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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. Atomistic simulations of fracture

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-31

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

  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 simulations of dislocation processes in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Jacobsen, K.W.

    2002-01-01

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

  6. 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

  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. Systematic evaluation of bundled SPC water for biomolecular simulations.

    Science.gov (United States)

    Gopal, Srinivasa M; Kuhn, Alexander B; Schäfer, Lars V

    2015-04-01

    In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. In the present work, we systematically validated and critically tested bundled SPC water models as solvent for biomolecular simulations. To that aim, we investigated both thermodynamic and structural properties of various biomolecular systems through molecular dynamics (MD) simulations. Potentials of mean force of dimerization of pairs of amino acid side chains as well as hydration free energies of single side chains obtained with bundled SPC and standard (unrestrained) SPC water agree closely with each other and with experimental data. Decomposition of the hydration free energies into enthalpic and entropic contributions reveals that in bundled SPC, this favorable agreement of the free energies is due to a larger degree of error compensation between hydration enthalpy and entropy. The Ramachandran maps of Ala3, Ala5, and Ala7 peptides are similar in bundled and unrestrained SPC, whereas for the (GS)2 peptide, bundled water leads to a slight overpopulation of extended conformations. Analysis of the end-to-end distance autocorrelation times of the Ala5 and (GS)2 peptides shows that sampling in more viscous bundled SPC water is about two times slower. Pronounced differences between the water models were found for the structure of a coiled-coil dimer, which is instable in bundled SPC but not in standard SPC. In addition, the hydration of the active site of the serine protease α-chymotrypsin depends on the water model. Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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,

  15. 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

  16. 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...

  17. 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

  18. 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...

  19. 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.

  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. 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

  2. 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)

  3. 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

  4. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-01-12

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

  5. 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.

  6. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-12-31

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

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

    Indian Academy of Sciences (India)

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

    2016-09-01

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

  8. 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.

  9. Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles.

    Science.gov (United States)

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

    2016-08-01

    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 supramolecular CG models, where several molecules are represented as a single CG bead, is challenging, but it provides higher computational gains and connection to the established MARTINI CG force field. Difficulties that arise from such coupling have been so far bypassed with bundled AT water models, where additional harmonic bonds between oxygen atoms within a given supramolecular water bundle are introduced. While these models simplify the supramolecular coupling, they also cause in certain situations spurious artifacts, such as partial unfolding of biomolecules. In this work, we present a new clustering algorithm SWINGER that can concurrently make, break, and remake water bundles and in conjunction with the AdResS permits the use of original AT water models. We apply our approach to simulate a hybrid SPC/MARTINI water system and show that the essential properties of water are correctly reproduced with respect to the standard monoscale simulations. The developed hybrid water model can be used in biomolecular simulations, where a significant speed up can be obtained without compromising the accuracy of the AT water model. PMID:27409519

  10. Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles.

    Science.gov (United States)

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

    2016-08-01

    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 supramolecular CG models, where several molecules are represented as a single CG bead, is challenging, but it provides higher computational gains and connection to the established MARTINI CG force field. Difficulties that arise from such coupling have been so far bypassed with bundled AT water models, where additional harmonic bonds between oxygen atoms within a given supramolecular water bundle are introduced. While these models simplify the supramolecular coupling, they also cause in certain situations spurious artifacts, such as partial unfolding of biomolecules. In this work, we present a new clustering algorithm SWINGER that can concurrently make, break, and remake water bundles and in conjunction with the AdResS permits the use of original AT water models. We apply our approach to simulate a hybrid SPC/MARTINI water system and show that the essential properties of water are correctly reproduced with respect to the standard monoscale simulations. The developed hybrid water model can be used in biomolecular simulations, where a significant speed up can be obtained without compromising the accuracy of the AT water model.

  11. 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.

  12. 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.

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

    International Nuclear Information System (INIS)

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

  14. Atomistic simulations of jog migration on extended screw dislocations

    DEFF Research Database (Denmark)

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

    2001-01-01

    We have performed large-scale atomistic simulations of the migration of elementary jogs on dissociated screw dislocations in Cu. The local crystalline configurations, transition paths. effective masses. and migration barriers for the jogs are determined using an interatomic potential based...... on the Effective Medium Theory, The minimum energy path through configuration space and the corresponding transition state energy are obtained using the Nudged Elastic Band path technique. We find very similar migration properties for elementary jogs on the (110){110} octahedral slip systems and the (110){110} non......-octahedral slip systems. with energy barriers in the 15-19 meV range. (C) 2001 Elsevier Science B.V. All rights reserved....

  15. Quantum-based Atomistic Simulation of Transition Metals

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-08-29

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

  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. Computer Science Techniques Applied to Parallel Atomistic Simulation

    Science.gov (United States)

    Nakano, Aiichiro

    1998-03-01

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

  18. 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...

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

    Science.gov (United States)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

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

  20. 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.

  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. 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.

  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. Linking Atomistic and Mesoscale Simulations of Water Soluble Polymers

    Science.gov (United States)

    Jones, J. L.

    2003-03-01

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2011-06-14

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-07

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

  8. 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 ...

  9. 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)

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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...

  16. Protein folding kinetics and thermodynamics from atomistic simulation

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  17. Molecular cooperativity and compatibility via full atomistic simulation

    Science.gov (United States)

    Kwan Yang, Kenny

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

  18. 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

  19. 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

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

    Science.gov (United States)

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

    2015-11-10

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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Atomistic Simulations of Material Properties under Extreme Conditions

    Science.gov (United States)

    An, Qi

    Extreme conditions involve low or high temperatures (> 1500 K), high pressures (> 30 MPa), high strains or strain rates, high radiation fluxes (> 100 dpa), and high electromagnetic fields (> 15T). Material properties under extreme conditions can be extremely different from those under normal conditions. Understanding material properties and performance under extreme conditions, including their dynamic evolution over time, plays an essential role in improving material properties and developing novel materials with desired properties. To understand material properties under extreme conditions, we use molecular dynamics (MD) simulations with recently developed reactive force fields (ReaxFF) and traditional embedded atom methods (EAM) potentials to examine various materials (e.g., energetic materials and binary liquids) and processes. The key results from the simulations are summarized below. Anisotropic sensitivity of RDX crystals: Based on the compress-and-shear reactive dynamics (CS-RD) simulations of cyclotrimethylene trinitramine (RDX) crystals, we predict that for mechanical shocks between 3 and 7 GPa, RDX is the most sensitive to shocks perpendicular to the (100) and (210) planes, while it is insensitive to those perpendicular to the (120), (111), and (110) planes. The simulations demonstrate that the molecular origin of anisotropic shock sensitivity is the steric hindrance to shearing of adjacent slip planes. Mechanisms of hotspot formation in polymer bonded explosives (PBXs): The simulations of a realistic model of PBXs reveal that hotspots may form at the nonplanar interfaces where shear relaxation leads to a dramatic temperature increase that persists long after the shock front has passed the interface. For energetic materials this temperature increase is coupled to chemical reactions that eventually lead to detonation. We show that decreasing the density of the binder eliminates the hotspots or reduces the sensitivity. Cavitation in binary metallic liquids

  7. 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.

  8. 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.

  9. 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

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

    Science.gov (United States)

    Noronha, S. J.; Farkas, D.

    2002-10-01

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

  11. 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...

  12. 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...

  13. 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

  14. 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.

  15. 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

  16. 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)

  17. 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

  18. 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

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

    Science.gov (United States)

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

    2014-01-21

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

  20. Atomistic Simulation of Intrinsic Defects and Trivalent and Tetravalent Ion Doping in Hydroxyapatite

    Directory of Open Access Journals (Sweden)

    Ricardo D. S. Santos

    2014-01-01

    Full Text Available Atomistic simulation techniques have been employed in order to investigate key issues related to intrinsic defects and a variety of dopants from trivalent and tetravalent ions. The most favorable intrinsic defect is determined to be a scheme involving calcium and hydroxyl vacancies. It is found that trivalent ions have an energetic preference for the Ca site, while tetravalent ions can enter P sites. Charge compensation is predicted to occur basically via three schemes. In general, the charge compensation via the formation of calcium vacancies is more favorable. Trivalent dopant ions are more stable than tetravalent dopants.

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

    Science.gov (United States)

    Stukowski, Alexander

    2010-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-10

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

  4. 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.

  5. 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

  6. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-08-04

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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.)

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

    CERN Document Server

    Mao, Yijin; Chen, C L

    2016-01-01

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

  14. 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).

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

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

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

    Science.gov (United States)

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

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

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

    NARCIS (Netherlands)

    Starikov, Sergey V.; Stegailov, Vladimir V.

    2009-01-01

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

  20. 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)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-06-30

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

  2. 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.

  3. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-12-30

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

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

    Science.gov (United States)

    Papaleo, Elena

    2015-01-01

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

  6. 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)

  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. 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

  9. 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.

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

    International Nuclear Information System (INIS)

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

  11. 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

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

    Science.gov (United States)

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

    2016-09-01

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

  13. 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.

  14. 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

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

    Science.gov (United States)

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

    2016-05-21

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

  16. 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. 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

  18. 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.

  19. 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...

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

    Science.gov (United States)

    Erhart, Paul; Albe, Karsten

    2005-01-01

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

  1. 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.

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

    Science.gov (United States)

    Makarov, Dmitrii

    2011-03-01

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

  3. 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.

  4. 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.

  5. 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

  6. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-02-21

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

  8. 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

  9. 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)

  10. Thermodynamic and mechanical properties of copper precipitates in α-iron from atomistic simulations

    Science.gov (United States)

    Erhart, Paul; Marian, Jaime; Sadigh, Babak

    2013-07-01

    Precipitate hardening is commonly used in materials science to control strength by acting on the number density, size distribution, and shape of solute precipitates in the hardened matrix. The Fe-Cu system has attracted much attention over the last several decades due to its technological importance as a model alloy for Cu steels. In spite of these efforts several aspects of its phase diagram remain unexplained. Here we use atomistic simulations to characterize the polymorphic phase diagram of Cu precipitates in body-centered cubic (BCC) Fe and establish a consistent link between their thermodynamic and mechanical properties in terms of thermal stability, shape, and strength. The size at which Cu precipitates transform from BCC to a close-packed 9R structure is found to be strongly temperature dependent, ranging from approximately 4 nm in diameter (˜2700atoms) at 200 K to about 8 nm (˜22800atoms) at 700 K. These numbers are in very good agreement with the interpretation of experimental data given Monzen [Philos. Mag. APMAADG0141-861010.1080/01418610008212077 80, 711 (2000)]. The strong temperature dependence originates from the entropic stabilization of BCC Cu, which is mechanically unstable as a bulk phase. While at high temperatures the transition exhibits first-order characteristics, the hysteresis, and thus the nucleation barrier, vanish at temperatures below approximately 300 K. This behavior is explained in terms of the mutual cancellation of the energy differences between core and shell (wetting layer) regions of BCC and 9R nanoprecipitates, respectively. The proposed mechanism is not specific for the Fe-Cu system but could generally be observed in immiscible systems, whenever the minority component is unstable in the lattice structure of the host matrix. Finally, we also study the interaction of precipitates with screw dislocations as a function of both structure and orientation. The results provide a coherent picture of precipitate strength that unifies

  11. 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)

  12. Tailoring Pull-out Properties of Single-Walled Carbon Nanotube Bundles by Varying Binding Structures through Molecular Dynamics Simulation.

