracture simulations into the piecewise linear form needed by a cohesive zone model. We discuss the effects of grain boundary microparameters (the choice of section of the interface, the translations of the grains relative to one another and the cutting plane of each lattice orientation) on the cohesive laws and polycrystal fracture. We find that the atomistic simulations fracture at lower levels of external stress, indicating that the initiation of fracture in the atomistic simulations is likely dominated by irregular atomic structures at external faces, internal edges, corners and junctions of grains. Thus, the cohesive properties of interfaces alone are not likely to be sufficient for modelling the fracture of polycrystals using continuum methods

  7. CANFLEX fuel bundle strength tests (test report)

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Seok Kyu; Chung, C. H.; Kim, B. D.

    1997-08-01

    This document outlines the test results for the strength tests of the CANFLEX fuel bundle. Strength tests are performed to determine and verify the amount of the bundle shape distortion which is against the side-stops when the bundles are refuelling. There are two cases of strength test; one is the double side-stop test which simulates the normal bundle refuelling and the other is the single side-stop test which simulates the abnormal refuelling. the strength test specification requires that the fuel bundle against the side-stop(s) simulators for this test were fabricated and the flow rates were controlled to provide the required conservative hydraulic forces. The test rig conditions of 120 deg C, 11.2 MPa were retained for 15 minutes after the flow rate was controlled during the test in two cases, respectively. The bundle loading angles of number 13- number 15 among the 15 bundles were 67.5 deg CCW and others were loaded randomly. After the tests, the bundle shapes against the side-stops were measured and inspected carefully. The important test procedures and measurements were discussed as follows. (author). 5 refs., 22 tabs., 5 figs.

  8. CANFLEX fuel bundle strength tests (test report)

    International Nuclear Information System (INIS)

    This document outlines the test results for the strength tests of the CANFLEX fuel bundle. Strength tests are performed to determine and verify the amount of the bundle shape distortion which is against the side-stops when the bundles are refuelling. There are two cases of strength test; one is the double side-stop test which simulates the normal bundle refuelling and the other is the single side-stop test which simulates the abnormal refuelling. the strength test specification requires that the fuel bundle against the side-stop(s) simulators for this test were fabricated and the flow rates were controlled to provide the required conservative hydraulic forces. The test rig conditions of 120 deg C, 11.2 MPa were retained for 15 minutes after the flow rate was controlled during the test in two cases, respectively. The bundle loading angles of number 13- number 15 among the 15 bundles were 67.5 deg CCW and others were loaded randomly. After the tests, the bundle shapes against the side-stops were measured and inspected carefully. The important test procedures and measurements were discussed as follows. (author). 5 refs., 22 tabs., 5 figs

  9. Bundling in Telecommunications

    OpenAIRE

    Begoña García-Mariñoso; Xavier Martinez-Giralt; Pau Olivella

    2008-01-01

    The paper offers an overview of the literature on bundling in the telecommunications sector and its application in the Spanish market. We argue that the use of bundling in the provision of services is associated to technological reasons. Therefore, there appears no need to regulate bundling activities. However, this is not to say that other related telecom markets should not be scrutinized and regulated, or that the regulator should not pay attention to other bundling-related anticompetitive ...

  10. Thermodynamics of low-temperature phyllosilicates: from a macroscopic perspective towards achieving atomistic simulation; Thermodynamique des phyllosilicates de basse temperature: de l'approche macroscopique a la simulation atomistique

    Energy Technology Data Exchange (ETDEWEB)

    Dubacq, B.

    2008-12-15

    suggest several improvements to these methods. We used atomistic simulation to calculate the mixing enthalpy along two solid solutions binaries of interest in low-temperature petrology. Results are in agreement with observations in natural systems and confirm the importance of hydration in clay minerals stability. (author)

  11. Bundling and Tying

    OpenAIRE

    Nicholas Economides

    2014-01-01

    We discuss strategic ways that sellers can use tying and bundling with requirement conditions to extract consumer surplus. We analyze different types of tying and bundling creating (i) intra-product price discrimination; (ii) intra-consumer price discrimination; and (iii) inter-product price discrimination, and assess the antitrust liability that these practices may entail. We also discuss the impact on consumers and competition, as well as potential antitrust liability of bundling “incontest...

  12. Influence of partial blockage of a BWR bundle on heat transfer, cladding temperature, and quenching during bottom flooding or top spraying under simulated LOCA conditions

    International Nuclear Information System (INIS)

    In a test facility with two parallel boiling water reactor fuel assemblies, experiments were carried out with top spray and bottom flooding, simulating loss-of-coolant accident (LOCA) conditions. The flow area restriction, caused by the ballooning of fuel rod cladding within one of the bundles, was provided by blockage plates, which had reductions of 37% in one case and in a second series 70% of the flow area. Test parameters were system pressure (1, 5, and 10 bars), spray (0.68 and 1.02 m3/h) and flooding rates (1.5,2, and 3.3 cm/s), power input (520 and 614 kW), and the initial cladding temperature (600 and 8000C at midplane) of the heaters. The test results showed no significant variations from those without blockage, except in the blocked region. An enhancement of heat transfer was observed in a close region downstream from the blockage in cases such as bottom flooding and top spray tests. The results will serve the purpose of code verification for reactor LOCA analysis

  13. Contact fiber bundles

    OpenAIRE

    Lerman, Eugene

    2003-01-01

    We define contact fiber bundles and investigate conditions for the existence of contact structures on the total space of such a bundle. The results are analogous to minimal coupling in symplectic geometry. The two applications are construction of K-contact manifolds generalizing Yamazaki's fiber join construction and a cross-section theorem for contact moment maps

  14. Principal noncommutative torus bundles

    DEFF Research Database (Denmark)

    Echterhoff, Siegfried; Nest, Ryszard; Oyono-Oyono, Herve

    2008-01-01

    of bivariant K-theory (denoted RKK-theory) due to Kasparov. Using earlier results of Echterhoff and Williams, we shall give a complete classification of principal non-commutative torus bundles up to equivariant Morita equivalence. We then study these bundles as topological fibrations (forgetting the...

  15. Atomistic Modeling of the U-Zr System

    International Nuclear Information System (INIS)

    Atomistic modeling using the BFS method for alloys and ab initio based parameters is proposed for the study of fundamental properties of U-Zr metallic nuclear fuels. Due to its basic atomistic nature and the universal character of the parametrization, the approach can be used for diverse problems such as the interaction between fuel and cladding and temperature gradient fuel constituent redistribution. In the first case, preliminary results for the formation of an interaction layer using large scale simulations are presented. For the second case, a mean field formalism is introduced in order to determine concentration profiles for arbitrary changes in temperature in the radial direction. (author)

  16. Bridging the Macroscopic and Atomistic Descriptions of the Electrocaloric Effect

    Science.gov (United States)

    Ponomareva, I.; Lisenkov, S.

    2012-04-01

    First-principles-based simulations are used to simulate the electrocaloric effect (ECE) in Ba0.5Sr0.5TiO3 alloys. In analogy with experimental studies we simulate the effect directly and indirectly (via the use of Maxwell thermodynamics). Both direct and indirect simulations utilize the same atomistic framework that allows us to compare them in a systematic way and with an atomistic precision for the very first time. Such precise comparison allows us to provide a bridge between the atomistic and macroscopic descriptions of the ECE and identify the factors that may critically compromise or even destroy their equivalence. Our computational data reveal the intrinsic features of ECE in ferroelectrics with multiple ferroelectric transitions and confirm the potential of these materials to exhibit giant electrocaloric response. The coexistence of negative and positive ECE in one material as well as an unusual field-driven transition between them is predicted, explained at an atomistic level, and proposed as a potential way to enhance the electrocaloric efficiency.

  17. Atomistic modeling of dropwise condensation

    Science.gov (United States)

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

    2016-05-01

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

  18. Amplitude death of coupled hair bundles with stochastic channel noise

    CERN Document Server

    Kim, Kyung-Joong

    2014-01-01

    Hair cells conduct auditory transduction in vertebrates. In lower vertebrates such as frogs and turtles, due to the active mechanism in hair cells, hair bundles(stereocilia) can be spontaneously oscillating or quiescent. Recently, the amplitude death phenomenon has been proposed [K.-H. Ahn, J. R. Soc. Interface, {\\bf 10}, 20130525 (2013)] as a mechanism for auditory transduction in frog hair-cell bundles, where sudden cessation of the oscillations arises due to the coupling between non-identical hair bundles. The gating of the ion channel is intrinsically stochastic due to the stochastic nature of the configuration change of the channel. The strength of the noise due to the channel gating can be comparable to the thermal Brownian noise of hair bundles. Thus, we perform stochastic simulations of the elastically coupled hair bundles. In spite of stray noisy fluctuations due to its stochastic dynamics, our simulation shows the transition from collective oscillation to amplitude death as inter-bundle coupling str...

  19. Restrictions of stable bundles

    CERN Document Server

    Balaji, V

    2011-01-01

    The Mehta-Ramanathan theorem ensures that the restriction of a stable vector bundle to a sufficiently high degree complete intersection curve is again stable. We improve the bounds for the "sufficiently high degree" and propose a possibly optimal conjecture.

  20. candu fuel bundle fabrication

    International Nuclear Information System (INIS)

    This paper describes works on CANDU fuel bundle fabrication in the Fuel Fabrication Development and Testing Section (FFDT) of AECL's Chalk River Laboratories. This work does not cover fuel design, pellet manufacturing, Zircaloy material manufacturing, but cover the joining of appendages to sheath tube, endcap preparation and welding, UO2 loading, end plate preparation and welding, and all inspections required in these steps. Materials used in the fabrication of CANDU fuel bundle are: 1)Ceramic UO2 Pellet 2)Zircaloy -4. Fuel Bundle Structural Material 3) Others (Zinc stearate, Colloidal graphite, Beryllium and Heium). Th fabrication of fuel element consist of three process: 1)pellet loading into the sheats, 2) endcap welding, and 3) the element profiling. Endcap welds is tested by metallography and He leak test. The endcaps of the elements are welded to the end plates to form the 37- element bundle assembly

  1. Subtleties Concerning Conformal Tractor Bundles

    CERN Document Server

    Graham, C Robin

    2012-01-01

    The realization of tractor bundles as associated bundles in conformal geometry is studied. It is shown that different natural choices of principal bundle with normal Cartan connection corresponding to a given conformal manifold can give rise to topologically distinct associated tractor bundles for the same inducing representation. Consequences for homogeneous models and conformal holonomy are described. A careful presentation is made of background material concerning standard tractor bundles and equivalence between parabolic geometries and underlying structures.

  2. Nano-hillock formation in diamond-like carbon induced by swift heavy projectiles in the electronic stopping regime: Experiments and atomistic simulations

    Science.gov (United States)

    Schwen, D.; Bringa, E.; Krauser, J.; Weidinger, A.; Trautmann, C.; Hofsäss, H.

    2012-09-01

    The formation of surface hillocks in diamond-like carbon is studied experimentally and by means of large-scale molecular dynamics simulations with 5 × 106 atoms combined with a thermal spike model. The irradiation experiments with swift heavy ions cover a large electronic stopping range between ˜12 and 72 keV/nm. Both experiments and simulations show that beyond a stopping power threshold, the hillock height increases linearly with the electronic stopping, and agree extremely well assuming an efficiency of approximately 20% in the transfer of electronic energy to the lattice. The simulations also show a transition of sp3 to sp2 bonding along the tracks with the hillocks containing almost no sp3 contribution.

  3. Nano-hillock formation in diamond-like carbon induced by swift heavy projectiles in the electronic stopping regime: Experiments and atomistic simulations

    International Nuclear Information System (INIS)

    The formation of surface hillocks in diamond-like carbon is studied experimentally and by means of large-scale molecular dynamics simulations with 5 × 106 atoms combined with a thermal spike model. The irradiation experiments with swift heavy ions cover a large electronic stopping range between ∼12 and 72 keV/nm. Both experiments and simulations show that beyond a stopping power threshold, the hillock height increases linearly with the electronic stopping, and agree extremely well assuming an efficiency of approximately 20% in the transfer of electronic energy to the lattice. The simulations also show a transition of sp3 to sp2 bonding along the tracks with the hillocks containing almost no sp3 contribution.

  4. Right bundle branch block

    DEFF Research Database (Denmark)

    Bussink, Barbara E; Holst, Anders Gaarsdal; Jespersen, Lasse;

    2013-01-01

    AimsTo determine the prevalence, predictors of newly acquired, and the prognostic value of right bundle branch block (RBBB) and incomplete RBBB (IRBBB) on a resting 12-lead electrocardiogram in men and women from the general population.Methods and resultsWe followed 18 441 participants included in...... men vs. 0.5%/2.3% in women, P <0.001). Significant predictors of newly acquired RBBB were male gender, increasing age, high systolic blood pressure, and presence of IRBBB, whereas predictors of newly acquired IRBBB were male gender, increasing age, and low BMI. Right bundle branch block was associated...... with significantly increased all-cause and cardiovascular mortality in both genders with age-adjusted hazard ratios (HR) of 1.31 [95% confidence interval (CI), 1.11-1.54] and 1.87 (95% CI, 1.48-2.36) in the gender pooled analysis with little attenuation after multiple adjustment. Right bundle branch...

  5. Principal -bundles on Nodal Curves

    Indian Academy of Sciences (India)

    Usha N Bhosle

    2001-08-01

    Let be a connected semisimple affine algebraic group defined over . We study the relation between stable, semistable -bundles on a nodal curve and representations of the fundamental group of . This study is done by extending the notion of (generalized) parabolic vector bundles to principal -bundles on the desingularization of and using the correspondence between them and principal -bundles on . We give an isomorphism of the stack of generalized parabolic bundles on with a quotient stack associated to loop groups. We show that if is simple and simply connected then the Picard group of the stack of principal -bundles on is isomorphic to ⊕ , being the number of components of .