    Science.gov (United States)

    Zhang, Liuyang; Wang, Xianqiao

    2014-08-12

    Single-walled carbon nanotubes (SWCNTs) have demonstrated a remarkable capacity for self-assembly into nanobundles through intermolecular van der Waals interactions, bestowing these agglomerates extraordinary mechanical, thermal, and electrical properties. However, how to improve the binding ability of SWCNT bundles to mitigate the delamination and sliding effects between individual nanotubes remains to be further investigated. By utilizing molecular dynamics simulation, here we present the construction of SWCNT bundles with discrete cylindrical and continuous helical binders by noncovalent coating of the bundle surface with sp(2)-hybridized carbon networks. Meanwhile, by modifying the binding potentials between the binder and SWCNT bundles to mimic the different binding types actually used, the bound SWCNT bundle presents a variety of distinct mechanical properties unmatched by unbound bundles. The pull-out tests with discrete binders portray an intriguing force-displacement curve which can help determine the number of discrete binders used in the system. SWCNT bundles with binders depict unique mechanical properties which can differentiate them from unbound SWCNT bundles. These findings provide compelling evidence that bound SWCNT bundles will open up novel avenues for a variety of applications, especially in nanocomposites.

  13. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-09-01

    This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel computers

  15. 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

  16. 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...

  17. Atomistic simulation of laser-pulse surface modification: Predictions of models with various length and time scales

    Energy Technology Data Exchange (ETDEWEB)

    Starikov, Sergey V., E-mail: starikov@ihed.ras.ru; Pisarev, Vasily V. [Moscow Institute of Physics and Technology, Dolgoprudny 141700 (Russian Federation); Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412 (Russian Federation)

    2015-04-07

    In this work, the femtosecond laser pulse modification of surface is studied for aluminium (Al) and gold (Au) by use of two-temperature atomistic simulation. The results are obtained for various atomistic models with different scales: from pseudo-one-dimensional to full-scale three-dimensional simulation. The surface modification after laser irradiation can be caused by ablation and melting. For low energy laser pulses, the nanoscale ripples may be induced on a surface by melting without laser ablation. In this case, nanoscale changes of the surface are due to a splash of molten metal under temperature gradient. Laser ablation occurs at a higher pulse energy when a crater is formed on the surface. There are essential differences between Al ablation and Au ablation. In the first step of shock-wave induced ablation, swelling and void formation occur for both metals. However, the simulation of ablation in gold shows an additional athermal type of ablation that is associated with electron pressure relaxation. This type of ablation takes place at the surface layer, at a depth of several nanometers, and does not induce swelling.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-08-01

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

  19. 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)

  20. Simulation of the response of the inner hair cell stereocilia bundle to an acoustical stimulus.

    Directory of Open Access Journals (Sweden)

    Sonya T Smith

    Full Text Available Mammalian hearing relies on a cochlear hydrodynamic sensor embodied in the inner hair cell stereocilia bundle. It is presumed that acoustical stimuli induce a fluid shear-driven motion between the tectorial membrane and the reticular lamina to deflect the bundle. It is hypothesized that ion channels are opened by molecular gates that sense tension in tip-links, which connect adjacent stepped rows of stereocilia. Yet almost nothing is known about how the fluid and bundle interact. Here we show using our microfluidics model how each row of stereocilia and their associated tip links and gates move in response to an acoustical input that induces an orbital motion of the reticular lamina. The model confirms the crucial role of the positioning of the tectorial membrane in hearing, and explains how this membrane amplifies and synchronizes the timing of peak tension in the tip links. Both stereocilia rotation and length change are needed for synchronization of peak tip link tension. Stereocilia length change occurs in response to accelerations perpendicular to the oscillatory fluid shear flow. Simulations indicate that nanovortices form between rows to facilitate diffusion of ions into channels, showing how nature has devised a way to solve the diffusive mixing problem that persists in engineered microfluidic devices.

  1. 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.

  2. Experimental approach and atomistic simulations to investigate the radiation tolerance of complex oxides: Application to the amorphization of pyrochlores

    Science.gov (United States)

    Sattonnay, G.; Thomé, L.; Sellami, N.; Monnet, I.; Grygiel, C.; Legros, C.; Tetot, R.

    2014-05-01

    Both experimental approach and atomistic simulations are performed in order to investigate the influence of the composition of pyrochlores on their radiation tolerance. Therefore, Gd2Ti2O7 and Gd2Zr2O7 were irradiated with 4 MeV Au and 92 MeV Xe ions in order to study the structural changes induced by low and high-energy irradiations. XRD results show that, for both irradiations, the structural modifications are strongly dependent on the sample composition: Gd2Ti2O7 is readily amorphized, whereas Gd2Zr2O7 is transformed into a radiation-resistant anion-deficient fluorite structure. Using atomistic simulations with new interatomic potentials derived from the SMTB-Q model, the lattice properties and the defect formation energies were calculated in Gd2Ti2O7 and Gd2Zr2O7. Calculations show that titanates have a more covalent character than zirconates. Moreover, in Gd2Ti2O7 the formation of cation antisite defects leads to strong local distortions around Ti-defects and to a decrease of the Ti coordination number, which are not observed in Gd2Zr2O7. Thus, the radiation resistance is related to the defect stability: the accumulation of structural distortions around Ti-defects could drive the Gd2Ti2O7 amorphization induced by irradiation.

  3. 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

  4. 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

    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......The lateral pressure profile of lipid bilayers has gained a lot of attention, since changes in the pressure profile have been suggested to shift the membrane protein conformational equilibrium. This relation has been mostly studied with theoretical methods, especially with molecular dynamics....../monomer fluorescence ratio has been assumed to represent the lateral pressure in the location of the pyrene moieties. Here, we consider the validity of this assumption through atomistic molecular dynamics simulations in a DOPC (dioleoylphosphatidylcholine) membrane, which hosts di-pyr-PC probes with different acyl...

  5. Mesoscale simulation of semiflexible chains. II. Evolution dynamics and stability of fiber bundle networks

    Science.gov (United States)

    Groot, Robert D.

    2013-06-01

    Network formation of associative semiflexible fibers and mixtures of fibers and colloidal particles is simulated for the Johnson-Kendall-Roberts model of elastic contacts, and a phase diagram in terms of particle elasticity and surface energy is presented. When fibers self-assemble, they form a network for sufficiently large fiber-solvent surface energy. If the surface energy is above the value where single particles crystallize, the adhesion forces drive diffusion-limited aggregation. Two mechanisms contribute to coarsening: non-associated chains joining existing bundles, and fiber bundles merging. Coarsening stops when the length of the network connections is roughly the persistence length, independent of surface energy. If the surface energy is below the value where single particles crystallize, a network can still be formed but at a much slower (reaction limited) rate. Loose (liquid-like) assemblies between chains form when they happen to run more-or-less parallel. These assemblies grow by diffusion and aggregation and form a loose network, which sets in micro-phase separation, i.e., syneresis. Only when the clusters crystallize, the coarsening process stops. In this case, the length of the network connections is larger than the persistence length of a single chain, and depends on the value of the surface energy. All networks of semiflexible homopolymers in this study show syneresis. Mixtures of fibers and colloid particles also form fiber bundle networks, but by choosing the colloid volume fraction sufficiently low, swelling gels are obtained. Applications of this model are in biological systems where fibers self-assemble into cell walls and bone tissue.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Judith C. [University of Pittsburgh

    2015-01-09

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

  7. Evidence of thin-film precursors formation in hydrokinetic and atomistic simulations of nano-channel capillary filling

    CERN Document Server

    Chibbaro, S; Diotallevi, F; Succi, S; Binder, K; Milchev, A; Dimitrov, D; Girardo, S; Pisignano, D

    2008-01-01

    We present hydrokinetic Lattice Boltzmann and Molecular Dynamics simulations of capillary filling of high-wetting fluids in nano-channels, which provide clear evidence of the formation of thin precursor films, moving ahead of the main capillary front. The dynamics of the precursor films is found to obey the Lucas-Washburn law as the main capillary front, z2(t) proportional to t, although with a larger prefactor, which we find to take the same value for both geometries under inspection. Both hydrokinetic and Molecular Dynamics approaches indicate a precursor film thickness of the order of one tenth of the capillary diameter. The quantitative agreement between the hydrokinetic and atomistic methods indicates that the formation and propagation of thin precursors can be handled at a mesoscopic/hydrokinetic level, thereby opening the possibility of using hydrokinetic methods to space-time scales and complex geometries of direct experimental relevance.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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...... with experimental results. The peak-to-peak interstitial potential (phi(epp)) at the active fiber surface was 38 mV, compared to 1.3 mV for the isolated fiber. A uniform increase of d from 0.35 to 1.2 mu m decreased phi(epp) from 38 to 25 mV, increased the velocity from 1.32 to 1.54 m/s, and decreased the maximum...

  14. 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.

  15. 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.

  16. 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)

  17. 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.

  18. 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.

  19. 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.

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

    Science.gov (United States)

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

    2010-02-25

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

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

    Science.gov (United States)

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

    2011-10-01

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

  2. 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 (B(4)C), 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 B(4)C, using the quantum-mechanics-derived reactive force field simulation. We examined the (0001)/⟨101̅0⟩ slip system related to deformation twinning and the (011̅1̅)/⟨1̅101⟩ slip system related to amorphous band formation. We find that brittle failure in B(4)C 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 B(4)C we propose alloying aimed at promoting shear relaxation through intericosahedral slip that avoids icosahedral fracture.

  3. A simulation study on the adsorption properties of linear alkanes on closed nanotube bundles

    NARCIS (Netherlands)

    J.J. Cannon; T.J.H. Vlugt; D. Dubbeldam; S. Maruyama; J. Shiomi

    2012-01-01

    Adsorption onto carbon nanotube bundles may find use in various applications such as gas pre-concentration and separation, and as a result it is of great interest to study the adsorption properties of such bundles. The adsorption of linear alkanes, with their systematic variation through chain lengt

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Lipid exchange mechanism of the cholesteryl ester transfer protein clarified by atomistic and coarse-grained simulations.