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

    OpenAIRE

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-01-01

    We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville von-Neumann equation approach of S\\'anchez et al. [J. Chem. Phys., 124, 214708 (2006)]. A key ingredient of our approach is a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to uniquely defi...

  7. Capacity efficiency of recovery request bundling

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Dittmann, Lars; Berger, Michael Stübert; Stidsen, Thomas Riis; Lagakos, Stephen; Perlovsky, Leonid; Jha, Manoi; Covaci, Brindusa; Zaharim, Azarni; Mastorakis, Nikos

    2010-01-01

    This paper presents a comparison of recovery methods in terms of capacity efficiency. In particular, a method where recovery requests are bundled towards the destination (Shortcut Span Protection) is evaluated against traditional recovery methods. Our simulation results show that Shortcut Span Pr...... Protection uses more capacity than the unbundled related methods, but this is compensated by easier control and management of the recovery actions....

  8. Capacity efficiency of recovery request bundling

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Dittmann, Lars; Berger, Michael Stübert; Stidsen, Thomas Riis; Lagakos, Stephen; Perlovsky, Leonid; Jha, Manoi; Covaci, Brindusa; Zaharim, Azarni; Mastorakis, Nikos

    2010-01-01

    This paper presents a comparison of recovery methods in terms of capacity efficiency. In particular, a method where recovery requests are bundled towards the destination (Shortcut Span Protection) is evaluated against traditional recovery methods. Our simulation results show that Shortcut Span...

  9. Atomistic modeling of carbon Cottrell atmospheres in bcc iron

    International Nuclear Information System (INIS)

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

  10. Scaling Shift in Multicracked Fiber Bundles

    Science.gov (United States)

    Manca, Fabio; Giordano, Stefano; Palla, Pier Luca; Cleri, Fabrizio

    2014-12-01

    Bundles of fibers, wires, or filaments are ubiquitous structures in both natural and artificial materials. We investigate the bundle degradation induced by an external damaging action through a theoretical model describing an assembly of parallel fibers, progressively damaged by a random population of cracks. Fibers in our model interact by means of a lateral linear coupling, thus retaining structural integrity even after substantial damage. Monte Carlo simulations of the Young's modulus degradation for increasing crack density demonstrate a remarkable scaling shift between an exponential and a power-law regime. Analytical solutions of the model confirm this behavior, and provide a thorough understanding of the underlying physics.

  11. Shear responses of [ 1-bar 1 0]-tilt {1 1 5}/{1 1 1} asymmetric tilt grain boundaries in fcc metals by atomistic simulations

    International Nuclear Information System (INIS)

    The shear response of the ∑3[ 1-bar 1 0]-tilt {1-bar 1-bar 5}/{1 1 1} and ∑9[ 1-bar 1 0]-tilt {1 1 5}/{1 1 1} asymmetric tilt grain boundaries (GBs) in fcc metals Cu and Al has been studied by atomistic simulation methods with the embedded atom method interatomic potentials and with a bicrystal model. It is found that the structure of the GBs studied can be well described by the coincidence site lattice (CSL) theory. Shear of these GBs at room temperature along eight different directions within the GB plane shows that these two types of GBs can transform between each other by the formation of a coherent twin boundary. The structure transformation of the GBs can also take the form of GB sliding, GB sliding–migration coupled motion, GB faceting, GB 9R structure formation, etc, depending on the shear directions adopted and the material involved (Cu or Al). The detailed structure transformation mechanisms have been analyzed with the aid of the CSL–DSC (displacement shift complete) theory. Several structure transformation paths adherent to these two types of GBs have been identified for the activation of the GB sliding–migration coupled motion. It is concluded that, although CSL–DSC theory can be applied to describe the sliding–migration coupled motion of the GBs studied, some other effects such as the shear direction within the GB plane and the bonding characteristics of the materials should also play a significant role in the shear response of these GBs. (paper)

  12. Hybrid bundle divertor design

    International Nuclear Information System (INIS)

    A hybrid bundle divertor design is presented that produces <0.3% magnetic ripple at the center of the plasma while providing adequate space for the coil shielding and structure for a tokamak fusion test reactor similar to the International Tokamak Reactor and the Engineering Test Facility (with R = 5 m, B = 5 T, and a /SUB wall/ = 1.5 m, in particular). This hybrid divertor consists of a set of quadrupole ''wing'' coils running tangent to the tokamak plasma on either side of a bundle divertor. The wing coils by themselves pull the edge of the plasma out 1.5 m and spread the thickness of the scrape-off layer from 0.1 to 0.7 m at the midplane. The clear aperture of the bundle divertor throat is 1.0 m high and 1.8 m wide. For maintenance or replacement, the hybrid divertor can be disassembled into three parts, with the bundle divertor part pulling straight out between toroidal field coils and the wing coils then sliding out through the same opening

  13. First Principles Based Reactive Atomistic Simulations to Understand the Effects of Molecular Hypervelocity Impact on Cassini's Ion and Neutral Mass Spectrometer

    Science.gov (United States)

    Jaramillo-Botero, A.; Cheng, M-J; Cvicek, V.; Beegle, Luther W.; Hodyss, R.; Goddard, W. A., III

    2011-01-01

    We report here on the predicted impact of species such as ice-water, CO2, CH4, and NH3, on oxidized titanium, as well as HC species on diamond surfaces. These simulations provide the dynamics of product distributions during and after a hypervelocity impact event, ionization fractions, and dissociation probabilities for the various species of interest as a function of impact velocity (energy). We are using these results to determine the relevance of the fragmentation process to Cassini INMS results, and to quantify its effects on the observed spectra.

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

    OpenAIRE

    Shluger, A. L.; Gavartin, J. L.; Szymanski, M. A.; Stoneham, A. M.

    2000-01-01

    This brief review is focused on recent results of atomistic modelling and simulation of exciton related processes in ionic materials. We present an analysis of thermal fluctuations of the electrostatic potential in cubic ionic crystals and their relation to formation of a tail in the electron density of states and localisation of electronic states. Then the possible 'fast' mechanism of formation of F-H pairs in KBr as a result of decomposition of relaxing excitons is discussed. We briefly des...

  15. Atomistic Determination of Cross-Slip Pathway and Energetics

    DEFF Research Database (Denmark)

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

    1997-01-01

    The mechanism for cross slip of a screw dislocation in Cu is determined by atomistic simulations that only presume the initial and final states of the process. The dissociated dislocation constricts in the primary plane and redissociates into the cross-slip plane while still partly in the primary...... dislocation is determined. The breakdown of linear elasticity theory for small splitting widths is studied. [S0031-9007(97)04444-X]....

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

    OpenAIRE

    Chen, Jie; Zhang, Gang; Li, Baowen

    2012-01-01

    By using non-equilibrium molecular dynamics simulations, we demonstrated that thermal conductivity of Germanium nanowires can be reduced more than 25% at room temperature by atomistic coating. There is a critical coating thickness beyond which thermal conductivity of the coated nanowire is larger than that of the host nanowire. The diameter dependent critical coating thickness and minimum thermal conductivity are explored. Moreover, we found that interface roughness can induce further reducti...

  17. Core structure and dissociation energetics of basal edge dislocation in α-Al2O3: A combined atomistic simulation and transmission electron microscopy analysis

    International Nuclear Information System (INIS)

    Using large-scale molecular dynamics (MD) simulations, we investigate the energetics and local structures/stresses of partial dislocations, 1/3〈011¯0〉 and 1/3〈101¯0〉, dissociated from the 1/3〈112¯0〉 perfect basal edge dislocation in α-Al2O3. The validity of the model adopted in the simulation is confirmed by comparing with theoretical stress/strain distributions and with those experimentally obtained from a high-resolution transmission electron microscopy (HRTEM) observation. Partial dislocation pairs have a stable inter-core distance (∼2 nm), which is also a phenomenon that is observed in the HRTEM experiments. The distance between the partials can be explained quantitatively by the balance between an elastic core–core repulsion and an effective attractive force against the extension of stacking faults (SFs). A comparison is made for two types of core structures of partial dislocations: a pair of partials with Al-terminated/O-terminated extra-half planes and that with Al-/Al-terminated ones. The overall tendency of the inter-core interaction and the equilibrium distances are the same in both cases, whereas the Al–O-terminated pair is slightly favourable in energy at the equilibrium distance. A residual shear stress on the SF plane is observed in the MD results, which can be attributed to local atomic structure in the SF

  18. Steady-flow characteristics of bundle fluid in drawing

    Energy Technology Data Exchange (ETDEWEB)

    Huh, You; Kim, Jong Seong [Kyunghee University, Suwon (Korea, Republic of)

    2006-07-15

    Drawing is a mechanical operation attenuating material thickness to an appropriate level for the next processing or end usage. When the input material has a form of bundle or bundles made of very thin and long shaped wires or fibers, this attenuation operation is called 'bundle drawing' or 'drafting'. Bundle drawing is being used widely in manufacturing micro sized wires or staple yarns. However, the bundle processed by this operation has more or less defects in the evenness of linear density. Such irregularities cause many problems not only for the product quality but also for the efficiency of the next successive processes. In this research a mathematical model for the dynamic behavior of the bundle fluid is to be set up on the basis of general physical laws containing physical variables, i.e. linear density and velocity as the dynamic state variables of the bundle fluid. The governing equations resulting from the modeling show that they appear in a slightly different form from what they do in a continuum fluid. Then, the governing equations system is simplified in a steady state and the bundle dynamics is simulated, showing that the shape of the velocity profiles depends on two model parameters. Experiments confirm that the model parameters are to be well adjusted to show a coincidence with the theoretical analysis. The higher the drawing ratio and drawing speed are, the more sensitive becomes the bundle flow to exogenous disturbances.

  19. On framed quantum principal bundles

    CERN Document Server

    Durdevic, M

    1995-01-01

    A noncommutative-geometric formalism of framed principal bundles is sketched, in a special case of quantum bundles (over quantum spaces) possessing classical structure groups. Quantum counterparts of torsion operators and Levi-Civita type connections are analyzed. A construction of a natural differential calculus on framed bundles is described. Illustrative examples are presented.

  20. Accurate Calculation of Solvation Free Energies in Supercritical Fluids by Fully Atomistic Simulations: Probing the Theory of Solutions in Energy Representation.

    Science.gov (United States)

    Frolov, Andrey I

    2015-05-12

    Accurate calculation of solvation free energies (SFEs) is a fundamental problem of theoretical chemistry. In this work we perform a careful validation of the theory of solutions in energy representation (ER method) developed by Matubayasi et al. [J. Chem. Phys. 2000, 113, 6070-6081] for SFE calculations in supercritical solvents. This method can be seen as a bridge between the molecular simulations and the classical (not quantum) density functional theory (DFT) formulated in energy representation. We performed extensive calculations of SFEs of organic molecules of different chemical natures in pure supercritical CO2 (sc-CO2) and in sc-CO2 with addition of 6 mol % of ethanol, acetone, and n-hexane as cosolvents. We show that the ER method reproduces SFE data calculated by a method free of theoretical approximations (the Bennett's acceptance ratio) with the mean absolute error of only 0.05 kcal/mol. However, the ER method requires by an order less computational resources. Also, we show that the quality of ER calculations should be carefully monitored since the lack of sampling can result into a considerable bias in predictions. The present calculations reproduce the trends in the cosolvent-induced solubility enhancement factors observed in experimental data. Thus, we think that molecular simulations coupled with the ER method can be used for quick calculations of the effect of variation of temperature, pressure, and cosolvent concentration on SFE and hence solubility of bioactive compounds in supercritical fluids. This should dramatically reduce the burden of experimental work on optimizing solvency of supercritical solvents. PMID:26574423

  1. In silico affinity profiling of neuroactive polyphenols for post-traumatic calpain inactivation: a molecular docking and atomistic simulation sensitivity analysis.

    Science.gov (United States)

    Kumar, Pradeep; Choonara, Yahya E; Pillay, Viness

    2015-01-01

    Calcium-activated nonlysosomal neutral proteases, calpains, are believed to be early mediators of neuronal damage associated with neuron death and axonal degeneration after traumatic neural injuries. In this study, a library of biologically active small molecular weight calpain inhibitors was used for model validation and inhibition site recognition. Subsequently, two natural neuroactive polyphenols, curcumin and quercetin, were tested for their sensitivity and activity towards calpain's proteolytic sequence and compared with the known calpain inhibitors via detailed molecular mechanics (MM), molecular dynamics (MD), and docking simulations. The MM and MD energy profiles (SJA6017 < AK275 < AK295 < PD151746 < quercetin < leupeptin < PD150606 < curcumin < ALLN < ALLM < MDL-28170 < calpeptin) and the docking analysis (AK275 < AK295 < PD151746 < ALLN < PD150606 < curcumin < leupeptin < quercetin < calpeptin < SJA6017 < MDL-28170 < ALLM) demonstrated that polyphenols conferred comparable calpain inhibition profiling. The modeling paradigm used in this study provides the first detailed account of corroboration of enzyme inhibition efficacy of calpain inhibitors and the respective calpain-calpain inhibitor molecular complexes' energetic landscape and in addition stimulates the polyphenol bioactive paradigm for post-SCI intervention with implications reaching to experimental in vitro, in cyto, and in vivo studies. PMID:25546626

  2. In Silico Affinity Profiling of Neuroactive Polyphenols for Post-Traumatic Calpain Inactivation: A Molecular Docking and Atomistic Simulation Sensitivity Analysis

    Directory of Open Access Journals (Sweden)

    Pradeep Kumar

    2014-12-01

    Full Text Available Calcium-activated nonlysosomal neutral proteases, calpains, are believed to be early mediators of neuronal damage associated with neuron death and axonal degeneration after traumatic neural injuries. In this study, a library of biologically active small molecular weight calpain inhibitors was used for model validation and inhibition site recognition. Subsequently, two natural neuroactive polyphenols, curcumin and quercetin, were tested for their sensitivity and activity towards calpain’s proteolytic sequence and compared with the known calpain inhibitors via detailed molecular mechanics (MM, molecular dynamics (MD, and docking simulations. The MM and MD energy profiles (SJA6017 < AK275 < AK295 < PD151746 < quercetin < leupeptin < PD150606 < curcumin < ALLN < ALLM < MDL-28170 < calpeptin and the docking analysis (AK275 < AK295 < PD151746 < ALLN < PD150606 < curcumin < leupeptin < quercetin < calpeptin < SJA6017 < MDL-28170 < ALLM demonstrated that polyphenols conferred comparable calpain inhibition profiling. The modeling paradigm used in this study provides the first detailed account of corroboration of enzyme inhibition efficacy of calpain inhibitors and the respective calpain–calpain inhibitor molecular complexes’ energetic landscape and in addition stimulates the polyphenol bioactive paradigm for post-SCI intervention with implications reaching to experimental in vitro, in cyto, and in vivo studies.

  3. Theinfluence of a hierarchical porous carbon network on the coherent dynamics of a nanoconfined room temperature ionic liquid: A neutron spin echo and atomistic simulation investigation

    Energy Technology Data Exchange (ETDEWEB)

    Banuelos, Jose Leo [ORNL; Feng, Guang [ORNL; Fulvio, Pasquale F [ORNL; Li, Song [Vanderbilt University, Nashville; Rother, Gernot [ORNL; Arend, Nikolas [ORNL; Faraone, Antonio [National Institute of Standards and Technology (NIST); Dai, Sheng [ORNL; Cummings, Peter T [ORNL; Wesolowski, David J [ORNL

    2014-01-01

    The molecular-scale dynamic properties of the room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, or [C4mim+ ][Tf2N ], confined in hierarchical microporous mesoporous carbon, were investigated using neutron spin echo (NSE) and molecular dynamics (MD) simulations. Both NSE and MD reveal pronounced slowing of the overall collective dynamics, including the presence of an immobilized fraction of RTIL at the pore wall, on the time scales of these approaches. A fraction of the dynamics, corresponding to RTIL inside 0.75 nm micropores located along the mesopore surfaces, are faster than those of RTIL in direct contact with the walls of 5.8 nm and 7.8 nm cylindrical mesopores. This behavior is ascribed to the near-surface confined-ion density fluctuations resulting from the ion ion and ion wall interactions between the micropores and mesopores as well as their confinement geometries. Strong micropore RTIL interactions result in less-coordinated RTIL within the micropores than in the bulk fluid. Increasing temperature from 296 K to 353 K reduces the immobilized RTIL fraction and results in nearly an order of magnitude increase in the RTIL dynamics. The observed interfacial phenomena underscore the importance of tailoring the surface properties of porous carbons to achieve desirable electrolyte dynamic behavior, since this impacts the performance in applications such as electrical energy storage devices.

  4. Comparative study of grain-boundary migration and grain-boundary self-diffusion of [0 0 1] twist-grain boundaries in copper by atomistic simulations

    International Nuclear Information System (INIS)

    Molecular-dynamics simulations were used to study grain-boundary migration as well as grain-boundary self-diffusion of low-angle and high-angle [0 0 1] planar twist grain boundaries (GBs) in copper. Elastic strain was imposed to drive the planar [0 0 1] twist GBs. The temperature dependence of the GB mobility was determined over a wide misorientation range. Additionally grain-boundary self-diffusion was studied for all investigated [0 0 1] planar twist GBs. A comparison of the activation energies determined shows that grain-boundary migration and self-diffusion are distinctly different processes. The behavior of atoms during grain-boundary migration was analyzed for all studied GBs. The analysis reveals that usually in absolute pure materials high-angle planar [0 0 1] twist GBs move by a collective shuffle mechanism while low-angle GBs move by a dislocation based mechanism. The obtained activation parameters were analyzed with respect to the compensation effect

  5. Simulation of Axial Flow in a Bare Rod Bundle Using a Non-Linear Turbulence Model With High and Low Reynolds Approximations

    International Nuclear Information System (INIS)

    This work presents a numerical investigation of fully developed turbulent flow in a triangular sub-channel of a bare rod bundle using a Non-Linear Eddy Viscosity Model (NLEVM). The numerical technique employed for discretizing the governing equations is the control-volume method with a boundary-fitted non-orthogonal coordinate system. The SIMPLE algorithm was used to correct the pressure field. The classical wall function and a low Reynolds model were used in order to handle flow calculations near the wall. In this work, the influence of constants of calibration existing in the non-linear terms of the model is analyzed. (authors)

  6. Bundles of Banach algebras

    Directory of Open Access Journals (Sweden)

    D. A. Robbins

    1994-12-01

    Full Text Available We study bundles of Banach algebras π:A→X, where each fiber Ax=π−1({x} is a Banach algebra and X is a compact Hausdorff space. In the case where all fibers are commutative, we investigate how the Gelfand representation of the section space algebra Γ(π relates to the Gelfand representation of the fibers. In the general case, we investigate how adjoining an identity to the bundle π:A→X relates to the standard adjunction of identities to the fibers.

  7. Helices and vector bundles

    CERN Document Server

    Rudakov, A N

    1990-01-01

    This volume is devoted to the use of helices as a method for studying exceptional vector bundles, an important and natural concept in algebraic geometry. The work arises out of a series of seminars organised in Moscow by A. N. Rudakov. The first article sets up the general machinery, and later ones explore its use in various contexts. As to be expected, the approach is concrete; the theory is considered for quadrics, ruled surfaces, K3 surfaces and P3(C).

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

    CERN Document Server

    Stephenson, David; Lockerby, Duncan A

    2016-01-01

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

  9. Bundled monocapillary optics

    Science.gov (United States)

    Hirsch, Gregory

    2002-01-01

    A plurality of glass or metal wires are precisely etched to form the desired shape of the individual channels of the final polycapillary optic. This shape is created by carefully controlling the withdrawal speed of a group of wires from an etchant bath. The etched wires undergo a subsequent operation to create an extremely smooth surface. This surface is coated with a layer of material which is selected to maximize the reflectivity of the radiation being used. This reflective surface may be a single layer of material, or a multilayer coating for optimizing the reflectivity in a narrower wavelength interval. The collection of individual wires is assembled into a close-packed multi-wire bundle, and the wires are bonded together in a manner which preserves the close-pack configuration, irrespective of the local wire diameter. The initial wires are then removed by either a chemical etching procedure or mechanical force. In the case of chemical etching, the bundle is generally segmented by cutting a series of etching slots. Prior to removing the wire, the capillary array is typically bonded to a support substrate. The result of the process is a bundle of precisely oriented radiation-reflecting hollow channels. The capillary optic is used for efficiently collecting and redirecting the radiation from a source of radiation which could be the anode of an x-ray tube, a plasma source, the fluorescent radiation from an electron microprobe, a synchrotron radiation source, a reactor or spallation source of neutrons, or some other source.

  10. Bundling harvester; Nippukorjausharvesteri

    Energy Technology Data Exchange (ETDEWEB)

    Koponen, K. [Eko-Log Oy, Kuopio (Finland)

    1996-12-31

    The staring point of the project was to design and construct, by taking the silvicultural point of view into account, a harvesting and processing system especially for energy-wood, containing manually driven bundling harvester, automatizing of the harvester, and automatized loading. The equipment forms an ideal method for entrepreneur`s-line harvesting. The target is to apply the system also for owner`s-line harvesting. The profitability of the system promotes the utilization of the system in both cases. The objectives of the project were: to construct a test equipment and prototypes for all the project stages, to carry out terrain and strain tests in order to examine the usability and durability, as well as the capacity of the machine, to test the applicability of the Eko-Log system in simultaneous harvesting of energy and pulp woods, and to start the marketing and manufacturing of the products. The basic problems of the construction of the bundling harvester have been solved using terrain-tests. The prototype machine has been shown to be operable. Loading of the bundles to form sufficiently economically transportable loads has been studied, and simultaneously, the branch-biomass has been tried to be utilized without loosing the profitability of transportation. The results have been promising, and will promote the profitable utilization of wood-energy

  11. International Standard problem ISP 14: behaviour of a fuel bundle simulator during a specified heatup and flooding period (Rebeka experiment): results of post-test analyses: final comparison report

    International Nuclear Information System (INIS)

    The test consisted in investigating the non-steady material behaviour of a bundle of electrically heated fuel rod simulators with respect to local fuel temperatures, cladding strain, time to burst and local strain at location of burst, together with the thermal hydraulic boundary conditions. The original aim has not been fully achievable. The applied codes for mechanical fuel behaviour largely demonstrated their capabilities for pretest predictions when certain local fluid dynamic parameters are well known to the code users. The difficulties expected with proper analysis of thermal hydraulics of the test were confirmed, caused by the coupling between pin cooling conditions, rod upper plenum calculations and the feedback to clad deformation and burst simulation

  12. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations--Existence of infinite overlapping networks in a fragile ionic liquid.

    Science.gov (United States)

    Habasaki, Junko; Ngai, K L

    2015-04-28

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO3), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, TB (or Tc) and the glass transition temperature Tg, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, NB, within the first minimum of the pair correlation function, g(r)min, increases. On crossing TB (>Tg), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at Tg. The glass transition temperature, Tg, is characterized by the saturation of the total number of "bonds," NB and the corresponding decrease in degree of freedom, F = [(3N - 6) - NB], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at Tg, the number of bonds shows a remarkable change at around TB. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, fg, of each coordination polyhedron, which can be defined by fg = [(3NV - 6) - Nb]. Here, 3Nv is the degree of freedom of NV vertices of the polyhedron, and Nb is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion in the cage is found to be correlated with the fluctuation of Nb of cation-cation (or anion-anion) pairs in the polyhedron, although the

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-01

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

  14. Atomistic mechanisms of fatigue in nanotwinned metals

    International Nuclear Information System (INIS)

    We investigate the fatigue behavior of nanotwinned Cu using a combination of molecular statics and molecular dynamics simulations. The presence of nanoscale twins is found to enhance fatigue crack growth resistance. For the twin-free nanocrystalline samples, the fatigue crack propagates by linking the nanovoids that are formed ahead of the crack tip. In the case of the nanotwinned samples, however, it advances as the crack tip alternately blunts and re-sharpens due to dislocation emission and slip. Both detwinning and crack closure are observed in the path of the fatigue crack in nanotwinned samples with a high density of twin boundaries. As the twin number per grain (quantified by the ratio of the mean grain size to the twin boundary spacing d/λ) increases, detwinning increases the dissipated energy of fatigue cracking, leading to enhanced fatigue resistance. The atomistic simulations show that fatigue crack growth in nanotwinned Cu conforms to Paris’ law. In conjunction with the experimental results, we obtain a quantitative estimation of the Paris’ law exponent (∼4.0), which is in agreement with the theoretical predictions from the damage accumulation model

  15. Correlation for cross-flow resistance coefficient using STAR-CCM+ simulation data for flow of water through rod bundle supported by spacer grid with split-type mixing vane

    International Nuclear Information System (INIS)

    Highlights: • Investigate spacer grid with split-type mixing vanes. • Extent of predictability of experimental data by STAR-CCM+. • Reliability of two equation turbulence models. • Resistance to cross-flow through gaps. - Abstract: Mass transfer by diversion cross-flow through gaps is an important inter-subchannel interaction in fuel bundle of power reactors. It is normally due to the lateral pressure difference between adjacent sub-channels. This phenomenon is augmented in the presence of flow deflectors and is referred to as, directed cross-flow. Diversion cross-flow carries the momentum and energy of flow and hence affects the velocity and temperature profile in the rod bundle. The resistance to cross-flow in the transverse momentum equations is specified by the cross-flow resistant coefficient which is the subject of concern in the present study. In order to obtain data to correlate cross-flow resistance coefficient, computational fluid dynamic simulation using STAR-CCM+ was performed for flow of water at the bundle Reynolds number of Re1 = 3.4×104 through a 5 × 5 rod bundle geometry supported by spacer grid with split mixing vanes for which the rod to rod pitch to diameter ratio was 1.33 and the rod to wall pitch to diameter ratio was 0.74. The two layer k-epsilon turbulence model with an all y+ automatic wall treatment function in STAR-CCM+ were adopted for an isothermal single phase (water) flow through the geometry. The objectives were to primarily investigate the extent of predictability of the experimental data by the computational fluid dynamic (CFD) simulation as a measure of reliability on the CFD code employed and also apply the simulation data to develop correlations for determining resistance coefficient to cross-flow. Validation of simulation results with experimental data showed good correlation of mean flow parameters with experimental data whiles turbulent fluctuations deviated largely from experimental trends. Generally, the agreement

  16. Kernel Bundle EPDiff

    DEFF Research Database (Denmark)

    Sommer, Stefan Horst; Lauze, Francois Bernard; Nielsen, Mads; Pennec, Xavier

    information to be automatically incorporated in registrations and promises to improve the standard framework in several aspects. We present the mathematical foundations of LDDKBM and derive the KB-EPDiff evolution equations, which provide optimal warps in this new framework. To illustrate the resulting......In the LDDMM framework, optimal warps for image registration are found as end-points of critical paths for an energy functional, and the EPDiff equations describe the evolution along such paths. The Large Deformation Diffeomorphic Kernel Bundle Mapping (LDDKBM) extension of LDDMM allows scale space...... diffeomorphism paths, we give examples showing the decoupled evolution across scales and how the method automatically incorporates deforma- tion at appropriate scales....