    Directory of Open Access Journals (Sweden)

    Artturi Koivuniemi

    2012-01-01

    Full Text Available Cholesteryl ester transfer protein (CETP transports cholesteryl esters, triglycerides, and phospholipids between different lipoprotein fractions in blood plasma. The inhibition of CETP has been shown to be a sound strategy to prevent and treat the development of coronary heart disease. We employed molecular dynamics simulations to unravel the mechanisms associated with the CETP-mediated lipid exchange. To this end we used both atomistic and coarse-grained models whose results were consistent with each other. We found CETP to bind to the surface of high density lipoprotein (HDL -like lipid droplets through its charged and tryptophan residues. Upon binding, CETP rapidly (in about 10 ns induced the formation of a small hydrophobic patch to the phospholipid surface of the droplet, opening a route from the core of the lipid droplet to the binding pocket of CETP. This was followed by a conformational change of helix X of CETP to an open state, in which we found the accessibility of cholesteryl esters to the C-terminal tunnel opening of CETP to increase. Furthermore, in the absence of helix X, cholesteryl esters rapidly diffused into CETP through the C-terminal opening. The results provide compelling evidence that helix X acts as a lid which conducts lipid exchange by alternating the open and closed states. The findings have potential for the design of novel molecular agents to inhibit the activity of CETP.

  9. 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

  10. Turbulent flow simulation in a wire-wrap rod bundle of an LMFBR

    Energy Technology Data Exchange (ETDEWEB)

    Natesan, K. [Thermal Hydraulics Section, Reactor Engineering Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Sundararajan, T. [Department of Mechanical Engineering, Indian Institute of Technology, Madras, Chennai 600036 (India); Narasimhan, Arunn, E-mail: arunn@iitm.ac.i [Department of Mechanical Engineering, Indian Institute of Technology, Madras, Chennai 600036 (India); Velusamy, K. [Thermal Hydraulics Section, Reactor Engineering Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India)

    2010-05-15

    The pressure drop and heat transfer characteristics of wire-wrapped 19-pin rod bundles in a nuclear reactor subassembly of liquid metal cooled fast breeder reactor (LMFBR) have been investigated through three-dimensional turbulent flow simulations. The predicted results of eddy viscosity based turbulence models (k-epsilon, k-omega) and the Reynolds stress model are compared with those of experimental correlations for friction factor and Nusselt number. The Re is varied between 50,000 and 150,000 and the ratio of helical pitch of wire wrap to the rod diameter is varied from 15 to 45. All the three turbulence models considered yield similar results. The friction factor increases with reduction in the wire-wrap pitch while the heat transfer coefficient remains almost unaltered. However, reduction in the wire-wrap pitch also enhances the transverse flow velocity in the cross-sectional plane as well as the local turbulence intensity, thereby improving the thermal mixing of coolant. Consequently, the presence of wire wrap reduces temperature variation within each section of the subassembly. The associated reduction in differential thermal expansion of rods is expected to improve the structural integrity of the fuel subassembly.

  11. Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena.

    Science.gov (United States)

    Prasad, Manish; Sinno, Talid

    2004-11-01

    An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.

  12. 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.

  13. Atomistic simulation of dislocation core structures in ordered TiAl

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-12-31

    Interatomic potentials of the Embedded Atom type were used in the simulation of the dislocation core structures in TiAl. Different orientations of the dislocation line were simulated for the most commonly observed TiAl slip systems. Low-temperature dislocation behavior is interpreted in terms of ordinary dislocation motion. The effect of applied stress on the shape of the dislocation core and its mobility is examined as well. For the superdislocations several possible types of dissociations were studied.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Radiation tolerance of ceramics—Insights from atomistic simulation of damage accumulation in pyrochlores

    Energy Technology Data Exchange (ETDEWEB)

    Devanathan, Ramaswami; Weber, William J.; Gale, Julian D.

    2010-10-01

    We have used molecular dynamics simulations to examine the effects of radiation damage accumulation in two pyrochlore-structured ceramics, namely Gd2Ti2O7 and Gd2Zr2O7. It is well known from experiment that the titanate is susceptible to radiation-induced amorphization, while the zirconate does not go amorphous under prolonged irradiation. Our simulations show that cation Frenkel pair accumulation eventually leads to amorphization of Gd2Ti2O7. Anion disorder occurs with cation disorder. The amorphization is accompanied by a density decrease of about 12.7% and a decrease of about 50% in the elastic modulus. In Gd2Zr2O7, amorphization does not occur, because the residual damage is not sufficiently energetic to drive the material amorphous. Subtle differences in damage accumulation and annealing between the two pyrochlores lead to drastically different radiation response as the damage accumulates.

  20. 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

  1. 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.

  2. 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

    The transport of aqueous solutions in artificial nanopores is of both fundamental and technological interest. Recently, carbon nano-structured materials (fullerenes) have attracted a great deal of attention in nanotechnology. In fact, due to their large specific surface area, high thermal...... conductivity, extremely low surface friction and superior mechanical properties, graphene channels and carbon nanotubes (CNTs) are promising candidates to be implemented as fluid conduits in nanosystems. Performing Non-equilibrium Molecular Dynamics simulations, we study the transport of water...... 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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.

  7. 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...

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Atomistic Simulations of Orientation and Shock Velocity Dependences on Pentaerythritol Tetranitrate Detonation

    Science.gov (United States)

    Shan, Tzu-Ray; Thompson, Aidan; Wixom, Ryan; Mattsson, Ann

    2012-02-01

    Predicting the behavior of energetic materials requires a detailed description of how chemical reaction, energy and pressure fronts propagate during initial stages of detonation. In this talk, classical molecular dynamics (MD) simulations are used to examine orientation and shock velocity dependences in single crystal pentaerythritol tetranitrate (PETN). This work utilizes an empirical, variable charge reactive force field (ReaxFF) that is implemented in the LAMMPS package with a time-averaged bond-order method for on-the-fly chemical species identification. The accuracy of ReaxFF is validated by comparisons of activation barriers for dissociation of a single PETN molecule along various dissociation channels with higher-fidelity, but more expensive, density functional theory (DFT) calculations. The response of single-crystal PETN to shock compression is simulated using the multi-scale shock technique (MSST) along the insensitive (100) directions, as well as the sensitive (001) and (110) directions, at steady shock velocities ranging from 6-10 km/s. Hugoniot curves, particle velocities of shocked molecules, and evolution of reaction products with time from MD simulations with ReaxFF will be discussed and compared to that from DFT calculations.

  14. Mechanical Behavior of Carbon Nanotubes Filled With Metal Nanowires By Atomistic Simulations

    Science.gov (United States)

    Danailov, Daniel; Keblinski, Pawel; Pulickel, Ajayan; Nayak, Saroj

    2002-03-01

    Using molecular dynamics simulations we studied mechanical behavior of (10,10) carbon nanotubes filled with a crystalline fcc metal wires. The interatomic interactions were described by a combination of Terfoff’s bond-order potential for carbon, embedded atom method (EAM) potential for metal and pair potential for carbon-metal interactions. The elastic properties, as well as failure mechanism were determined by simulating three point bending test, by pressing the center and the ends of relatively long tube in determined relatively small ring areas. We observed that following elastic response, at larger deformation, the metal wire yields well before the carbon bonding is affected. The behavior of filled tubes was compared with that of hollow tubes. Interesting is thet the hollow carbon (10,10) nanotube is more strong elastically than the same tube filled with Au-metal nanowire. We also simulated indentation of filled tubes residing on a hard flat surface. Similarly as in the bending test, metal wire yields first, is cut in between hard cylinder and hard plane and pushed away from under the indenter. Upon further increase of the indentation force, carbon tube is broken and forms two open ends that are rapidly zipped around the cut metal wire. Remarkably, the shape of the zipped tube ends strong depend of the speed of the punching of the tube. This result imply a possibility of designing tubes with various closed end shapes with applicationusing in the nanoscale manipulation procedures used for production.

  15. 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...

  16. Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study.

    Directory of Open Access Journals (Sweden)

    Vijayan ManickamAchari

    Full Text Available The rational design of a glycolipid application (e.g. drug delivery with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20% in the hydrophobic region of the lamellar crystal (LC phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.

  17. 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).

  18. 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

  19. Early and transient stages of Cu oxidation: Atomistic insights from theoretical simulations and in situ experiments

    Science.gov (United States)

    Zhu, Qing; Zou, Lianfeng; Zhou, Guangwen; Saidi, Wissam A.; Yang, Judith C.

    2016-10-01

    Understanding of metal oxidation is critical to corrosion control, catalysis synthesis, and advanced materials engineering. Although, metal oxidation process is rather complicated, different processes, many of them coupled, are involved from the onset of reaction. Since first introduced, there has been great success in applying heteroepitaxial theory to the oxide growth on a metal surface as demonstrated in the Cu oxidation experiments. In this paper, we review the recent progress in experimental findings on Cu oxidation as well as the advances in the theoretical simulations of the Cu oxidation process. We focus on the effects of defects such as step edges, present on realistic metal surfaces, on the oxide growth dynamics. We show that the surface steps can change the mass transport of both Cu and O atoms during oxide growth, and ultimately lead to the formation of different oxide morphology. We also review the oxidation of Cu alloys and explore the effect of a secondary element to the oxide growth on a Cu surface. From the review of the work on Cu oxidation, we demonstrate the correlation of theoretical simulations at multiple scales with various experimental techniques.

  20. 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.

  1. Atomistic simulation of point defects and diffusion in B2 NiAl

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-08-04

    NiAl is a strongly ordered compound with a large atomic size difference between the components. Due to these features it demonstrates the so-called triple-defect mechanism of compositional disorder with Ni anti-structural atoms in Ni-rich compositions and Ni vacancies in Al-rich compositions. Diffusion mechanisms in triple-defect compounds are more involved than in antisite disorder compounds. Because every Ni atom in the B2 structure is surrounded by Al atoms and vise versa, every nearest-neighbor (NN) jump of a vacancy induces local disorder, which is very unfavorable. The authors therefore have to consider diffusion of Ni and Al along their own sublattices by next-nearest-neighbor (NNN) vacancy jumps. Alternatively, one can think of cycled mechanisms in which the crystal order is destroyed only locally and temporarily, but is totally restored when the diffusion cycle is complete. In this study the authors apply molecular statics simulations to evaluate the energetics of the point defect formation and migration in NiAl by different mechanisms. The goal of their simulations is to predict the mechanisms that are the easiest, thus dominating, at different alloy compositions.

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

    Science.gov (United States)

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

    2015-11-12

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

  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. 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.

  5. 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.