  17. Twists of symmetric bundles

    OpenAIRE

    Cassou-Nogues, Ph.; Erez, B.; Taylor, M. J.

    2004-01-01

    We establish comparison results between the Hasse-Witt invariants w_t(E) of a symmetric bundle E over a scheme and the invariants of one of its twists E_{\\alpha}. For general twists we describe the difference between w_t(E) and w_t(E_{\\alpha}) up to terms of degree 3. Next we consider a special kind of twist, which has been studied by A. Fr\\"ohlich. This arises from twisting by a cocycle obtained from an orthogonal representation. We show how to explicitly describe the twist for representatio...

  18. Mechanical Models of Microtubule Bundle Collapse in Alzheimer's Disease

    Science.gov (United States)

    Sendek, Austin; Singh, Rajiv; Cox, Daniel

    2013-03-01

    Amyloid-beta aggregates initiate Alzheimer's disease, and downstream trigger degradation of tau proteins that act as microtubule bundle stabilizers and mechanical spacers. Currently it is unclear which of tau cutting by proteases, tau phosphorylation, or tau aggregation are responsible for cytoskeleton degradation., We construct a percolation simulation of the microtubule bundle using a molecular spring model for the taus and including depletion force attraction between microtubules and membrane/actin cytoskeletal surface tension. The simulation uses a fictive molecular dynamics to model the motion of the individual microtubules within the bundle as a result of random tau removal, and calculates the elastic modulus of the bundle as the tau concentration falls. We link the tau removal steps to kinetic tau steps in various models of tau degradation. Supported by US NSF Grant DMR 1207624

  19. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations.

    Directory of Open Access Journals (Sweden)

    Thomas Lemmin

    Full Text Available The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices.

  20. Robust atomistic calculation of dislocation line tension

    Science.gov (United States)

    Szajewski, B. A.; Pavia, F.; Curtin, W. A.

    2015-12-01

    The line tension Γ of a dislocation is an important and fundamental property ubiquitous to continuum scale models of metal plasticity. However, the precise value of Γ in a given material has proven difficult to assess, with literature values encompassing a wide range. Here results from a multiscale simulation and robust analysis of the dislocation line tension, for dislocation bow-out between pinning points, are presented for two widely-used interatomic potentials for Al. A central part of the analysis involves an effective Peierls stress applicable to curved dislocation structures that markedly differs from that of perfectly straight dislocations but is required to describe the bow-out both in loading and unloading. The line tensions for the two interatomic potentials are similar and provide robust numerical values for Al. Most importantly, the atomic results show notable differences with singular anisotropic elastic dislocation theory in that (i) the coefficient of the \\text{ln}(L) scaling with dislocation length L differs and (ii) the ratio of screw to edge line tension is smaller than predicted by anisotropic elasticity. These differences are attributed to local dislocation core interactions that remain beyond the scope of elasticity theory. The many differing literature values for Γ are attributed to various approximations and inaccuracies in previous approaches. The results here indicate that continuum line dislocation models, based on elasticity theory and various core-cut-off assumptions, may be fundamentally unable to reproduce full atomistic results, thus hampering the detailed predictive ability of such continuum models.

  1. Bundle Security Protocol for ION

    Science.gov (United States)

    Burleigh, Scott C.; Birrane, Edward J.; Krupiarz, Christopher

    2011-01-01

    This software implements bundle authentication, conforming to the Delay-Tolerant Networking (DTN) Internet Draft on Bundle Security Protocol (BSP), for the Interplanetary Overlay Network (ION) implementation of DTN. This is the only implementation of BSP that is integrated with ION.

  2. Fiber Bundles and Parseval Frames

    OpenAIRE

    Agrawal, Devanshu; Knisley, Jeff

    2015-01-01

    Continuous frames over a Hilbert space have a rich and sophisticated structure that can be represented in the form of a fiber bundle. The fiber bundle structure reveals the central importance of Parseval frames and the extent to which Parseval frames generalize the notion of an orthonormal basis.

  3. Fiber bundle phase conjugate mirror

    Science.gov (United States)

    Ward, Benjamin G.

    2012-05-01

    An improved method and apparatus for passively conjugating the phases of a distorted wavefronts resulting from optical phase mismatch between elements of a fiber laser array are disclosed. A method for passively conjugating a distorted wavefront comprises the steps of: multiplexing a plurality of probe fibers and a bundle pump fiber in a fiber bundle array; passing the multiplexed output from the fiber bundle array through a collimating lens and into one portion of a non-linear medium; passing the output from a pump collection fiber through a focusing lens and into another portion of the non-linear medium so that the output from the pump collection fiber mixes with the multiplexed output from the fiber bundle; adjusting one or more degrees of freedom of one or more of the fiber bundle array, the collimating lens, the focusing lens, the non-linear medium, or the pump collection fiber to produce a standing wave in the non-linear medium.

  4. Twisted Vector Bundles on Pointed Nodal Curves

    Indian Academy of Sciences (India)

    Ivan Kausz

    2005-05-01

    Motivated by the quest for a good compactification of the moduli space of -bundles on a nodal curve we establish a striking relationship between Abramovich’s and Vistoli’s twisted bundles and Gieseker vector bundles.

  5. 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.

  6. Atomistic k ⋅ p theory

    International Nuclear Information System (INIS)

    Pseudopotentials, tight-binding models, and k ⋅ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ⋅ p theory. In its usual formulation, k ⋅ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ⋅ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp3 tight-binding model. We can thus directly derive the parameters in the sp3 tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III–V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ⋅ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ⋅ p models to be combined in the same system

  7. Steric effects induce geometric remodeling of actin bundles in filopodia

    CERN Document Server

    Dobramysl, Ulrich; Erban, Radek

    2016-01-01

    Filopodia are ubiquitous fingerlike protrusions, spawned by many eukaryotic cells, to probe and interact with their environments. Polymerization dynamics of actin filaments, comprising the structural core of filopodia, largely determine their instantaneous lengths and overall lifetimes. The polymerization reactions at the filopodial tip require transport of G-actin, which enter the filopodial tube from the filopodial base and diffuse toward the filament barbed ends near the tip. Actin filaments are mechanically coupled into a tight bundle by cross-linker proteins. Interestingly, many of these proteins are relatively short, restricting the free diffusion of cytosolic G-actin throughout the bundle and, in particular, its penetration into the bundle core. To investigate the effect of steric restrictions on G-actin diffusion by the porous structure of filopodial actin filament bundle, we used a particle-based stochastic simulation approach. We discovered that excluded volume interactions result in partial and the...

  8. Interactive hypermedia training manual for spent-fuel bundle counters

    International Nuclear Information System (INIS)

    Spent-fuel bundle counters, developed by the Canadian Safeguards Support Program for the International Atomic Energy Agency, provide a secure and independent means of counting the number of irradiated fuel bundles discharged into the fuel storage bays at CANDU nuclear power stations. Paper manuals have been traditionally used to familiarize IAEA inspectors with the operation, maintenance and extensive reporting capabilities of the bundle counters. To further assist inspectors, an interactive training manual has been developed on an Apple Macintosh computer using hypermedia software. The manual uses interactive animation and sound, in conjunction with the traditional text and graphics, to simulate the underlying operation and logic of the bundle counters. This paper presents the key features of the interactive manual and highlights the advantages of this new technology for training

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

    Science.gov (United States)

    Turner, C. Heath; Lei, Yu; Bao, Yuping

    2016-04-01

    The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

  10. First principles view on chemical compound space: Towards atomistic control of molecular properties

    CERN Document Server

    von Lilienfeld, O A

    2012-01-01

    A well-defined notion of chemical space is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we revisit the atomistic first principles perspective on chemical compound space. First, we review chemical space in terms of conceptual density functional and molecular grand-canonical ensemble theory. Subsequently, compound-pairs, "alchemical" interpolation and reference compounds, and the relevance of property non-linearity are discussed. Thereafter, we will focus on recent contributions for accelerating atomistic simulations based on modern statistical data analysis methods (artificial intelligence). The crucial role of good descriptors for chemical compounds will be addressed.

  11. The Atiyah Bundle and Connections on a Principal Bundle

    Indian Academy of Sciences (India)

    Indranil Biswas

    2010-06-01

    Let be a ∞ manifold and a Lie a group. Let $E_G$ be a ∞ principal -bundle over . There is a fiber bundle $\\mathcal{C}(E_G)$ over whose smooth sections correspond to the connections on $E_G$. The pull back of $E_G$ to $\\mathcal{C}(E_G)$ has a tautological connection. We investigate the curvature of this tautological connection.

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

    NARCIS (Netherlands)

    Rzepiela, Andrzej J.; Sengupta, Durba; Goga, Nicolae; Marrink, Siewert J.

    2010-01-01

    Antimicrobial peptides (AMPs) comprise a large family of peptides that include small cationic peptides, such as magainins, which permeabilize lipid membranes. Previous atomistic level simulations of magainin-H2 peptides show that they act by forming toroidal transmembrane pores. However, due to the

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

    Science.gov (United States)

    Chen, Youping

    2006-02-01

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

  14. Left bundle-branch block

    DEFF Research Database (Denmark)

    Risum, Niels; Strauss, David; Sogaard, Peter;

    2013-01-01

    The relationship between myocardial electrical activation by electrocardiogram (ECG) and mechanical contraction by echocardiography in left bundle-branch block (LBBB) has never been clearly demonstrated. New strict criteria for LBBB based on a fundamental understanding of physiology have recently...

  15. Bundling ecosystem services in Denmark

    DEFF Research Database (Denmark)

    Turner, Katrine Grace; Odgaard, Mette Vestergaard; Bøcher, Peder Klith; Dalgaard, Tommy; Svenning, J.-C.

    2014-01-01

    We made a spatial analysis of 11 ecosystem services at a 10 km × 10 km grid scale covering most of Denmark. Our objective was to describe their spatial distribution and interactions and also to analyze whether they formed specific bundle types on a regional scale in the Danish cultural landscape....... We found clustered distribution patterns of ecosystem services across the country. There was a significant tendency for trade-offs between on the one hand cultural and regulating services and on the other provisioning services, and we also found the potential of regulating and cultural services to...... form synergies. We identified six distinct ecosystem service bundle types, indicating multiple interactions at a landscape level. The bundle types showed specialized areas of agricultural production, high provision of cultural services at the coasts, multifunctional mixed-use bundle types around urban...

  16. Structure of the acrosomal bundle.

    Science.gov (United States)

    Schmid, Michael F; Sherman, Michael B; Matsudaira, Paul; Chiu, Wah

    2004-09-01

    In the unactivated Limulus sperm, a 60- micro m-long bundle of actin filaments crosslinked by the protein scruin is bent and twisted into a coil around the base of the nucleus. At fertilization, the bundle uncoils and fully extends in five seconds to support a finger of membrane known as the acrosomal process. This biological spring is powered by stored elastic energy and does not require the action of motor proteins or actin polymerization. In a 9.5-A electron cryomicroscopic structure of the extended bundle, we show that twist, tilt and rotation of actin-scruin subunits deviate widely from a 'standard' F-actin filament. This variability in structural organization allows filaments to pack into a highly ordered and rigid bundle in the extended state and suggests a mechanism for storing and releasing energy between coiled and extended states without disassembly. PMID:15343340

  17. Locking means for fuels bundles

    International Nuclear Information System (INIS)

    A nuclear power reactor fuel bundle is described which has a plurality of fuel rods disposed between two end plates positioned by tie rods extending therebetween. The assembled bundle is secured by one or more locking forks which pass through slots in the tie rod ends. Springs mounted on the fuel rods and tie rods are compressed by assembling the bundle and forcing one end plate against the locking fork to maintain the fuel rods and tie rods in position between the end plates. Downward pressure on the end plate permits removal of the locking fork so that the end plates may be removed, thus giving access to the fuel rods. This construction facilitates disassembly of an irradiated fuel bundle under water

  18. Damage in Fiber Bundle Models

    OpenAIRE

    Kun, Ferenc; Zapperi, Stefano; Herrmann, Hans J.

    1999-01-01

    We introduce a continuous damage fiber bundle model that gives rise to macroscopic plasticity and compare its behavior with that of dry fiber bundles. Several interesting constitutive behaviors are found in this model depending on the value of the damage parameter and on the form of the disorder distribution. In addition, we compare the behavior of global load transfer models with local load transfer models and study in detail the damage evolution before failure. We emphasize the analogies be...

  19. Atomistically-informed Dislocation Dynamics in fcc Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, E; Marian, J; Arsenlis, T; Victoria, M; Perlado, J M

    2006-09-06

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

  20. Holomorphic bundles over elliptic manifolds

    International Nuclear Information System (INIS)

    In this lecture we shall examine holomorphic bundles over compact elliptically fibered manifolds. We shall examine constructions of such bundles as well as (duality) relations between such bundles and other geometric objects, namely K3-surfaces and del Pezzo surfaces. We shall be dealing throughout with holomorphic principal bundles with structure group GC where G is a compact, simple (usually simply connected) Lie group and GC is the associated complex simple algebraic group. Of course, in the special case G = SU(n) and hence GC = SLn(C), we are considering holomorphic vector bundles with trivial determinant. In the other cases of classical groups, G SO(n) or G = Sympl(2n) we are considering holomorphic vector bundles with trivial determinant equipped with a non-degenerate symmetric, or skew symmetric pairing. In addition to these classical cases there are the finite number of exceptional groups. Amazingly enough, motivated by questions in physics, much interest centres around the group E8 and its subgroups. For these applications it does not suffice to consider only the classical groups. Thus, while often first doing the case of SU(n) or more generally of the classical groups, we shall extend our discussions to the general semi-simple group. Also, we shall spend a good deal of time considering elliptically fibered manifolds of the simplest type, namely, elliptic curves

  1. Structure and dynamics of the pore-lining helix of the nicotinic receptor : MD simulations in water, lipid bilayers, and transbilayer bundles

    NARCIS (Netherlands)

    Law, RJ; Forrest, LR; Ranatunga, KM; La Rocca, P; Tieleman, DP; Sansom, MSP

    2000-01-01

    Multiple nanosecond duration molecular dynamics simulations on the pore-lining M2 helix of the nicotinic acetylcholine receptor reveal how its structure and dynamics change as a function of environment. In water, the M2 helix partially unfolds to form a molecular hinge in the vicinity of a central L

  2. Does size matter? : disentangling consumers' bundling preferences

    OpenAIRE

    Manoj K. Agarwal; Frambach, Ruud T.; Stremersch, Stefan

    2000-01-01

    Previous marketing literature has focused to a large extent on the effect of bundle characteristics on a consumer’s decision to buy a (fixed) bundle in a non-competitive setting. This study extends this narrow focus in four major ways. First, the authors address bundles that are customizable. Second, they distinguish between a consumer’s decision of whether to bundle (bundle choice) and the decision of how many goods or services to include in a bundle (bundle size). Third, they extend the foc...

  3. Atomistic Processes of Catalyst Degradation

    Energy Technology Data Exchange (ETDEWEB)

    None

    2004-11-27

    The purpose of this cooperative research and development agreement (CRADA) between Sasol North America, Inc., and the oak Ridge National Laboratory (ORNL) was to improve the stability of alumina-based industrial catalysts through the combination of aberration-corrected scanning transmission electron microscopy (STEM) at ORNL and innovative sample preparation techniques at Sasol. Outstanding progress has been made in task 1, 'Atomistic processes of La stabilization'. STEM investigations provided structural information with single-atom precision, showing the lattice location of La dopant atoms, thus enabling first-principles calculations of binding energies, which were performed in collaboration with Vanderbilt University. The stabilization mechanism turns out to be entirely due to a particularly strong binding energy of the La tom to the {gamma}-alumina surface. The large size of the La atom precludes incorporation of La into the bulk alumina and also strains the surface, thus preventing any clustering of La atoms. Thus highly disperse distribution is achieved and confirmed by STEM images. la also affects relative stability of the exposed surfaces of {gamma}-alumina, making the 100 surface more stable for the doped case, unlike the 110 surface for pure {gamma}-alumina. From the first-principles calculations, they can estimate the increase in transition temperature for the 3% loading of La used commercially, and it is in excellent agreement with experiment. This task was further pursued aiming to generate useable recommendations for the optimization of the preparation techniques for La-doped aluminas. The effort was primarily concentrated on the connection between the boehmitre-{gamma}-Al{sub 2}O{sub 3} phase transition (i.e. catalyst preparation) and the resulting dispersion of La on the {gamma}-Al{sub 2}O{sub 3} surface. It was determined that the La distribution on boehmite was non-uniform and different from that on the {gamma}-Al{sub 2}O{sub 3} and thus

  4. Design and fabrication of a remote fuel bundle welding system

    International Nuclear Information System (INIS)

    A remote fuel bundle welding system in the hot-cell was designed and fabricated. To achieve this, a preliminary investigation of a hands-on fuel fabrication outside the hot-cell was conducted with a consideration of the constraints caused by welding in the hot-cell. Some basic experiments were also carried out to improve the end-plate welding process for fuel bundle manufacturing. The resistance welding system using the end-plate welding was also improved. It was found that resistance welding was more suitable for joining and end-plate to end caps in the hot-cell. The optimum conditions for end-plate welding for remote operation were also obtained. Preliminary performances to improve the resistance welding process were also examined, and the resistance welding process was determined to be the best in the hot-cell environment for fuel bundle manufacturing. The greatest advantage of fuel bundle welding system would be a qualified process for resistance welding in which there is extensive production experience. This paper presents an outline of the developed welding system for fuel bundle manufacturing and reviews the conceptual design of remote welding system using a master-slave manipulator. The design of a remote welding system using the 3-dimensional modeling method was also designed. Furthermore the mechanical considerations and the mock-up simulation test were described. Finally, its performance test results were presented for a mock-up of a remote fuel bundle welding system. (Author)

  5. Validation of SOCRAT-BN code on rod bundle experiments

    International Nuclear Information System (INIS)

    SOCRAT-BN code is developed for the analysis of design and beyond design basis accidents at NPPs with liquid sodium as a coolant. To simulate the behavior of the coolant in the reactor core heat transfer and friction in rod bundle geometry are required to consider. The code SOCRAT-BN uses specialized closing relations to simulate rod bundles. The article describes the validation of the code SOCRAT-BN on experiments with fuel rod imitators in the triangular geometry with a wire-wound. (author)

  6. Advanced Fuel Bundles for PHWRS

    International Nuclear Information System (INIS)

    The fuel used by NPCIL presently is natural uranium dioxide in the form of 19- element fuel bundles for 220 MWe PHWRs and 37-element fuel bundles for the TAPP-3&4 540 MWe units. The new 700 MWe PHWRs also use 37-element fuel bundles. These bundles are of short 0.5 m length of circular geometry. The cladding is of collapsible type made of Zircaloy-4 material. PHWRs containing a string of short length fuel bundles and the on-power refueling permit flexibility in using different advanced fuel designs and in core fuel management schemes. Using this flexibility, alternative fuel concepts are tried in Indian PHWRs. The advances in PHWR fuel designs are governed by the desire to use resources other than uranium, improve fuel economics by increasing fuel burnup and reduce overall spent nuclear fuel waste and improve reactor safety. The rising uranium prices are leading to a relook into the Thorium based fuel designs and reprocessed Uranium based and Plutonium based MOX designs and are expected to play a major role in future. The requirement of synergism between different type of reactors also plays a role. Increase in fuel burnup beyond 15 000 MW∙d/TeU in PHWRs, using higher fissile content materials like slightly enriched uranium, Mixed Oxide and Thorium Oxide in place of natural uranium in fuel elements, was studied many PHWR operating countries. The work includes reactor physics studies and test irradiation in research reactors and power reactors. Due to higher fissile content these bundles will be capable of delivering higher burnup than the natural uranium bundles. In India the fuel cycle flexibility of PHWRs is demonstrated by converting this type of technical flexibility to the real economy by irradiating these different types of advanced fuel materials namely Thorium, MOX, SEU, etc. The paper gives a review of the different advanced fuel design concepts studied for Indian PHWRs. (author)

  7. 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...

  8. Studying the vibrations of rod bundles under asymmetrical flow-round

    International Nuclear Information System (INIS)

    The results of experimental invesigation into vibrations of peripheral tubes in a rod bundle initiated by coolant flow are presented. Conditions of flowing around the rod bundles with different deflections in the channel geometry and hydrodynamics of coolant flow are simulated on special models. Data characterizing the dependence of the rod vibration amplitudes on the value of the gap between the bundle and the channel as well as the effect of the transverse constituent of the coolant overflow from the centre of the bundle to periphery on the rod vibration amplitude in one- and two-phase flows are obtained

  9. An atomistically validated continuum model for strain relaxation and misfit dislocation formation

    Science.gov (United States)

    Zhou, X. W.; Ward, D. K.; Zimmerman, J. A.; Cruz-Campa, J. L.; Zubia, D.; Martin, J. E.; van Swol, F.

    2016-06-01

    In this paper, molecular dynamics (MD) calculations have been used to examine the physics behind continuum models of misfit dislocation formation and to assess the limitations and consequences of approximations made within these models. Without compromising the physics of misfit dislocations below a surface, our MD calculations consider arrays of dislocation dipoles constituting a mirror imaged "surface". This allows use of periodic boundary conditions to create a direct correspondence between atomistic and continuum representations of dislocations, which would be difficult to achieve with free surfaces. Additionally, by using long-time averages of system properties, we have essentially reduced the errors of atomistic simulations of large systems to "zero". This enables us to deterministically compare atomistic and continuum calculations. Our work results in a robust approach that uses atomistic simulation to accurately calculate dislocation core radius and energy without the continuum boundary conditions typically assumed in the past, and the novel insight that continuum misfit dislocation models can be inaccurate when incorrect definitions of dislocation spacing and Burgers vector in lattice-mismatched systems are used. We show that when these insights are properly incorporated into the continuum model, the resulting energy density expression of the lattice-mismatched systems is essentially indistinguishable from the MD results.

  10. Atomistic modelling of the hydration of CaSO 4

    Science.gov (United States)

    Adam, Craig D.

    2003-08-01

    Atomistic modelling techniques, using empirical potentials, have been used to simulate a range of structures formed by the hydration of γ-CaSO 4 and described as CaSO 4· nH 2O (0commercial importance and has been subjected to much experimental study. These simulation studies demonstrate significant water-matrix interactions that influence the crystallography of the hydrated phase. The existence of two types of hydration site has been predicted, including one within the Ca 2+coordination sphere. Close correlation between water molecule bonding energy, Ca 2+-O w bond length and unit-cell volume have been established. This shows that as the number of water molecules within the unit cell increases, the bonding energy increases and the unit cell contracts. However around n=0.5, this process reaches a turning point with the incorporation of further waters resulting in reduced binding energy and an expanding unit cell.

  11. Asymmetric dynamics of ion channel forming proteins - Hepatitis C virus (HCV) p7 bundles.

    Science.gov (United States)

    Kalita, Monoj Mon; Fischer, Wolfgang B

    2016-07-01

    Protein p7 of hepatitis C virus (HCV) is a short 63 amino acid membrane protein which homo-oligomerises in the lipid membrane to form ion and proton conducting bundles. Two different genotypes (GTs) of p7, 1a and 5a, are used to simulate hexameric bundles of the protein embedded in a fully hydrated lipid bilayer during 400ns molecular dynamics (MD) simulations. Whilst the bundle of GT 1a is based on a fully computational derived structure, the bundle of GT 5a is based on NMR spectroscopic data. Results of a full correlation analysis (FCA) reveal that albeit structural differences both bundles screen local minima during the simulation. The collective motion of the protein domains is asymmetric. No 'breathing-mode'-like dynamics is observed. The presence of divalent ions, such as Ca-ions affects the dynamics of especially solvent exposed parts of the protein, but leaves the asymmetric domain motion unaffected. PMID:27079148

  12. Modelling of transient dynamic bundle deformation using time integration scheme

    International Nuclear Information System (INIS)

    The BOW code has been examined whether its modeling capability can be extended to the simulation of interactions (i.e., fretting) between neighbouring fuel elements in a fuel bundle and between the fuel bundle and the pressure tube in a fuel channel. The current BOW code is specialized in simulating the static problems, such as the deflection of each element and interactions between neighbouring elements in a fuel bundle, and interactions between neighbouring bundles and between a bundle and the pressure tube in a fuel channel. The Wilson θ time integration scheme has been implemented in the BOW code, for the extension of its capability to modelling dynamic contact problems. As part of verification to ensure that the modification in the code functions exactly as designed, the dynamic-modelling capability of the BOW code has been applied to simple support beam cases subjected to a uniform step load at the middle of the beam. The calculation results confirmed that the modified BOW code, where the contact algorithm is implemented in the step-by-step integration manner using the Wilson θ time integration scheme, can solve the dynamic problem with unconditional convergence. This paper describes the theory and models for the new capabilities of the BOW code. (author)

  13. Numerical model for thermal and mechanical behaviour of a CANDU 37-element bundle

    International Nuclear Information System (INIS)

    Prediction of transient fuel bundle deformations is important for assessing the integrity of fuel and the surrounding structural components under different operating conditions including accidents. For numerical simulation of the interactions between fuel bundle and pressure tube, a reliable numerical bundle model is required to predict thermal and mechanical behaviour of the fuel bundle assembly under different thermal loading conditions. To ensure realistic representations of the bundle behaviour, this model must include all of the important thermal and mechanical features of the fuel bundle, such as temperature-dependent material properties, thermal viscoplastic deformation in sheath, fuel-to-sheath interactions, endplate constraints and contacts between fuel elements. In this paper, we present a finite element based numerical model for predicting macroscopic transient thermal-mechanical behaviour of a complete 37-element CANDU nuclear fuel bundle under accident conditions and demonstrate its potential for being used to investigate fuel bundle to pressure tube interaction in future nuclear safety analyses. This bundle model has been validated against available experimental and numerical solutions and applied to various simulations involving steady-state and transient loading conditions. (author)

  14. Effect of Reynolds number and bundle geometry on the turbulent flow in tight lattice bundle

    International Nuclear Information System (INIS)

    The flow structure in tight lattice is still of great interest to nuclear industry. The accurate prediction of flow parameter in subchannels of tight lattice is likable. Unsteady Reynolds Averaged Navier Stokes (URANS) is a promising approach to achieve this goal. The implementation of URANS (Unsteady Reynolds Averaged Navier Stokes) approach will be validated by comparing computational results with the experimental data of Krauss (1998). In this paper, the turbulent flow with different Reynolds number (5000~215000) and different P/D(1.005~1.2) are simulated with CFD code CFX12.The effects of the Reynolds number and the bundle geometry(P/D) on wall shear stress, turbulent kinetic energy, turbulent mixing and large scale coherent structure in tight lattice are analyzed in details. It is hoped that the present work will contribute to the understanding of these important flow phenomena and facilitate the prediction and design of rod bundles. (author)

  15. Cohomology of line bundles: Applications

    Science.gov (United States)

    Blumenhagen, Ralph; Jurke, Benjamin; Rahn, Thorsten; Roschy, Helmut

    2012-01-01

    Massless modes of both heterotic and Type II string compactifications on compact manifolds are determined by vector bundle valued cohomology classes. Various applications of our recent algorithm for the computation of line bundle valued cohomology classes over toric varieties are presented. For the heterotic string, the prime examples are so-called monad constructions on Calabi-Yau manifolds. In the context of Type II orientifolds, one often needs to compute cohomology for line bundles on finite group action coset spaces, necessitating us to generalize our algorithm to this case. Moreover, we exemplify that the different terms in Batyrev's formula and its generalizations can be given a one-to-one cohomological interpretation. Furthermore, we derive a combinatorial closed form expression for two Hodge numbers of a codimension two Calabi-Yau fourfold.