  6. Atomistic Simulation of Solubilization of Polycyclic Aromatic Hydrocarbons in a Sodium Dodecyl Sulfate Micelle.

    Science.gov (United States)

    Liang, Xujun; Marchi, Massimo; Guo, Chuling; Dang, Zhi; Abel, Stéphane

    2016-04-19

    Solubilization of two polycyclic aromatic hydrocarbons (PAHs), naphthalene (NAP, 2-benzene-ring PAH) and pyrene (PYR, 4-benzene-ring PAH), into a sodium dodecyl sulfate (SDS) micelle was studied through all-atom molecular dynamics (MD) simulations. We find that NAP as well as PYR could move between the micelle shell and core regions, contributing to their distribution in both regions of the micelle at any PAH concentration. Moreover, both NAP and PYR prefer to stay in the micelle shell region, which may arise from the greater volume of the micelle shell, the formation of hydrogen bonds between NAP and water, and the larger molecular volume of PYR. The PAHs are able to form occasional clusters (from dimer to octamer) inside the micelle during the simulation time depending on the PAH concentration in the solubilization systems. Furthermore, the micelle properties (i.e., size, shape, micelle internal structure, alkyl chain conformation and orientation, and micelle internal dynamics) are found to be nearly unaffected by the solubilized PAHs, which is irrespective of the properties and concentrations of PAHs.

  7. Simulating surface-enhanced Raman optical activity using atomistic electrodynamics-quantum mechanical models.

    Science.gov (United States)

    Chulhai, Dhabih V; Jensen, Lasse

    2014-10-01

    Raman optical activity has proven to be a powerful tool for probing the geometry of small organic and biomolecules. It has therefore been expected that the same mechanisms responsible for surface-enhanced Raman scattering may allow for similar enhancements in surface-enhanced Raman optical activity (SEROA). However, SEROA has proved to be an experimental challenge and mirror-image SEROA spectra of enantiomers have so far not been measured. There exists a handful of theories to simulate SEROA, all of which treat the perturbed molecule as a point-dipole object. To go beyond these approximations, we present two new methods to simulate SEROA: the first is a dressed-tensors model that treats the molecule as a point-dipole and point-quadrupole object; the second method is the discrete interaction model/quantum mechanical (DIM/QM) model, which considers the entire charge density of the molecule. We show that although the first method is acceptable for small molecules, it fails for a medium-sized one such as 2-bromohexahelicene. We also show that the SEROA mode intensities and signs are highly sensitive to the nature of the local electric field and gradient, the orientation of the molecule, and the surface plasmon frequency width. Our findings give some insight into why experimental SEROA, and in particular observing mirror-image SEROA for enantiomers, has been difficult.

  8. 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)

  9. Micron-scale Reactive Atomistic Simulation of Void Collapse and Hotspot Growth in PETN

    Science.gov (United States)

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

    2015-06-01

    Material defects and other heterogeneities such as dislocations, micro-porosity, and grain boundaries play key roles in the shock-induced initiation of detonation in energetic materials. We performed non-equilibrium molecular dynamics simulations to explore the effect of nanoscale voids on hotspot growth and initiation in micron-scale pentaerythritol tetranitrate (PETN) crystals under weak shock loading (Up = 1.25 km/s; Us = 4.5 km/s). We used the ReaxFF potential implemented in LAMMPS. We built a pseudo-2D PETN crystal with dimensions 0.3 μm × 0.22 μm × 1.3 nm containing a 20 nm cylindrical void. Once the initial shockwave traversed the entire sample, the shock-front absorbing boundary condition was applied, allowing the simulation to continue beyond 1 nanosecond. Results show an exponentially increasing hotspot growth rate. The hotspot morphology is initially symmetric about the void axis, but strong asymmetry develops at later times, due to strong coupling between exothermic chemistry, temperature, and divergent secondary shockwaves emanating from the collapsing void. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  10. 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.

  11. 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)

  12. 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

  13. Atomistic simulations of the load dependant friction force between silicon tip and diamond substrate.

    Science.gov (United States)

    Bu, Hao; Chen, Yunfei

    2010-11-01

    In this paper, the load dependence on the interfacial friction between a cubic silicon tip and diamond substrate was investigated using molecular dynamics simulations. With the increase of the applied load, the sliding process experiences the states of superlubricity, single slip instability, double slip instability and plastic stage. The transitions from one state to the next one occur at the contact pressure 5.3 GPa, 8.0 GPa and 10.8 GPa, sequentially. In the superlubricity state, both friction and dissipated energy approach zero, independent of the load. However, in the single slip state the friction has a linear relationship with load, while the double slip mode induces decreased frictional force and lower damping. The coupling of the structure and forces in the plastic regime leads to the reduction of friction. These behaviors show good agreement with the recent experimental observations and theoretical predictions. PMID:21137969

  14. 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.

  15. Orientation and Rate Dependence of Wave Propagation in Shocked Beta-SiC from Atomistic Simulations

    Institute of Scientific and Technical Information of China (English)

    CHENG Qin; WU Heng-An; WANG Yu; WANG Xiu-Xi

    2009-01-01

    The orientation dependence of planax wave propagation in beta-SiC is studied via the molecular dynamics (MD) method. Simulations axe implemented under impact loadings in four main crystal directions, i.e., , ,, and . The dispersion of stress states in different directions increases with rising impact velocity, which implies the anisotropic characteristic of shock wave propagation for beta-SiC materials. We also obtain the Hugoniot relations between the shock wave velocity and the impact velocity, and find that the shock velocity falls into a plateau above a threshold of impact velocity. The shock velocity of the plateaux is dependent on the shock directions, while and can be regarded as equivalent directions as they almost reach the same plateau.A comparison between the atomic stress from MD and the stress from Rankine--Hugoniot jump conditions is also made, and it is found that they agree with each other very well.

  16. 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.

  17. Investigation of the thermal stability of Cu nanowires using atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Granberg, F.; Parviainen, S., E-mail: stefan.parviainen@helsinki.fi; Djurabekova, F.; Nordlund, K. [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, Helsinki, FIN-00014 (Finland)

    2014-06-07

    We present a method for determining the melting point of copper nanowires based on classical molecular dynamics simulations and use it to investigate the dependence of the melting point on wire diameter. The melting point is determined as the temperature at which there is a significant change in the fraction of liquid atoms in the wire, according to atomic bond angle analysis. The results for the wires with diameters in the range 1.5 nm to 20 nm show that the melting point is inversely proportional to the diameter while the cross-sectional shape of the wire does not have a significant impact. Comparison of results obtained using different potentials show that while the absolute values of the melting points may differ substantially, the melting point depression is similar for all potentials. The obtained results are consistent with predictions based on the semi-empirical liquid drop model.

  18. Force-Field Derivation and Atomistic Simulation of HMX/Graphite Interface and Polycrystal Systems

    Institute of Scientific and Technical Information of China (English)

    龙瑶; 刘永刚; 聂福德; 陈军

    2012-01-01

    Interface is the key issue to understand the performance of composite materials. In this work, we study the interface between octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and graphite, try to find out its contribution to mixture explosives. The work starts from the force-field derivation. We get ab initio based pair potentials across the interface, and then use them to study the interface structural and mechanical properties. A series of large scale molecular dynamics simulations are performed. The structure evolution, energy variation and elastic/plastic transformation of interface and polycrystal systems are calculated. The desensitizing mechanism of graphite to HMX is discussed.

  19. 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

  20. 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.

  1. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations

    Science.gov (United States)

    Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue

    2016-05-01

    Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.

  2. 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.

  3. Atomistic simulation of the homogeneous nucleation and of the growth of N2 crystallites.

    Science.gov (United States)

    Leyssale, Jean-Marc; Delhommelle, Jerome; Millot, Claude

    2005-03-01

    We report on a computer simulation study of the early stages of the crystallization of molecular nitrogen. First, we study how homogeneous nucleation takes place in supercooled liquid N(2) for a moderate degree of supercooling. Using the umbrella sampling technique, we determine the free energy barrier of formation for a critical nucleus of N(2). We show that, in accord with Ostwald's rule of stages, the structure of the critical nucleus is predominantly that of a metastable polymorph (alpha-N(2) for the state point investigated). We then monitor the evolution of several critical nuclei through a series of unbiased molecular dynamics trajectories. The growth of N(2) crystallites is accompanied by a structural evolution toward the stable polymorph beta-N(2). The microscopic mechanism underlying this evolution qualitatively differs from that reported previously. We do not observe any dissolution or reorganization of the alpha-like core of the nucleus. On the contrary, we show that alpha-like and beta-like blocks coexist in postcritical nuclei. We relate the structural evolution to a greater adsorption rate of beta-like molecules on the surface and show that this transition actually starts well within the precritical regime. We also carefully investigate the effect of the system size on the height of the free energy barrier of nucleation and on the structure and size of the critical nucleus. PMID:15836335

  4. Atomistic Simulation Studies of the Bulk Lithiated TiO2

    Science.gov (United States)

    Ngoepe, Phuti; Matshaba, Malili; Sayle, Dean

    2013-03-01

    TiO2 has been confirmed as a safe anode material in lithium ion batteries due to its higher Li-insertion potential, (1.5V) in comparison with commercialised carbon anode materials. In the current study, amorphisation recrystallization method is used to produce bulk TiO2 with a brookite structure and lithium is inserted at different concentrations. In accordance with pair distribution function experiments, it is found that lithiation tends to amorphise the structures. Simulated X-ray diffraction patterns are produced from such structures and compared with the experimental XRDs. Microstructures of TiO2 are generated and are found to be highly twinned hence forming straight and zigzag tunnels. The microstructures of lithiated TiO2 display limited twinning and tunnels with less pathways available for lithium transport. The microstructures are compared with those of nanostructural TiO2 and suggestions for the preference of the latter in anodes are put forward. SARChI Chair, under the National Research Foundation, Pretoria

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

    Science.gov (United States)

    Safi, E.; Björkas, C.; Lasa, A.; Nordlund, K.; Sukuba, I.; Probst, M.

    2015-08-01

    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.

  6. 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.

  7. 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.

  8. 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

  9. Transfer-matrix simulations of field emission from bundles of open and closed (5,5) carbon nanotubes

    Science.gov (United States)

    Mayer, A.; Miskovsky, N. M.; Cutler, P. H.; Lambin, Ph.

    2003-12-01

    We present simulations of field emission from bundles of metallic (5,5) carbon nanotubes, which are either ideally open or closed. The scattering calculations are achieved using a transfer-matrix methodology for consideration of three-dimensional aspects of both the emitting structure and the surface barrier. Band-structure effects are reproduced by using pseudopotentials and enforcing the incident states to first travel through a periodic repetition of the tubes’ basic cell before entering the region containing the fields. The bundles consist of three and six identical structures, which are placed at the corners of equilateral triangles. In all cases, the closed emitters are found to emit less current than the open ones and to be more sensitive to the electric field in their response to neighboring tubes. Due to the enhanced screening of the electric field, the bundles’ emission rates are reduced compared to those of the isolated tubes. It turns out that the rates characterizing bundle and isolated emitters are related by a simple formula, whose dependence on the electric field suggests deviations from the Fowler-Nordheim equation at high fields. Finally, the position of peaks associated with quasilocalized states on top of the closed emitters appears to be a strong indicator of the tubes’ environment.