  16. CFD simulations of the single-phase and two-phase coolant flow of water inside the original and modified CANDU 37-element bundles

    International Nuclear Information System (INIS)

    Single-phase (inlet temperature of 180° C, outlet pressure of 9 MPa, total power of 2 MW and flow rate of 13.5 Kg/s), and two-phase (inlet temperature of 265° C, outlet pressure of 10 MPa, total power of 7.126 MW and flow rate of 19 Kg/s) water flows inside a CANDU thirty seven element fuel string are simulated using a Computational Fluid Dynamics (CFD) code with parallel processing and results are presented in this paper. The analyses have been performed for the original and modified (11.5 mm center element diameter) designs with skewed cosine axial heat flux distribution and 5.1% diametral creep of the pressure tube. The CFD results are in good agreement with the expected temperature and velocity cross-sectional distributions. The effect of the pressure tube creep on the flow bypass is detected, and the CHF improvement in the core region of the modified design is confirmed. The two-phase flow model reasonably predicted the void distribution and the role of interfacial drag on increasing the pressure drop. In all CFD models, the appendages were shown to enhance the production of cross flows and their corresponding flow mixing and asymmetry. (author)

  17. Principal bundles the classical case

    CERN Document Server

    Sontz, Stephen Bruce

    2015-01-01

    This introductory graduate level text provides a relatively quick path to a special topic in classical differential geometry: principal bundles.  While the topic of principal bundles in differential geometry has become classic, even standard, material in the modern graduate mathematics curriculum, the unique approach taken in this text presents the material in a way that is intuitive for both students of mathematics and of physics. The goal of this book is to present important, modern geometric ideas in a form readily accessible to students and researchers in both the physics and mathematics communities, providing each with an understanding and appreciation of the language and ideas of the other.

  18. ASSERT and COBRA predictions of flow distribution in vertical bundles

    International Nuclear Information System (INIS)

    COBRA and ASSERT are subchannel codes which compute flow and enthalpy distributions in rod bundles. COBRA is a well known code, ASSERT is under development at CRNL. This paper gives a comparison of the two codes with boiling experiments in vertical seven rod bundles. ASSERT predictions of the void distribution are shown to be in good agreement with reported experimental results, while COBRA predictions are unsatisfactory. The mixing models in both COBRA and ASSERT are briefly discussed. The reasons for the failure of COBRA-IV and the success of ASSERT in simulating the experiments are highlighted

  19. Exploring Bundling Theory with Geometry

    Science.gov (United States)

    Eckalbar, John C.

    2006-01-01

    The author shows how instructors might successfully introduce students in principles and intermediate microeconomic theory classes to the topic of bundling (i.e., the selling of two or more goods as a package, rather than separately). It is surprising how much students can learn using only the tools of high school geometry. To be specific, one can…

  20. Hydrodynamic behavior of a bare rod bundle

    International Nuclear Information System (INIS)

    The temperature distribution within the rod bundle of a nuclear reactor is of major importance in nuclear reactor design. However temperature information presupposes knowledge of the hydrodynamic behavior of the coolant which is the most difficult part of the problem due to complexity of the turbulence phenomena. In the present work a 2-equation turbulence model--a strong candidate for analyzing actual three dimensional turbulent flows--has been used to predict fully developed flow of infinite bare rod bundle of various aspect ratios (P/D). The model has been modified to take into account anisotropic effects of eddy viscosity. Secondary flow calculations have been also performed although the model seems to be too rough to predict the secondary flow correctly. Heat transfer calculations have been performed to confirm the importance of anisotropic viscosity in temperature predictions. All numerical calculations for flow and heat have been performed by two computer codes based on the TEACH code. Experimental measurements of the distribution of axial velocity, turbulent axial velocity, turbulent kinetic energy and radial Reynolds stresses were performed in the developing and fully developed regions. A 2-channel Laser Doppler Anemometer working on the Reference mode with forward scattering was used to perform the measurements in a simulated interior subchannel of a triangular rod array with P/D = 1.124. Comparisons between the analytical results and the results of this experiment as well as other experimental data in rod bundle array available in literature are presented. The predictions are in good agreement with the results for the high Reynolds numbers

  1. Bundled Discounts and EC Judicial Review

    OpenAIRE

    Christian Roques

    2008-01-01

    The Community Courts' case law is rich with cases relating to tying or bundling practices in their classical economic form. However, the same cannot be said for the second acceptance of bundled discounts.

  2. Thermal hydraulics of rod bundles: The effect of eccentricity

    International Nuclear Information System (INIS)

    Highlights: • Present CFD investigation explores, whole bundle eccentricity for the first time. • Fluid flow and thermal characteristics in various subchannels are analyzed. • Mass flux distribution is particularly analyzed to study eccentricity effect. • Higher eccentricity resulted in a shoot up in rod surface temperature distribution. • Both tangential and radial flow in rod bundles has resulted due to eccentricity. -- Abstract: The effect of eccentricity on the fluid flow and heat transfer through a 19-rod bundle is numerically carried out. When the whole bundle shifts downwards with respect to the outer (pressure) tube, flow redistribution happens. This in turn is responsible for changes in mass flux, pressure and differential flow development in various subchannels. The heat flux imposed on the surface of the fuel rods and the mass flux through the subchannels determines the coolant outlet temperatures. The simulations are performed for a coolant flow Reynolds number of 4 × 105. For an eccentricity value of 0.7, the mass flux in the bottom most subchannel (l) was found to decrease by 10%, while the surface temperature of the fuel rod in the vicinity of this subchannel increased by 250% at the outlet section. Parameters of engineering interest including skin friction coefficient, Nusselt number, etc., have been systematically explored to study the effect of eccentricity on the rod bundle

  3. Failure properties of fiber bundle models

    OpenAIRE

    Pradhan, Srutarshi; Chakrabarti, Bikas K.

    2003-01-01

    We study the failure properties of fiber bundles when continuous rupture goes on due to the application of external load on the bundles. We take the two extreme models: equal load sharing model (democratic fiber bundles) and local load sharing model. The strength of the fibers are assumed to be distributed randomly within a finite interval. The democratic fiber bundles show a solvable phase transition at a critical stress (load per fiber). The dynamic critical behavior is obtained analyticall...

  4. Bundling Information Goods: Pricing, Profits, and Efficiency

    OpenAIRE

    Yannis Bakos; Erik Brynjolfsson

    1999-01-01

    We study the strategy of bundling a large number of information goods, such as those increasingly available on the Internet, and selling them for a fixed price. We analyze the optimal bundling strategies for a multiproduct monopolist, and we find that bundling very large numbers of unrelated information goods can be surprisingly profitable. The reason is that the law of large numbers makes it much easier to predict consumers' valuations for a bundle of goods than their valuations for the indi...

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

    Science.gov (United States)

    Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten

    2009-02-01

    We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

  6. Atomistic processes during nanoindentation of amorphous silicon carbide

    International Nuclear Information System (INIS)

    Atomistic mechanisms of nanoindentation of a-SiC have been studied by molecular dynamics simulations. The load displacement curve exhibits a series of load drops, reflecting the short-range topological order similar to crystalline 3C-SiC. In contrast to 3C-SiC, the load drops are irregularly spaced and less pronounced. The damage is spatially more extended than in 3C-SiC, and it exhibits long-range oscillations consistent with the indenter size. Hardness is ∼60% lower than in 3C-SiC and is in agreement with experiment. The onset of plastic deformation occurs at depth ∼75% lower than in 3C-SiC

  7. Quantum principal bundles and corresponding gauge theories

    CERN Document Server

    Durdevic, M

    1995-01-01

    A generalization of classical gauge theory is presented, in the framework of a noncommutative-geometric formalism of quantum principal bundles over smooth manifolds. Quantum counterparts of classical gauge bundles, and classical gauge transformations, are introduced and investigated. A natural differential calculus on quantum gauge bundles is constructed and analyzed. Kinematical and dynamical properties of corresponding gauge theories are discussed.

  8. Strategic and welfare implications of bundling

    DEFF Research Database (Denmark)

    Martin, Stephen

    1999-01-01

    A standard oligopoly model of bundling shows that bundling by a firm with a monopoly over one product has a strategic effect because it changes the substitution relationships between the goods among which consumers choose. Bundling in appropriate proportions is privately profitable, reduces rivals...

  9. On Volumes of Arithmetic Line Bundles

    OpenAIRE

    Yuan, Xinyi

    2008-01-01

    We show an arithmetic generalization of the recent work of Lazarsfeld-Mustata which uses Okounkov bodies to study linear series of line bundles. As applications, we derive a log-concavity inequality on volumes of arithmetic line bundles and an arithmetic Fujita approximation theorem for big line bundles.

  10. Mixture of ionic liquid and carbon nanotubes: comparative studies of the structural characteristics and dispersion of the aggregated non-bundled and bundled carbon nanotubes.

    Science.gov (United States)

    Mohammadi, Morteza; Foroutan, Masumeh

    2013-02-21

    In this work, the two mixtures of ionic liquid 1-n-propyl-4-amino-1,2,4-triazolium bromide and each type of the aggregated single-walled carbon nanotubes (SWCNTs), i.e. bundled SWCNTs and non-bundled, were investigated using molecular dynamics (MD) simulations. The structural characteristics of a SWCNT in the ionic liquid (IL) were examined by analyzing the radial distribution functions and the results show that the nearest IL cations to the SWCNT surface can approach it from three different positions. Also, the possibility of the dispersion of the bundled SWCNTs containing three and seven carbon nanotubes was investigated. The obtained results showed that under the investigated conditions, the IL cannot disperse the bundled SWCNTs, but it can disperse six and seven aggregated non-bundled ones. Moreover, we investigated the underlying dispersion mechanism of the aggregated SWCNTs in the IL, using MD simulations. The self diffusion coefficients and transport numbers of the cations and anions were computed in the systems containing pure IL, the mixtures of IL and one, six and seven non-bundled SWCNTs and the systems containing IL and bundled SWCNTs with three and seven carbon nanotubes. The obtained results showed that the diffusion coefficients and the transport numbers of the cations are more than anions in all mentioned systems. PMID:23318467

  11. Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

    Science.gov (United States)

    Sarukhanyan, Edita; De Nicola, Antonio; Roccatano, Danilo; Kawakatsu, Toshihiro; Milano, Giuseppe

    2014-03-01

    The processes of CNTs bundle formation and insertion/rearrangement inside lipid bilayers, as models of cellular membranes, is described and analyzed in details using simulations on the microsecond scale. Molecular Dynamics simulations employing hybrid particle-field models (MD-SCF) show that during the insertion process lipid molecules coat bundles surfaces. The distortions of bilayers are more pronounced for systems undergoing to insertion of bundles made of longer CNTs. In particular, when the insertion occurs in perpendicular orientation, adsorption of lipids on CNTs surfaces promotes a transient poration. This result suggests mechanism of membrane disruption operated by bundles causing the formation of solvent-rich pockets.

  12. Simplicial principal bundles in parametrized spaces

    CERN Document Server

    Roberts, David M

    2012-01-01

    In this paper, motivated by recent interest in higher gauge theory, we prove that the fiberwise geometric realization functor takes a certain class of simplicial principal bundles in a suitable category of spaces over a fixed space $B$ to fiberwise principal bundles. As an application we show that the fiberwise geometric realization of the universal simplicial principal bundle for a simplicial group $G$ in the category of spaces over $B$ gives rise to a fiberwise principal bundle with structure group $|G|$. An application to classifying theory for fiberwise principal bundles is described.

  13. Multipath packet switch using packet bundling

    DEFF Research Database (Denmark)

    Berger, Michael Stubert

    The basic concept of packet bundling is to group smaller packets into larger packets based on, e.g., quality of service or destination within the packet switch. This paper presents novel applications of bundling in packet switching. The larger packets created by bundling are utilized to extend...... switching capacity by use of parallel switch planes. During the bundling operation, packets will experience a delay that depends on the actual implementation of the bundling and scheduling scheme. Analytical results for delay bounds and buffer size requirements are presented for a specific scheduling...

  14. Atomistic Failure Mechanism of Single Wall Carbon Nanotubes with Small Diameters

    Institute of Scientific and Technical Information of China (English)

    JI Dong; GAO Xiang; KONG Xiang-Yang; LI Jia-Ming

    2007-01-01

    @@ Single wall carbon nanotubes with small diameters (< 5.0 (A)) subjected to bending deformation are simulated by orthogonal tight-binding molecular dynamics approach. Based on the calculations of C-C bond stretching and breaking in the bending nanotubes, we elucidate the atomistic failure mechanisms of nanotube with small diameters. In the folding zone of bending nanotube, a large elongation of C-C bonds occurs, accounting for the superelastic behaviour.

  15. A numerical method for the time coarsening of transport processes at the atomistic scale

    Science.gov (United States)

    Gonzalez-Ferreiro, B.; Romero, I.; Ortiz, M.

    2016-05-01

    We propose a novel numerical scheme for the simulation of slow transport processes at the atomistic scale. The scheme is based on a model for non-equilibrium statistical thermodynamics recently proposed by the authors, and extends it by formulating a variational integrator, i.e. a discrete functional whose optimality conditions provide all the governing equations of the problem. The method is employed to study surface segregation of AuAg alloys and its convergence is confirmed numerically.