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

    Science.gov (United States)

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

    2012-07-01

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

  11. Numerical Simulation for Frictional Loss and Local Loss of a 5*5 SMART Rod Bundle

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jong-Pil; Kim, Seong Jin; Kwon, Hyuk; Seo, Kyong-Won; Hwang, Dae-Hyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-10-15

    The results showed good agreement with experimental data and/or reasonable values. However, these results were dependent on computational meshes and turbulence models and it still remains important issues in CFD analysis. The aim of present work is to assess the pressure drop in a 5*5 SMART rod bundle using 3D CFD code with various computational meshes and turbulence models. In the present work, 3D CFD code was utilized to investigate pressure drop in a SMART 5*5 rod bundle. The predicted pressure drop was strongly dependent with computational meshes and turbulence models. Based on CFD results in this study, least five of six meshes within the subchannel gap are required to get reliable result which is insensitive to the number of meshes. The friction factor predicted by k - ε model is good agreement with McAdams's correlation while SST model overestimate McAdams's correlation. However, it is difficult to judge performance of turbulence model because of lock of experimental data for a 5*5 SMART bare rod bundle. For nominal condition (Re-194,000) of SMART, SST model predict k-factor of MV and IFM grid as 1.304 and 0.748, respectively. This value is reasonable as compared with designed k-factor, 1.320 and 0.78.

  12. 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.

  13. 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

  14. Behavior of AgInCd absorber material in Zry/UO{sub 2} fuel rod simulator bundles tested at high temperatures in the CORA facility

    Energy Technology Data Exchange (ETDEWEB)

    Sepold, L.; Hagen, S.; Hofmann, P.; Schanz, G.

    2009-01-15

    The CORA experiments carried out in an out-of-pile facility at the Kernforschungszentrum Karlsruhe (KfK), Federal Republic of Germany, are part of the ''Severe Fuel Damage'' (SFD) program. The experimental program is to provide information on the failure mechanisms of Light Water Reactor (LWR) fuel elements in a temperature range from 1200 C to 2000 C and in a few cases up to 2400 C. In the CORA experiments two different bundle configurations are tested: PWR (Pressurized Water Reactor) and BWR (Boiling Water Reactor) bundles. The PWR-type assemblies usually consist of 25 rods with 16 electrically heated fuel rod simulators and nine unheated rods (full-pellet and absorber rods). Bundle CORA-5 contained one Ag/In/Cd - steel absorber rod whereas two absorber rods were used in CORA-12, CORA-15, and CORA-9. The larger bundle CORA-7 contained 5 absorber rods. CORA-12 was terminated by quenching with water from the bottom. In CORA-15 the heated and unheated rods were pressurized to achieve pronounced clad ballooning. Bundle CORA-9 was tested with a system pressure of 1.0 MPa instead of 0.22 MPa. The test bundles were subjected to temperature transients of a slow heatup rate in a steam environment. Thus, an accident sequence is simulated, which may develop from a small-break loss-of-coolant accident of a LWR. The transient phases of the tests were initiated with a temperature ramp rate of 1 K/s. The temperature escalation due to the exothermal zircaloy (Zry)-steam reaction started at about 1100 C, leading the bundles to maximum temperatures of approximately 2000 C. Rod destruction started with the failure of the absorber rod cladding at about 1200 C, i.e. about 250 K below the melting regime of steel. Penetration of the steel cladding was presumably caused by a eutectic interaction between steel and the zircaloy guide tube. The test bundles resulted in severe oxidation and partial melting of the cladding, fuel dissolution by Zry/UO{sub 2} interaction

  15. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Despite being chemically inert as a bulk material, nanoscale gold can pose harmful side effects to living organisms. In particular, cationic Au nanoparticles (AuNP+) of 2 nm diameter or less permeate readily through plasma membranes and induce cell death. We report atomistic simulations of cationic...... Au nanoparticles interacting with realistic membranes and explicit solvent using a model system that comprises two cellular compartments, extracellular and cytosolic, divided by two asymmetric lipid bilayers. The membrane-AuNP+ binding and membrane reorganization processes are discovered...... of the zwitterionic lipids and nanoparticle side groups in the contact area, giving rise to the initial stage of pore formation on the membrane surface. Such behavior is not seen on the cytosolic side, where AuNP+ is spontaneously captured by the negatively charged phosphatidylserine lipids that diffuse to enrich...

  17. Systematic Structural Change in Selected Rare Earth Oxide Pyrochlores as Determined by Wide-Angle CBED and a Comparison with the Results of Atomistic Computer Simulation

    Science.gov (United States)

    Tabira, Yasunori; Withers, Ray L.; Minervini, Licia; Grimes, Robin W.

    2000-08-01

    An unknown oxygen atom fractional co-ordinate characteristic of the pyrochlore structure type has been determined for selected rare earth zirconate and titanate pyrochlores via a systematic row wide-angle CBED technique and shown to vary systematically with rare earth ion size. In the case of the titanate pyrochlore Gd2Ti2O7, the obtained results contrast with previously published X-ray results. Atomistic computer simulation is used to predict the value of the same parameter for a wide range of oxide pyrochlores. Comparison of calculated values with experimentally determined values shows that the general trends are correctly predicted although there appears to be systematic underestimation of both the observed values (by approximately 0.007) as well as their rate of change with rare earth ion size. Cation anti-site disorder is proposed as the origin of these discrepancies.

  18. 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.

  19. Simulation of the fuel rod bundle test QUENCH-03 using the integral code ASTEC V2

    Energy Technology Data Exchange (ETDEWEB)

    Kruse, Philipp; Koch, Marco K. [Bochum Univ. (Germany). Chair of Energy Systems and Energy Economics

    2010-05-15

    Failure of the main and emergency cooling-systems can lead to an accident with severe core degradation even with core meltdown. To prevent total meltdown of the uncovered and overheated core reflooding with water is an unavoidable accident management measure. The fast supply of water and the resulting increased available amount of steam can lead to crack formations and break up of the oxide layer of the fuel rods. The additionally exposed surface could result in an increased release of hydrogen due to a supplementary exothermal zirconium- steam-oxidation reaction. Within the frame of the QUENCH test-program - realised by FZK - loss of coolant accidents in LWR (Light Water Reactor) are analysed using an experimental reactor core to determine the produced amount of hydrogen, the so-called hydrogen source term. Additionally, the behaviour of the bundle with different absorber rod and cladding materials is being analysed. Based on the post-test calculations of the QUENCH tests with the severe accident code system ASTEC the capability of the code can be established and evaluated. In the following the post-test calculations of the QUENCH-03 test with ASTEC V2 are discussed. (orig.)

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

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

    Science.gov (United States)

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

    2012-01-01

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

  6. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.

    Science.gov (United States)

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

    Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

  7. 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)

  8. 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...

  9. 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.

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

    Science.gov (United States)

    Ji, Pengfei; Zhang, Yuwen

    2016-03-01

    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 provides a general way that is accessible to other metals in laser heating.

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Jonane, Inga; Timoshenko, Janis; Kuzmin, Alexei

    2016-10-01

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

  14. Surface structure of (10(-)10) and (11(-)20) surfaces of ZnO with density functional theory and atomistic simulation.

    Science.gov (United States)

    Cooke, David J; Marmier, Arnaud; Parker, Stephen C

    2006-04-20

    We have calculated the stability of two of the low-index surfaces known to dominate the morphology of ZnO as a function of stoichiometry. These two surfaces are (10(-)10) and (11(-)20). In each case, two terminations only are stable for a significant range of oxygen and hydrogen chemical potential: the pure stoichiometric surface and a surface covered in a monolayer of water. The mode by which the water adsorbs is however different for the two surfaces considered. On the (10(-)10) surface the close proximity of the water molecules means hydrogen bonding can occur between adjacent chemiabsorbed water molecules and hence there is little difference in the stability of the hydrated and hydroxylated surface, and in fact the most stable surface occurs with a combination of dissociated and undissociated water adsorption. In the case of the (11(-)20) surface, it is only when full dissociation has occurred that a hydrogen-bonding network can form. Our results also show good agreement between DFT and atomistic simulations, suggesting that potential based methods can usefully be applied to ZnO. PMID:16610898

  15. 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

  16. 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

  17. 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

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how...... transitions occur in membrane proteins-not to mention numerous applications in drug design. Here, we present a full 1 micros atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements...... process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5-1 micros). Together with lipids binding in matching positions...

  18. 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)

  19. 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 ...

  20. 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

    studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter...

  1. 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.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics...

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  4. 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

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

    OpenAIRE

    Ji, Pengfei; Zhang, Yuwen

    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 ...

  6. Evidence of thin-film precursors formation in hydrokinetic and atomistic simulations of nano-channel capillary filling

    OpenAIRE

    Chibbaro, S.; BIFERALE, L.; Diotallevi, F.; Succi, S.; Binder, K.; Milchev, A.; Dimitrov, D.; Girardo, S.; Pisignano, D.

    2008-01-01

    We present hydrokinetic Lattice Boltzmann and Molecular Dynamics simulations of capillary filling of high-wetting fluids in nano-channels, which provide clear evidence of the formation of thin precursor films, moving ahead of the main capillary front. The dynamics of the precursor films is found to obey the Lucas-Washburn law as the main capillary front, z2(t) proportional to t, although with a larger prefactor, which we find to take the same value for both geometries under inspection. Both h...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. 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)

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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

  19. Bundling dynamics regulates the active mechanics and transport in carbon nanotube networks and their nanocomposites.

    Science.gov (United States)

    Hahm, Myung Gwan; Wang, Hailong; Jung, Hyun Young; Hong, Sanghyun; Lee, Sung-Goo; Kim, Sung-Ryong; Upmanyu, Moneesh; Jung, Yung Joon

    2012-06-01

    High-density carbon nanotube networks (CNNs) continue to attract interest as active elements in nanoelectronic devices, nanoelectromechanical systems (NEMS) and multifunctional nanocomposites. The interplay between the network nanostructure and its properties is crucial, yet current understanding remains limited to the passive response. Here, we employ a novel superstructure consisting of millimeter-long vertically aligned single walled carbon nanotubes (SWCNTs) sandwiched between polydimethylsiloxane (PDMS) layers to quantify the effect of two classes of mechanical stimuli, film densification and stretching, on the electronic and thermal transport across the network. The network deforms easily with an increase in the electrical and thermal conductivities, suggestive of a floppy yet highly reconfigurable network. Insight from atomistically informed coarse-grained simulations uncover an interplay between the extent of lateral assembly of the bundles, modulated by surface zipping/unzipping, and the elastic energy associated with the bent conformations of the nanotubes/bundles. During densification, the network becomes highly interconnected yet we observe a modest increase in bundling primarily due to the reduced spacing between the SWCNTs. The stretching, on the other hand, is characterized by an initial debundling regime as the strain accommodation occurs via unzipping of the branched interconnects, followed by rapid rebundling as the strain transfers to the increasingly aligned bundles. In both cases, the increase in the electrical and thermal conductivity is primarily due to the increase in bundle size; the changes in network connectivity have a minor effect on the transport. Our results have broad implications for filamentous networks of inorganic nanoassemblies composed of interacting tubes, wires and ribbons/belts.

  20. 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

  1. 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)

  2. 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)

  3. 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

  4. 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)

  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. 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 ...

  7. Atomistic Properties of Solids

    CERN Document Server

    Sirdeshmukh, Dinker B; Subhadra, K G

    2011-01-01

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

  8. Atomistic Mechanisms of Fatigue in Nanocrystalline Metals

    Science.gov (United States)

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

    2005-04-01

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

  9. Parabolic k-ample bundles

    CERN Document Server

    Biswas, Indranil

    2011-01-01

    We construct projectivization of a parabolic vector bundle and a tautological line bundle over it. It is shown that a parabolic vector bundle is ample if and only if the tautological line bundle is ample. This allows us to generalize the notion of a k-ample bundle, introduced by Sommese, to the context of parabolic bundles. A parabolic vector bundle $E_*$ is defined to be k-ample if the tautological line bundle ${\\mathcal O}_{{\\mathbb P}(E_*)}(1)$ is $k$--ample. We establish some properties of parabolic k-ample bundles.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-09-01

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

  11. 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)

  12. 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

  13. Principal noncommutative torus bundles

    DEFF Research Database (Denmark)

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

    2008-01-01

    action) and give necessary and sufficient conditions for any non-commutative principal torus bundle being RKK-equivalent to a commutative one. As an application of our methods we shall also give a K-theoretic characterization of those principal torus-bundles with H-flux, as studied by Mathai...... and Rosenberg which possess "classical" T-duals....

  14. 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...

  15. 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.

  16. Liquid Flow in Shaped Fiber Bundle

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yan; WANG Hua-ping; CHEN Yue-hua

    2006-01-01

    By computation and comparison of the critical spreading coefficient parameter, it was found that shaped fiber bundle is better for wetting. Liquid-air interface tension of liquid arising the shaped fiber bundle body is considered as one critical factor besides liquid viscosity, inertia force and liquid-fiber interface tension. Experimental result simulation demonstrated that the liquid-air interface tension is correlated with the geometric size of the liquid arising in body, φ0 (x) and which is affected by the cross sectional shape of fiber and the radius of single fiber. The shaped fiber bundle model is introduced to investigate liquid flow in fiber assembly. The model is generated based on a random function for stochastic forming of fibers in bundle and it is necessary to combine this fundamental model with physical explanation for investigation of liquid flow in fiber assembly.

  17. 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.

  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. Atomistic Modeling of Gas Adsorption in Nanocarbons

    Directory of Open Access Journals (Sweden)

    G. Zollo

    2012-01-01

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

  20. 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.

  1. 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.

  2. 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.

  3. Computer simulation in materials science

    Energy Technology Data Exchange (ETDEWEB)

    Arsenault, R.J.; Beeler, J.R.; Esterling, D.M.

    1988-01-01

    This book contains papers on the subject of modeling in materials science. Topics include thermodynamics of metallic solids and fluids, grain-boundary modeling, fracture from an atomistic point of view, and computer simulation of dislocations on an atomistic level.

  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.......5%/2.3% in women, P 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 block was associated...

  5. 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...

  6. 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 .

  7. Bundles of Banach algebras

    Directory of Open Access Journals (Sweden)

    J. W. Kitchen

    1994-01-01

    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.

  8. On projective space bundle with nef normalized tautological line bundle

    CERN Document Server

    Yasutake, Kazunori

    2011-01-01

    In this paper, we study the structure of projective space bundles whose relative anti-canonical line bundle is nef. As an application, we get a characterization of abelian varieties up to finite etale covering.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-31

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

  10. Atomistic modeling of carbon Cottrell atmospheres in bcc iron

    Science.gov (United States)

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

    2013-01-01

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

  11. 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.

  12. Capacity efficiency of recovery request bundling

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Dittmann, Lars; Berger, Michael Stübert;

    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...

  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. Detailed atomistic simulation of the nano-sorption and nano-diffusivity of water, tyrosol, vanillic acid, and p-coumaric acid in single wall carbon nanotubes.

    Science.gov (United States)

    Anastassiou, Alexandros; Karahaliou, Elena K; Alexiadis, Orestis; Mavrantzas, Vlasis G

    2013-10-28

    We report results from a detailed computer simulation study for the nano-sorption and mobility of four different small molecules (water, tyrosol, vanillic acid, and p-coumaric acid) inside smooth single-wall carbon nanotubes (SWCNTs). Most of the results have been obtained with the molecular dynamics (MD) method, but especially for the most narrow of the CNTs considered, the results for one of the molecules addressed here (water) were further confirmed through an additional Grand Canonical (μVT) Monte Carlo (GCMC) simulation using a value for the water chemical potential μ pre-computed with the particle deletion method. Issues addressed include molecular packing and ordering inside the nanotube for the four molecules, average number of sorbed molecules per unit length of the tube, and mean residence time and effective axial diffusivities, all as a function of tube diameter and tube length. In all cases, a strong dependence of the results on tube diameter was observed, especially in the way the different molecules are packed and organized inside the CNT. For water for which predictions of properties such as local structure and packing were computed with both methods (MD and GCMC), the two sets of results were found to be fully self-consistent for all types of SWCNTs considered. Water diffusivity inside the CNT (although, strongly dependent on the CNT diameter) was computed with two different methods, both of which gave identical results. For large enough CNT diameters (larger than about 13 Å), this was found to be higher than the corresponding experimental value in the bulk by about 55%. Surprisingly enough, for the rest of the molecules simulated (phenolic), the simulations revealed no signs of mobility inside nanotubes with a diameter smaller than the (20, 20) tube. This is attributed to strong phenyl-phenyl attractive interactions, also to favorable interactions of these molecules with the CNT walls, which cause them to form highly ordered, very stable

  15. 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...

  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. 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

  18. ALUMINUM BOX BUNDLING PRESS

    Directory of Open Access Journals (Sweden)

    Iosif DUMITRESCU

    2015-05-01

    Full Text Available In municipal solid waste, aluminum is the main nonferrous metal, approximately 80- 85% of the total nonferrous metals. The income per ton gained from aluminum recuperation is 20 times higher than from glass, steel boxes or paper recuperation. The object of this paper is the design of a 300 kN press for aluminum box bundling.

  19. Universal Lagrangian bundles

    NARCIS (Netherlands)

    Sepe, D.

    2013-01-01

    The obstruction to construct a Lagrangian bundle over a fixed integral affine manifold was constructed by Dazord and Delzant (J Differ Geom 26:223–251, 1987) and shown to be given by ‘twisted’ cup products in Sepe (Differ GeomAppl 29(6): 787–800, 2011). This paper uses the topology of universal Lagr

  20. Thermodynamic integration based on classical atomistic simulations to determine the Gibbs energy of condensed phases: Calculation of the aluminum-zirconium system

    Science.gov (United States)

    Harvey, J.-P.; Gheribi, A. E.; Chartrand, P.

    2012-12-01

    In this work, an in silico procedure to generate a fully coherent set of thermodynamic properties obtained from classical molecular dynamics (MD) and Monte Carlo (MC) simulations is proposed. The procedure is applied to the Al-Zr system because of its importance in the development of high strength Al-Li alloys and of bulk metallic glasses. Cohesive energies of the studied condensed phases of the Al-Zr system (the liquid phase, the fcc solid solution, and various orthorhombic stoichiometric compounds) are calculated using the modified embedded atom model (MEAM) in the second-nearest-neighbor formalism (2NN). The Al-Zr MEAM-2NN potential is parameterized in this work using ab initio and experimental data found in the literature for the AlZr3-L12 structure, while its predictive ability is confirmed for several other solid structures and for the liquid phase. The thermodynamic integration (TI) method is implemented in a general MC algorithm in order to evaluate the absolute Gibbs energy of the liquid and the fcc solutions. The entropy of mixing calculated from the TI method, combined to the enthalpy of mixing and the heat capacity data generated from MD/MC simulations performed in the isobaric-isothermal/canonical (NPT/NVT) ensembles are used to parameterize the Gibbs energy function of all the condensed phases in the Al-rich side of the Al-Zr system in a CALculation of PHAse Diagrams (CALPHAD) approach. The modified quasichemical model in the pair approximation (MQMPA) and the cluster variation method (CVM) in the tetrahedron approximation are used to define the Gibbs energy of the liquid and the fcc solid solution respectively for their entire range of composition. Thermodynamic and structural data generated from our MD/MC simulations are used as input data to parameterize these thermodynamic models. A detailed analysis of the validity and transferability of the Al-Zr MEAM-2NN potential is presented throughout our work by comparing the predicted properties obtained

  1. First principles molecular dynamics simulation of a task-specific ionic liquid based on silver-olefin complex: atomistic insight into separation process

    CERN Document Server

    Jiang, De-en

    2008-01-01

    First principles molecular dynamics based on density functional theory is applied to a hypothetical ionic liquid whose cations and anions are silver-ethylene complex [Ag(C2H4)2+] and tetrafluoroborate [BF4-], respectively. This ionic liquid represents a group of task-specific silver complex-based ionic liquids synthesized recently. Molecular dynamics simulations at two temperatures are performed for five picoseconds. Events of association, dissociation, exchange, and recombination of ethylene with silver cation are observed. A mechanism of ethylene transfer similar to the Grotthus type of proton transfer in water is identified, where a silver cation accepts one ethylene molecule and donates another to a neighboring silver cation. This mechanism may contribute to fast transport of olefins through ionic liquid membranes based on silver complexes for olefin/paraffin separation.

  2. 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

    on the simulations we are able to show the atom-level binding modes of two substrate forms: quinol (QH(2)) and quinone (Q). The QH(2) binding at the Q(o)-site involves a coordinated water arrangement that produces an exceptionally close and stable interaction between the cyt b and iron sulfur protein subunits....... In this arrangement water molecules are positioned suitably in relation to the hydroxyls of the QH(2) ring to act as the primary acceptors of protons detaching from the oxidized substrate. In contrast, water does not have a similar role in the Q binding at the Q(o)-site. Moreover, the coordinated water molecule...... is also a prime candidate to act as a structural element, gating for short-circuit suppression at the Q(o)-site. (c) 2013 Elsevier B.V. All rights reserved....