  16. A genetic algorithm for the atomistic design and global optimisation of substitutionally disordered materials

    OpenAIRE

    Mohn, Chris E.; Kob, Walter

    2008-01-01

    We present a genetic algorithm for the atomistic design and global optimisation of substitutionally disordered bulk materials and surfaces. Premature convergence which hamper conventional genetic algorithms due to problems with synchronisation is avoided using a symmetry adapted crossover. The algorithm outperforms previously reported Monte Carlo and genetic algorithm simulations for finding low energy minima of two simple alloy models without the need for any redesign.

  17. Atomistic calculation of the thermal conductance of large scale bulk-nanowire junctions

    OpenAIRE

    Duchemin, Ivan; Donadio, Davide

    2011-01-01

    We have developed an efficient scalable kernel method for thermal transport in open systems, with which we have computed the thermal conductance of a junction between bulk silicon and silicon nanowires with diameter up to 10 nm. We have devised scaling laws for transmission and reflection spectra, which allow us to predict the thermal resistance of bulk-nanowire interfaces with larger cross sections than those achievable with atomistic simulations. Our results indicate the characteristic size...

  18. Model of turbine blades bundles

    Czech Academy of Sciences Publication Activity Database

    Půst, Ladislav; Pešek, Luděk

    Prague : Institute of Thermomechanics, Academy of Sciences of the Czech Republic, v. v. i., 2013 - (Zolotarev, I.), s. 467-477 ISBN 978-80-87012-47-5. ISSN 1805-8256. [Engineering Mechanics 2013 /19./. Svratka (CZ), 13.05.2013-16.05.2013] R&D Projects: GA ČR GA101/09/1166 Institutional support: RVO:61388998 Keywords : free and forced vibrations * eigenmodes * mathematical model * bundle of blades Subject RIV: BI - Acoustics

  19. Model of turbine blades bundles

    Czech Academy of Sciences Publication Activity Database

    Půst, Ladislav; Pešek, Luděk

    Praha : Insitute of Thermomechanics ASCR, v. v. i., 2013 - (Zolotarev, I.). s. 125-126 ISBN 978-80-87012-46-8. ISSN 1805-8248. [Engineering Mechanics 2013 /19./. 13.05.2013-16.05.2013, Svratka] R&D Projects: GA ČR GA101/09/1166 Institutional support: RVO:61388998 Keywords : free and forced vibrations * eigenmodes * bundle of blades Subject RIV: BI - Acoustics

  20. Competitive nonlinear pricing and bundling

    OpenAIRE

    Armstrong, Mark; Vickers, John

    2006-01-01

    We examine the impact of multiproduct nonlinear pricing on profit, consumer surplus and welfare in a duopoly. When consumers buy all their products from one firm (the one-stop shopping model), nonlinear pricing leads to higher profit and welfare, but often lower consumer surplus, than linear pricing. By contrast, in a unit-demand model where consumers may buy one product from one firm and another product from another firm, bundling generally acts to reduce profit and welfare and to boost cons...

  1. A Gaussian mixture modelling approach to the data-driven estimation of atomistic support for continuum stress

    International Nuclear Information System (INIS)

    Recent developments in multiscale modelling include the treatment of atomistic scale interactions via molecular dynamics simulations. The atomistic stress definition at a given continuum point contains a space-averaging volume over nearby atoms to provide an averaged macroscopic stress measure. Previous work on atomistic stress measures introduce the size of this volume as an a priori given parameter. In this contribution we let the atomistic data speak for itself by hypothesizing that the influence between atoms can be effectively estimated from their relative spatial position and stress. Atoms with highly similar spatial position and stress should therefore be contained within the same space-averaging volume. We motivate the application of Gaussian mixture modelling as a principled probabilistic means of estimating this similarity directly from the atomistic data. This model enables the discovery of homogeneous sub-populations of atoms in an entirely data-driven manner. The size of the space-averaging volume then follows naturally from the average maximum extent of the sub-populations. Furthermore, we demonstrate how the model can be used to compute the stress at arbitrary continuum points. Thorough evaluation is conducted on a numerical example of an edge dislocation in a single crystal. We find that our results are in excellent agreement with the corresponding analytical solution. (paper)

  2. Quantum bundles and their symmetries

    International Nuclear Information System (INIS)

    Wave functions in the domain of observables such as the Hamiltonian are not always smooth functions on the classical configuration space Q. Rather, they are often best regarded as functions on a G bundle EG over Q or as sections of an associated bundle. If H is a classical group which acts on Q, its quantum version HG, which acts on EG, is not always H, but an extension of H by G. A powerful and physically transparent construction of EG and HG, where G = U(1) and H1(Q,Z) = 0, has been developed using the path space P. (P consists of paths on Q from a fixed point). In this paper the authors show how to construct EG and HG when G is U(1) or U(1) x π1(Q) and there is no restriction on H1(Q,Z). The method is illustrated with concrete examples, such as a system of charges and monopoles. The method is illustrated with concrete examples, such as a system of charges and monopoles. The authors argue also that P is a sort of superbundle from which a large variety of bundles can be obtained by imposing suitable equivalence relations

  3. Photonic bandgap fiber bundle spectrometer

    CERN Document Server

    Hang, Qu; Syed, Imran; Guo, Ning; Skorobogatiy, Maksim

    2010-01-01

    We experimentally demonstrate an all-fiber spectrometer consisting of a photonic bandgap fiber bundle and a black and white CCD camera. Photonic crystal fibers used in this work are the large solid core all-plastic Bragg fibers designed for operation in the visible spectral range and featuring bandgaps of 60nm - 180nm-wide. 100 Bragg fibers were chosen to have complimentary and partially overlapping bandgaps covering a 400nm-840nm spectral range. The fiber bundle used in our work is equivalent in its function to a set of 100 optical filters densely packed in the area of ~1cm2. Black and white CCD camera is then used to capture spectrally "binned" image of the incoming light at the output facet of a fiber bundle. To reconstruct the test spectrum from a single CCD image we developed an algorithm based on pseudo-inversion of the spectrometer transmission matrix. We then study resolution limit of this spectroscopic system by testing its performance using spectrally narrow test peaks (FWHM 5nm-25nm) centered at va...

  4. Compressive force generation by a bundle of living biofilaments

    Science.gov (United States)

    Ramachandran, Sanoop; Ryckaert, Jean-Paul

    2013-08-01

    To study the compressional forces exerted by a bundle of living stiff filaments pressing on a surface, akin to the case of an actin bundle in filopodia structures, we have performed particulate molecular dynamics simulations of a grafted bundle of parallel living (self-assembling) filaments, in chemical equilibrium with a solution of their constitutive monomers. Equilibrium is established as these filaments, grafted at one end to a wall of the simulation box, grow at their chemically active free end, and encounter the opposite confining wall of the simulation box. Further growth of filaments requires bending and thus energy, which automatically limit the populations of longer filaments. The resulting filament sizes distribution and the force exerted by the bundle on the obstacle are analyzed for different grafting densities and different sub- or supercritical conditions, these properties being compared with the predictions of the corresponding ideal confined bundle model. In this analysis, non-ideal effects due to interactions between filaments and confinement effects are singled out. For all state points considered at the same temperature and at the same gap width between the two surfaces, the force per filament exerted on the opposite wall appears to be a function of a rescaled free monomer density hat{ρ }_1^eff. This quantity can be estimated directly from the characteristic length of the exponential filament size distribution P observed in the size domain where these grafted filaments are not in direct contact with the wall. We also analyze the dynamics of the filament contour length fluctuations in terms of effective polymerization (U) and depolymerization (W) rates, where again it is possible to disentangle non-ideal and confinement effects.

  5. Single and two-phase flow pressure drop for CANFLEX bundle

    Energy Technology Data Exchange (ETDEWEB)

    Park, Joo Hwan; Jun, Ji Su; Suk, Ho Chun [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of); Dimmick, G. R.; Bullock, D. E. [Atomic Energy of Canada Limited, Ontario (Canada)

    1998-12-31

    Friction factor and two-phase flow frictional multiplier for a CANFLEX bundle are newly developed and presented in this paper. CANFLEX as a 43-element fuel bundle has been developed jointly by AECL/KAERI to provide greater operational flexibility for CANDU reactor operators and designers. Friction factor and two-phase flow frictional multiplier have been developed by using the experimental data of pressure drops obtained from two series of Freon-134a (R-134a) CHF tests with a string of simulated CANFLEX bundles in a single phase and a two-phase flow conditions. The friction factor for a CANFLEX bundle is found to be about 20% higher than that of Blasius for a smooth circular pipe. The pressure drop predicted by using the new correlations of friction factor and two-phase frictional multiplier are well agreed with the experimental pressure drop data of CANFLEX bundle within {+-} 5% error. 11 refs., 5 figs. (Author)

  6. Experimentally driven atomistic model of 1,2 polybutadiene

    International Nuclear Information System (INIS)

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

  7. THEBES: a thermal hydraulic code for the calculation of transient two phase flow in bundle geometry

    International Nuclear Information System (INIS)

    The three dimensional thermal hydraulic code THEBES, capable to calculate transient boiling of sodium in rod bundles is described here. THEBES, derived from the transient single phase code SABRE-2A, was developed in CADARACHE by the SIES to analyse the SCARABEE N loss of flow experiments. This paper also presents the results of tests which were performed against various types of experiments: (1) transient boiling in a 7 pin bundle simulating a partial blockage at the bottom of a subassembly (rapid transient SCARABEE 7.2 experiment), (2) transient boiling in a 7 pin bundle simulating a coolant coast down (slow transient SCARABEE 7.3 experiment), (3) steady local and generalised boiling in a 19 pin bundle (GR 19 I experiment), (4) transient boiling in a 19 pin bundle simulating a coolant coast down (GR 19 I experiment), (5) steady local boiling in a 37 pin bundle with internal blockage (MOL 7C experiment). Excellent agreement was found between calculated and experimental results for these different situations. Our conclusion is that THEBES is able to calculate transient boiling of sodium in rod bundles in a quite satisfying way

  8. CFD analysis of flow and heat transfer in Canadian supercritical water reactor bundle

    International Nuclear Information System (INIS)

    Highlights: • Flow and heat transfer in SCWR fuel bundle design by AECL is studied using CFD. • Bare-rod bundle geometry is tested at 23.5, 25 and 28 MPa using STAR-CCM+ code. • SST k–ω low-Re model was used to study occurrence of heat transfer deterioration. - Abstract: Within the Gen-IV International Forum, AECL is leading the effort in developing a conceptual design for the Canadian SCWR. AECL proposed a new fuel bundle design with two rings of fuel elements placed between central flow tube and the pressure tube. In line with the scope of the conceptual design, the objective of the present CFD work is to aid in developing a bundle heat transfer correlation for the Canadian SCWR fuel bundle design. This paper presents results from an ongoing effort in determining the conditions favorable for occurrence of HTD in the supercritical bundle flows. In the current investigation, bare-rod bundle geometry was tested for the proposed fuel bundle design at 23.5, 25 and 28 MPa using STAR-CCM+ CFD code. Taking advantage of the design symmetry of the fuel bundle, only 1/32 of the computational domain was simulated. The low-Reynolds number modification of SST k–ω turbulence model along with y+ < 1 was used in the simulations. For lower mass flow simulations, the increase of inlet temperature and operational pressure was found effective in reducing the occurrence of HTD. For higher mass flow simulations, normal heat transfer behaviour was observed except for the lower pressure range (23.5 MPa)

  9. CANFLEX fuel bundle strength tests during normal and abnormal refuelling procedure

    International Nuclear Information System (INIS)

    As one of verifications of the CANFLEX fuel bundle, the strength tests were performed by the double side-stop test for the simulation of normal fuel loading and the single side-stop test for the simulation of abnormal fuel loading. In both tests the load was applied by controlling the flow to obtain a desired pressure drop across the whole fuel string resulting in a specified hydraulic drag force on the test bundle. The test rig conditions for each test were 120 .deg. C and 11.2 MPa for 15 minutes. The test bundles against the side-stop simulators were measured and inspected carefully after the tests according to the measurement procedures. The inspection results showed the test bundles were intact and met the acceptance criteria

  10. Atomistic modeling of diffusional phasetransformations with elastic strain

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-10-31

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

  11. 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.

  12. Hybrid continuum–atomistic modelling of swift heavy ion radiation damage in germanium

    International Nuclear Information System (INIS)

    The response of germanium to swift heavy ion irradiation is simulated using a hybrid continuum–atomistic approach. The continuum part of the model, which characterises the electronic excitations is an extension of the inelastic thermal spike based on an approximation to the Boltzmann transport equation; while the atomistic part is represented with molecular dynamics. This integrated method can realistically account for the non-equilibrium carrier dynamics in band-gap materials under irradiation, unlike earlier developments based on the two-temperature approach. The model is used to obtain temporal and spatial evolution of carrier density, electronic temperature and lattice temperature for germanium irradiated with carbon cluster ions. Good agreement with experimental data of amorphised latent track radii for different stopping powers is obtained by fitting a constant value for the electron–phonon coupling strength – the only parameter treated as free in the model

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

    Science.gov (United States)

    He, Yang; Gu, Meng; Xiao, Haiyan; Luo, Langli; Shao, Yuyan; Gao, Fei; Du, Yingge; Mao, Scott X; Wang, Chongmin

    2016-05-17

    Intercalation and conversion are two fundamental chemical processes for battery materials in response to ion insertion. The interplay between these two chemical processes has never been directly seen and understood at atomic scale. Here, using in situ HRTEM, we captured the atomistic conversion reaction processes during Li, Na, Ca insertion into a WO3 single crystal model electrode. An intercalation step prior to conversion is explicitly revealed at atomic scale for the first time for Li, Na, Ca. Nanoscale diffraction and ab initio molecular dynamic simulations revealed that after intercalation, the inserted ion-oxygen bond formation destabilizes the transition-metal framework which gradually shrinks, distorts and finally collapses to an amorphous W and Mx O (M=Li, Na, Ca) composite structure. This study provides a full atomistic picture of the transition from intercalation to conversion, which is of essential importance for both secondary ion batteries and electrochromic devices. PMID:27071488

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

    Institute of Scientific and Technical Information of China (English)

    R ANSARI; S ROUHI; M ARYAYI

    2013-01-01

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

  15. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    Energy Technology Data Exchange (ETDEWEB)

    Zavadlav, Julija; Praprotnik, Matej, E-mail: praprot@cmm.ki.si [Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Melo, Manuel N.; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl [Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen (Netherlands)

    2015-06-28

    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.