  3. First principles molecular dynamics simulation of a task-specific ionic liquid based on silver-olefin complex: atomistic insights into a separation process.

    Science.gov (United States)

    Jiang, De-en; Dai, Sheng

    2008-08-21

    First principles molecular dynamics based on density functional theory is applied to a hypothetical ionic liquid whose cations and anions are silver-ethylene complex [Ag(C2H4)2+] and tetrafluoroborate [BF4-], respectively. This ionic liquid represents a group of task-specific silver complex-based ionic liquids synthesized recently. Molecular dynamics simulations at two temperatures are performed for five picoseconds. Events of association, dissociation, exchange, and recombination of ethylene with silver cation are found. A mechanism of ethylene transfer similar to the Grotthus type of proton transfer in water is identified, where a silver cation accepts one ethylene molecule and donates another to a neighboring silver cation. This mechanism may contribute to fast transport of olefins through ionic liquid membranes based on silver complexes for olefin/paraffin separation.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Deformation quantization of principal bundles

    CERN Document Server

    Aschieri, Paolo

    2016-01-01

    We outline how Drinfeld twist deformation techniques can be applied to the deformation quantization of principal bundles into noncommutative principal bundles, and more in general to the deformation of Hopf-Galois extensions. First we twist deform the structure group in a quantum group, and this leads to a deformation of the fibers of the principal bundle. Next we twist deform a subgroup of the group of authomorphisms of the principal bundle, and this leads to a noncommutative base space. Considering both deformations we obtain noncommutative principal bundles with noncommutative fiber and base space as well.

  9. 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...

  10. 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).

  11. 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.

  12. 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

  13. Superconductivity in an Inhomogeneous Bundle of Metallic and Semiconducting Nanotubes

    Directory of Open Access Journals (Sweden)

    Ilya Grigorenko

    2013-01-01

    Full Text Available Using Bogoliubov-de Gennes formalism for inhomogeneous systems, we have studied superconducting properties of a bundle of packed carbon nanotubes, making a triangular lattice in the bundle's transverse cross-section. The bundle consists of a mixture of metallic and doped semiconducting nanotubes, which have different critical transition temperatures. We investigate how a spatially averaged superconducting order parameter and the critical transition temperature depend on the fraction of the doped semiconducting carbon nanotubes in the bundle. Our simulations suggest that the superconductivity in the bundle will be suppressed when the fraction of the doped semiconducting carbon nanotubes will be less than 0.5, which is the percolation threshold for a two-dimensional triangular lattice.

  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. 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

  16. Atomistic simulations of semiconductor and metallic nanoparticles

    OpenAIRE

    Zonias, Nicholas

    2011-01-01

    Semiconductor and metallic nanoparticles have recently become an attractive area of intensive research due to their unique and diverse properties, that differ significantly from bulk materials. With a wide range of applications and potential uses in nanoelectronics, catalysis, medicine, chemistry or physics an important amount of experimental and theoretical investigations aim to facilitate deeper understating in their physical and chemical behaviour. Within this context, this thesis is focus...

  17. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

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

  18. Managing bundled payments.

    Science.gov (United States)

    Draper, Andrew

    2011-04-01

    Results of Medicare's ACE demonstration project and Geisinger Health System's ProvenCare initiative provide insight into the challenges hospitals will face as bundled payment proliferates. An early analysis of these results suggests that hospitals would benefit from bringing full automation using clinical IT tools to bear in their efforts to meet these challenges. Other important factors contributing to success include board and physician leadership, organizational structure, pricing methodology for bidding, evidence-based medical practice guidelines, supply cost management, process efficiency management, proactive and aggressive case management, business development and marketing strategy, and the financial management system.

  19. Managing bundled payments.

    Science.gov (United States)

    Draper, Andrew

    2011-04-01

    Results of Medicare's ACE demonstration project and Geisinger Health System's ProvenCare initiative provide insight into the challenges hospitals will face as bundled payment proliferates. An early analysis of these results suggests that hospitals would benefit from bringing full automation using clinical IT tools to bear in their efforts to meet these challenges. Other important factors contributing to success include board and physician leadership, organizational structure, pricing methodology for bidding, evidence-based medical practice guidelines, supply cost management, process efficiency management, proactive and aggressive case management, business development and marketing strategy, and the financial management system. PMID:21548437

  20. 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...

  1. Differential calculi on noncommutative bundles

    OpenAIRE

    Pflaum, Markus J.; Schauenburg, Peter

    1996-01-01

    We introduce a category of noncommutative bundles. To establish geometry in this category we construct suitable noncommutative differential calculi on these bundles and study their basic properties. Furthermore we define the notion of a connection with respect to a differential calculus and consider questions of existence and uniqueness. At the end these constructions are applied to basic examples of noncommutative bundles over a coquasitriangular Hopf algebra.

  2. 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

    Energy Technology Data Exchange (ETDEWEB)

    Agbodemegbe, V.Y., E-mail: vincevalt@gmail.com [Karlsruhe Institute of Technology, Institute of Fusion and Reactor Technique, Kaiserstrasse 12, Karlsruhe (Germany); Cheng, Xu, E-mail: xu.cheng@kit.edu [Karlsruhe Institute of Technology, Institute of Fusion and Reactor Technique, Kaiserstrasse 12, Karlsruhe (Germany); Akaho, E.H.K, E-mail: akahoed@yahoo.com [School of Nuclear and Allied Sciences, University of Ghana, PO Box AE 1, Kwabenya, Accra (Ghana); Allotey, F.K.A, E-mail: fkallotey@gmail.com [Institute of Mathematical Sciences, PO Box LG 197, Legon, Accra (Ghana)

    2015-04-15

    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 = 3.4×10{sup 4} 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

  3. Thermal Characteristics of Tube Bundles in Ultra-Supercritical Boilers

    Directory of Open Access Journals (Sweden)

    Seok Min Choi

    2016-09-01

    Full Text Available In this study, flow and thermal characteristics of tube bundles in ultra-supercritical boilers were analyzed. The local heat transfer around the tube bundles was measured to predict the local temperature distribution and vulnerable positions of the superheated tube bundles. The maximally superheated tube bundles were simulated in the laboratory and local heat transfer was measured by using the naphthalene sublimation method. The experiment was conducted on three lines of tube bundles, all with in-line arrangements. Each line consist of six tubes. The distance in the streamwise direction (Sx/∅ was 1.99 and that in the spanwise direction (Sz/∅ was 5.45. The Reynolds number varied from 5000 to 30,000, which covers a range of different operating conditions. Thermal and stress analyses were conducted numerically, based on the experimental data. The results showed that the flow characteristic changes the local heat transfer of the tube bundles. The flow impinged on the stagnation point of Tube 1 and reattached at 60° of Tube 2. The high heat transfer occurred at those positions of the tube bundles. The temperature and stress distributions on the surface of each tube bundle also varied. The reattachment point on Tube 2 had the highest heat transfer and temperature distribution. That position on Tube 2 was subjected to the highest stress due to the large temperature gradient. This result indicates that Tube 2 of the ultra-supercritical (USC boiler is the weakest of the tube bundles, changing the pitch of the streamwise direction of Tube 2 is one method to reduce the highest stress in superheater tube bundles in the USC boiler.

  4. 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.

  5. Stress in titania nanoparticles: An atomistic study

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-24

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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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...

  16. Semiflexible Biopolymers in Bundled Arrangements

    Directory of Open Access Journals (Sweden)

    Jörg Schnauß

    2016-07-01

    Full Text Available Bundles and networks of semiflexible biopolymers are key elements in cells, lending them mechanical integrity while also enabling dynamic functions. Networks have been the subject of many studies, revealing a variety of fundamental characteristics often determined via bulk measurements. Although bundles are equally important in biological systems, they have garnered much less scientific attention since they have to be probed on the mesoscopic scale. Here, we review theoretical as well as experimental approaches, which mainly employ the naturally occurring biopolymer actin, to highlight the principles behind these structures on the single bundle level.

  17. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-23

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

  19. 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.

  20. 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

  1. 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.

  2. Bundling ecosystem services in Denmark

    DEFF Research Database (Denmark)

    Turner, Katrine Grace; Odgaard, Mette Vestergaard; Bøcher, Peder Klith;

    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...

  3. 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...

  4. 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

  5. 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.

  6. 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...

  7. 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

  8. 基于接触耦合算法的捆绑火箭接头仿真分析%Joint simulation analysis of bundled carrier rocket based on contact couplling algorithm

    Institute of Scientific and Technical Information of China (English)

    黄海峰; 万小朋; 赵美英

    2011-01-01

    针对捆绑火箭主接头受力特点提出一种耳片构型方案,根据工程算法进行了初步尺寸设计;基于ANSYS有限元非线性接触算法,设置刚性体和柔性体接触,对刚体添加载荷控制点进行非线性分析:通过有限元仿真分析,证明了较原方案耳片方案不仅安全余度较大,而且结构总重量减轻了犯%,具有工程应用前景.%It gives a scheme of main joint connector according the loading character of bundled roceket,and designs the basic parameter based on project Algorithm,based on ANSYS nonlinear contact algorithm,set contact face between rigid and soft body,then set load control point of the rigid body so as to continue simulation analysis.It proved that the safety redundancy is big enungh,and the structure weight reduce for 32%,the blue print of the project is great.

  9. 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.

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

    Science.gov (United States)

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

    2015-12-10

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

  11. 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)

  12. 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.

  13. Bundle Formation in Biomimetic Hydrogels.

    Science.gov (United States)

    Jaspers, Maarten; Pape, A C H; Voets, Ilja K; Rowan, Alan E; Portale, Giuseppe; Kouwer, Paul H J

    2016-08-01

    Bundling of single polymer chains is a crucial process in the formation of biopolymer network gels that make up the extracellular matrix and the cytoskeleton. This bundled architecture leads to gels with distinctive properties, including a large-pore-size gel formation at very low concentrations and mechanical responsiveness through nonlinear mechanics, properties that are rarely observed in synthetic hydrogels. Using small-angle X-ray scattering (SAXS), we study the bundle formation and hydrogelation process of polyisocyanide gels, a synthetic material that uniquely mimics the structure and mechanics of biogels. We show how the structure of the material changes at the (thermally induced) gelation point and how factors such as concentration and polymer length determine the architecture, and with that, the mechanical properties. The correlation of the gel mechanics and the structural parameters obtained from SAXS experiments is essential in the design of future (synthetic) mimics of biopolymer networks.

  14. 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)

  15. 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)

  16. 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.

  17. 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

  18. 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…

  19. 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.

  20. 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...

  1. 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...