  16. Quadratic bundle and nonlinear equations

    International Nuclear Information System (INIS)

    The paper is aimed at giving an exhaustive description of the nonlinear evolution equations (NLEE), connected with the quadratic bundle (the spectral parameter lambda, which enters quadratically into the equations) and at describing Hamiltonian structure of these equations. The equations are solved through the inverse scattering method (ISM). The basic formulae for the scattering problem are given. The spectral expansion of the integrodifferential operator is used so that its eigenfunctions are the squared solutions of the equation. By using the notions of Hamiltonian structure hierarchy and gauge transformations it is shown how to single out physically interesting NLEE

  17. Static stress analysis of CANFLEX fuel bundles

    International Nuclear Information System (INIS)

    The static stress analysis of CANFLEX bundles is performed to evaluate the fuel structural integrity during the refuelling service. The structure analysis is carried out by predicting the drag force, stress and displacements of the fuel bundle. By the comparison of strength tests and analysis results, the displacement values are well agreed within 15%. The analysis shows that the CANFLEX fuel bundle keep its structural integrity. 24 figs., 6 tabs., 12 refs. (Author) .new

  18. Damping Properties of the Hair Bundle

    OpenAIRE

    Baumgart, Johannes; Kozlov, Andrei S.; Risler, Thomas; Hudspeth, A. James

    2015-01-01

    The viscous liquid surrounding a hair bundle dissipates energy and dampens oscillations, which poses a fundamental physical challenge to the high sensitivity and sharp frequency selectivity of hearing. To identify the mechanical forces at play, we constructed a detailed finite-element model of the hair bundle. Based on data from the hair bundle of the bullfrog's sacculus, this model treats the interaction of stereocilia both with the surrounding liquid and with the liquid in the narrow gaps b...

  19. Tying, Bundling, and Loyalty/Requirement Rebates

    OpenAIRE

    Nicholas Economides

    2011-01-01

    I discuss the impact of tying, bundling, and loyalty/requirement rebates on consumer surplus in the affected markets. I show that the Chicago School Theory of a single monopoly surplus that justifies tying, bundling, and loyalty/requirement rebates on the basis of efficiency typically fails. Thus, tying, bundling, and loyalty/requirement rebates can be used to extract consumer surplus and enhance profit of firms with market power. I discuss the various setups when this occurs.

  20. Bundling and Competition on the Internet

    OpenAIRE

    Yannis Bakos; Erik Brynjolfsson

    2000-01-01

    The Internet has signi.cantly reduced the marginal cost of producing and distributing digital information goods. It also coincides with the emergence of new competitive strategies such as large-scale bundling. In this paper, we show that bundling can create “economies of aggregation” for information goods if their marginal costs are very low, even in the absence of network externalities or economies of scale or scope. We extend the Bakos-Brynjolfsson bundling model (1999) to settings with sev...

  1. Bundling and joint marketing by rival firms

    OpenAIRE

    Jeitschko, Thomas D.; Jung, Yeonjei; Kim, Jaesoo

    2014-01-01

    We study joint marketing arrangements by competing firms who engage in price discrimination between consumers who patronize only one firm (single purchasing) and those who purchase from both competitors (bundle purchasers). Two types of joint marketing are considered. Firms either commit to a component-price that applies to bundle-purchasers and then firms set stand-alone prices for single purchasers; or firms commit to a rebate off their stand alone price that will be applied to bundle-purch...

  2. Dimer model for Tau proteins bound in microtubule bundles

    Science.gov (United States)

    Hall, Natalie; Kluber, Alexander; Hayre, N. Robert; Singh, Rajiv; Cox, Daniel

    2013-03-01

    The microtubule associated protein tau is important in nucleating and maintaining microtubule spacing and structure in neuronal axons. Modification of tau is implicated as a later stage process in Alzheimer's disease, but little is known about the structure of tau in microtubule bundles. We present preliminary work on a proposed model for tau dimers in microtubule bundles (dimers are the minimal units since there is one microtubule binding domain per tau). First, a model of tau monomer was created and its characteristics explored using implicit solvent molecular dynamics simulation. Multiple simulations yield a partially collapsed form with separate positively/negatively charged clumps, but which are a factor of two smaller than required by observed microtubule spacing. We argue that this will elongate in dimer form to lower electrostatic energy at a cost of entropic ``spring'' energy. We will present preliminary results on steered molecular dynamics runs on tau dimers to estimate the actual force constant. Supported by US NSF Grant DMR 1207624.

  3. Statistical Constitutive Equation of Aramid Fiber Bundles

    Institute of Scientific and Technical Information of China (English)

    熊杰; 顾伯洪; 王善元

    2003-01-01

    Tensile impact tests of aramid (Twaron) fiber bundles were carried om under high strain rates with a wide range of 0. 01/s~1000/s by using MTS and bar-bar tensile impact apparatus. Based on the statistical constitutive model of fiber bundles, statistical constitutive equations of aramid fiber bundles are derived from statistical analysis of test data at different strain rates. Comparison between the theoretical predictions and experimental data indicates statistical constitutive equations fit well with the experimental data, and statistical constitutive equations of fiber bundles at different strain rates are valid.

  4. Hydraulic characteristics of HANARO fuel bundles

    Energy Technology Data Exchange (ETDEWEB)

    Cho, S.; Chung, H. J.; Chun, S. Y.; Yang, S. K.; Chung, M. K. [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1997-12-31

    This paper presents the hydraulic characteristics measured by using LDV (Laser Doppler Velocimetry) in subchannels of HANARO, KAERI research reactor, fuel bundle. The fuel bundle consists of 18 axially finned rods with 3 spacer grids, which are arranged in cylindrical configuration. The effects of the spacer grids on the turbulent flow were investigated by the experimental results. Pressure drops for each component of the fuel bundle were measured, and the friction factors of fuel bundle and loss coefficients for the spacer grids were estimated from the measured pressure drops. Implications regarding the turbulent thermal mixing were discussed. Vibration test results measured by using laser vibrometer were presented. 9 refs., 12 figs. (Author)

  5. Universality Class of Fiber Bundle Model on Complex Networks

    OpenAIRE

    Kim, Dong-Hee; Kim, Beom Jun; Jeong, Hawoong

    2004-01-01

    We investigate the failure characteristics of complex networks within the framework of the fiber bundle model subject to the local load sharing rule in which the load of the broken fiber is transferred only to its neighbor fibers. Although the load sharing is strictly local, it is found that the critical behavior belongs to the universality class of the global load sharing where the load is transferred equally to all fibers in the system. From the numerical simulations and the analytical appr...

  6. Extension of holomorphic bundles to the disc (and Serre's Problem on Stein bundles)

    OpenAIRE

    Rosay, Jean-Pierre

    2006-01-01

    We show how to extend some holomorphic bundles with fifer C^2 and base an open set in C, to bundles on the Riemann Sphere, by an extremely simple technique. In particular, it applies to examples of non-Stein bundles constructed by Skoda and Demailly. It gives an example on C, with polynomial transition automorphisms.

  7. Atomistic nano-scale 3D simulations about effects of Cr percentage on the molecular dynamics parameters of Fe-9-12% Cr alloys at fusion reactor temperature conditions

    International Nuclear Information System (INIS)

    9-12% Cr ferritic steel structures at atomic scale were modeled by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) Molecular Dynamics package with high accuracy. Embedded-Atom Model (EAM) potential parameters were applied for Fe-Fe, Fe-Cr and Cr-Cr atomic interactions. Nuclear reactor temperature conditions were used in the simulations. Heat flux, kinetic energy, potential energy, total energy, pressures, and atomic displacements of Fe-Cr steels including 9%, 10%, 11%, and 12% Cr were given.

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

    Science.gov (United States)

    Strong, Steven E; Eaves, Joel D

    2016-05-19

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

  9. Rotational viscosity of a liquid crystal mixture:a fully atomistic molecular dynamics study

    Institute of Scientific and Technical Information of China (English)

    Zhang Ran; Peng Zeng-Hui; Liu Yong-Gang; Zheng Zhi-Gang; Xuan Li

    2009-01-01

    Fully atomistic molecular dynamics(MD)simulations at 293, 303 and 313 K have been performed for the four. component liquid crystal mixture, E7, using the software package Material Studio. Order parameters and orientational time correlation functions(TCFs)were calculated from MD trajectories. The rotational viscosity coefficients(RVCs)of the mixture were ca]culated using the Nemtsov-Zakharov and Fialkowski methods based on statistical-mechanical approaches. Temperature dependences of RVC and density were discussed in detall. Reasonable agreement between the simulated and experimental values was found.

  10. Design verification of the CANFLEX fuel bundle - quality assurance requirements for mechanical flow testing

    International Nuclear Information System (INIS)

    As part of the design verification program for the new fuel bundle, a series of out-reactor tests was conducted on the CANFLEX 43-element fuel bundle design. These tests simulated current CANDU 6 reactor normal operating conditions of flow, temperature and pressure. This paper describes the Quality Assurance (QA) Program implemented for the tests that were run at the testing laboratories of Atomic Energy of Canada Limited (AECL) and Korea Atomic energy Research Institute (KAERI). (author)

  11. Nucleation and growth of dislocation loops in Cu, Al and Si by a concurrent atomistic-continuum method

    International Nuclear Information System (INIS)

    Submicron-sized samples with 42,000 finite elements containing up to ∼86 million atoms have been simulated using a concurrent atomistic-continuum method. The simulations reproduce not only nucleation and growth of semicircular dislocation loops in Cu and Al, but also hexagonal shuffle dislocation loops in Si, with the loop radius approaching ∼75 nm. Details of leading and trailing partial dislocations connected by intrinsic stacking faults, dislocation loop coalescence through annihilation, and formation of junctions are reproduced.

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

    Science.gov (United States)

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

    2013-11-01

    The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O/H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O/H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

  13. Theoretical modeling of the PEMFC catalyst layer: A review of atomistic methods

    International Nuclear Information System (INIS)

    This article reviews recent progress in the catalyst layer modeling of polymer electrolyte membrane fuel cells. Theoretical modeling is important to understand the basic chemical, and physical phenomena at the atomistic level in materials and relating these fundamentals to the properties and performance of the catalyst layer. Two fundamentally important theoretical methods have been chosen to represent atomistic models, namely density functional theory (DFT) and classical molecular dynamics. In addition, some reactive force field models are highlighted, and the mathematical framework is sufficiently described. The literature review includes important contributions that help to understand the oxygen reduction reaction including gas-phase reaction trends, and the solvation effects are also presented. Moreover, the electric field effect is discussed along with the recently established double reference method in the DFT framework. Using two atomistic simulations based on different axiomatic theories, the production of current density in the molecular junctions is considered with respect to voltage, elucidating applications to simple systems. The models of water transportation via polymer electrolyte membrane, as well as the catalyst and support oxidation are described. Epoxidized carbon support, oxidizable metal-oxide support and electron localization function analysis have provided insights for improving catalyst support material and enable characterization of the bonding between the catalyst and support. Conclusions and future outlook are outlined at the end. Thus the present work enlightens the future of the catalyst modeling towards more realistic models

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

    Science.gov (United States)

    Zhang, W.; Mi, J.

    2016-03-01

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

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

    International Nuclear Information System (INIS)

    The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O/H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O/H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials

  16. Principal Bundles on the Projective Line

    Indian Academy of Sciences (India)

    V B Mehta; S Subramanian

    2002-08-01

    We classify principal -bundles on the projective line over an arbitrary field of characteristic ≠ 2 or 3, where is a reductive group. If such a bundle is trivial at a -rational point, then the structure group can be reduced to a maximal torus.

  17. The Verlinde formula for Higgs bundles

    CERN Document Server

    Andersen, Jørgen Ellegaard; Pei, Du

    2016-01-01

    We propose and prove the Verlinde formula for the quantization of the Higgs bundle moduli spaces and stacks for any simple and simply-connected group. This generalizes the equivariant Verlinde formula for the case of $SU(n)$ proposed previously by the second and third author. We further establish a Verlinde formula for the quantization of parabolic Higgs bundle moduli spaces and stacks.

  18. k-Gerbes, Line Bundles and Anomalies

    CERN Document Server

    Ekstrand, C

    2000-01-01

    We use sets of trivial line bundles for the realization of gerbes. For1-gerbes the structure arises naturally for the Weyl fermion vacuum bundle at afixed time. The Schwinger term is an obstruction in the triviality of a1-gerbe.

  19. k-Gerbes, Line Bundles and Anomalies

    International Nuclear Information System (INIS)

    We use sets of trivial line bundles for the realization of gerbes. For 1-gerbes the structure arises naturally for the Weyl fermion vacuum bundle at a fixed time. The Schwinger term is an obstruction in the triviality of a 1-gerbe. (author)

  20. k-Gerbes, Line Bundles and Anomalies

    OpenAIRE

    Ekstrand, C.

    2000-01-01

    We use sets of trivial line bundles for the realization of gerbes. For 1-gerbes the structure arises naturally for the Weyl fermion vacuum bundle at a fixed time. The Schwinger term is an obstruction in the triviality of a 1-gerbe.