  2. Thermal hydraulics of rod bundles: The effect of eccentricity

    Energy Technology Data Exchange (ETDEWEB)

    Chauhan, Amit K., E-mail: amit_fmlab@yahoo.co.in [Fluid Mechanics Laboratory, Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai 600036 (India); Prasad, B.V.S.S.S., E-mail: prasad@iitm.ac.in [Thermal Turbomachines Laboratory, Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai 600036 (India); Patnaik, B.S.V., E-mail: bsvp@iitm.ac.in [Fluid Mechanics Laboratory, Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai 600036 (India)

    2013-10-15

    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 × 10{sup 5}. 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. 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.

  4. Multiscale Simulations Using Particles

    DEFF Research Database (Denmark)

    Walther, Jens Honore

    We are developing particle methods as a general framework for large scale simulations of discrete and continuous systems in science and engineering. The specific application and research areas include: discrete element simulations of granular flow, smoothed particle hydrodynamics and particle...... 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...

  5. Higher order jet prolongations type gauge natural bundles over vector bundles

    Directory of Open Access Journals (Sweden)

    Jan Kurek

    2004-05-01

    Full Text Available Let $rgeq 3$ and $mgeq 2$ be natural numbers and $E$ be a vector bundle with $m$-dimensional basis. We find all gauge natural bundles ``similar" to the $r$-jet prolongation bundle $J^rE$ of $E$. We also find all gauge natural bundles ``similar" to the vector $r$-tangent bundle $(J^r_{fl}(E,R_0^*$ of $E$.

  6. 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.

  7. 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

  8. 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...

  9. 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)

  10. 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)

  11. Atomistic modeling of H absorption in Pd nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-04-16

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2015-02-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-21

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

  15. 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

  16. 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.

  17. 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.

  18. 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...

  19. 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

  20. 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...

  1. General frame structures on quantum principal bundles

    CERN Document Server

    Durdevic, M

    1996-01-01

    A noncommutative-geometric generalization of the classical formalism of frame bundles is developed, incorporating into the theory of quantum principal bundles the concept of the Levi-Civita connection. The construction of a natural differential calculus on quantum principal frame bundles is presented, including the construction of the associated differential calculus on the structure group. General torsion operators are defined and analyzed. Illustrative examples are presented.

  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. Parallel transport on principal bundles over stacks

    Science.gov (United States)

    Collier, Brian; Lerman, Eugene; Wolbert, Seth

    2016-09-01

    In this paper we introduce a notion of parallel transport for principal bundles with connections over differentiable stacks. We show that principal bundles with connections over stacks can be recovered from their parallel transport thereby extending the results of Barrett, Caetano and Picken, and Schreiber and Waldorf from manifolds to stacks. In the process of proving our main result we simplify Schreiber and Waldorf's original definition of a transport functor for principal bundles with connections over manifolds and provide a more direct proof of the correspondence between principal bundles with connections and transport functors.

  5. 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)

  6. 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.

  7. Jacobi Structures on Affine Bundles

    Institute of Scientific and Technical Information of China (English)

    J. GRABOWSKI; D. IGLESIAS; J. C. MARRERO; E. PADR(O)N; P. URBA(N)SKI

    2007-01-01

    We study affine Jacobi structures (brackets) on an affine bundle π: A→M, i.e. Jacobi brackets that close on affine functions. We prove that if the rank of A is non-zero, there is a one-to- one correspondence between affine Jacobi structures on A and Lie algebroid structures on the vector bundle A+=∪p∈M Aff(Ap, R) of affine functionals. In the case rank A = 0, it is shown that there is a one-to-one correspondence between affins Jacobi structures on A and local Lie algebras on A+. Some examples and applications, also for the linear case, are discussed. For a special type of affine Jacobi structures which are canonically exhibited (strongly-affine or affine-homogeneous Jacobi structures) over a real vector space of finite dimension, we describe the leaves of its characteristic foliation as the orbits of an affine representation. These afline Jacobi structures can be viewed as an analog of the Kostant-Arnold-LiouviUe linear Poisson structure on the dual space of a real finite-dimensional Lie algebra.

  8. 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...

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. Anatomic Double-bundle ACL Reconstruction

    NARCIS (Netherlands)

    V.M. Schreiber; C.F. van Eck; F.H. Fu

    2010-01-01

    Rupture of the anterior cruciate ligament (ACL) is one of the most frequent forms of knee trauma. The traditional surgical treatment for ACL rupture is single-bundle reconstruction. However, during the past few years there has been a shift in interest toward double-bundle reconstruction to closely r

  15. 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.

  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. Fock modules and noncommutative line bundles

    Science.gov (United States)

    Landi, Giovanni

    2016-09-01

    To a line bundle over a noncommutative space there is naturally associated a Fock module. The algebra of corresponding creation and annihilation operators is the total space algebra of a principal U(1) -bundle over the noncommutative space. We describe the general construction and illustrate it with examples.

  18. Damping Properties of the Hair Bundle

    Science.gov (United States)

    Baumgart, Johannes; Kozlov, Andrei S.; Risler, Thomas; Hudspeth, A. J.

    2011-11-01

    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 between the individual stereocilia. The investigation revealed that grouping stereocilia in a bundle dramatically reduces the total drag. During hair-bundle deflections, the tip links potentially induce drag by causing small but very dissipative relative motions between stereocilia; this effect is offset by the horizontal top connectors that restrain such relative movements at low frequencies. For higher frequencies the coupling liquid is sufficient to assure that the hair bundle moves as a unit with a low total drag. This work reveals the mechanical characteristics originating from hair-bundle morphology and shows quantitatively how a hair bundle is adapted for sensitive mechanotransduction.

  19. Properties of the microcirculation in capillary bundles of rat spinotrapezius muscle fascia

    Science.gov (United States)

    Jacobitz, Frank; Engebrecht, Cheryn; Metzger, Ian; Porterfield, Colin

    2006-11-01

    Properties of the microcirculation in capillary bundles of rat spinotrapezius muscle fascia are investigated using microscope observations, empirical modeling, and numerical simulations. Capillary bundles consist of a network of feeding arterioles, draining venules, and capillary vessels. A dozen samples of muscle fascia tissue were prepared for microscope observation. The chosen method of preparation allows for the long-term preservation of the tissue samples for future studies. Capillary bundles are photographed under a microscope with 40x magnification. From the images, the microvasculature of the tissue samples is reconstructed. It was found, for example, that the distribution of vessel length in a capillary bundle follows a log-normal law. In addition to a statistical analysis of the vessel data, the network topology is used for numerical simulations of the flow in the capillary bundles. The numerical approach uses a sparse-matrix solver and it considers vessel elasticity and blood rheology. The numerical simulations show, for example, a strong pressure drop across the capillary vessels of the bundle.

  20. Line bundle embeddings for heterotic theories

    Energy Technology Data Exchange (ETDEWEB)

    Groot Nibbelink, Stefan [Muenchen Univ. (Germany). Arnold Sommerfeld Center for Theoretical Physics; Ruehle, Fabian [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2016-03-15

    In heterotic string theories consistency requires the introduction of a non-trivial vector bundle. This bundle breaks the original ten-dimensional gauge groups E{sub 8} x E{sub 8} or SO(32) for the supersymmetric heterotic string theories and SO(16) x SO(16) for the non-supersymmetric tachyon-free theory to smaller subgroups. A vast number of MSSM-like models have been constructed up to now, most of which describe the vector bundle as a sum of line bundles. However, there are several different ways of describing these line bundles and their embedding in the ten-dimensional gauge group. We recall and extend these different descriptions and explain how they can be translated into each other.

  1. Requirements for disordered actomyosin bundle contractility

    CERN Document Server

    Lenz, Martin

    2011-01-01

    Actomyosin contractility is essential for biological force generation, and is well understood in highly ordered structures such as striated muscle. In vitro experiments have shown that non-sarcomeric bundles comprised only of F-actin and myosin thick filaments can also display contractile behavior, which cannot be described by standard muscle models. Here we investigate the microscopic symmetries underlying this process in large non-sarcomeric bundles with long actin filaments. We prove that contractile behavior requires non-identical motors that generate large enough forces to probe the nonlinear elastic behavior of F-actin. A simple disordered bundle model demonstrates a contraction mechanism based on these assumptions and predicts realistic bundle deformations. Recent experimental observations of F-actin buckling in in vitro contractile bundles support our model.

  2. Double Fell bundles and Spectral triples

    CERN Document Server

    Martins, Rachel A D

    2007-01-01

    As a natural and canonical extension of Kumjian's Fell bundles over groupoids \\cite{fbg}, we give a definition for a double Fell bundle (a double category) over a double groupoid. We show that finite dimensional double category Fell line bundles tensored with their dual with $S^o$-reality satisfy the finite real spectral triples axioms but not necessarily orientability. This means that these product bundles with noncommutative algebras can be regarded as noncommutative compact manifolds more general than real spectral triples as they are not necessarily orientable. By construction, they unify the noncommutative geometry axioms and hence provide an algebraic enveloping structure for finite spectral triples to give the Dirac operator $D$ new algebraic and geometric structures that are otherwise missing in the transition from Fredholm operator to Dirac operator. The Dirac operator in physical applications as a result becomes less ad hoc. The new noncommutative space we present is a complex line bundle over a dou...

  3. Line bundle embeddings for heterotic theories

    CERN Document Server

    Nibbelink, Stefan Groot

    2016-01-01

    In heterotic theories consistency requires the introduction of a non-trivial vector bundle. This bundle breaks the original ten-dimensional gauge groups E_8 x E_8 or SO(32) for the supersymmetric heterotic theories and SO(16) x SO(16) for the non-supersymmetric tachyon-free theory to smaller subgroups. A vast number of MSSM-like models have been constructed up to now, most of which describe the vector bundle as a sum of line bundles. However, there are several different ways of describing these line bundles and their embedding in the ten-dimensional gauge group. We recall and extend these different descriptions and explain how they can be translated into each other.

  4. On Harder–Narasimhan Reductions for Higgs Principal Bundles

    Indian Academy of Sciences (India)

    Arijit Dey; R Parthasarathi

    2005-05-01

    The existence and uniqueness of – reduction for the Higgs principal bundles over nonsingular projective variety is shown. We also extend the notion of – reduction for (, )-bundles and ramified -bundles over a smooth curve.

  5. Unravelling the Effects of Grain Boundary and Chemical Doping on Electron-Hole Recombination in CH3NH3PbI3 Perovskite by Time-Domain Atomistic Simulation.

    Science.gov (United States)

    Long, Run; Liu, Jin; Prezhdo, Oleg V

    2016-03-23

    Advancing organohalide perovskite solar cells requires understanding of carrier dynamics. Electron-hole recombination is a particularly important process because it constitutes a major pathway of energy and current losses. Grain boundaries (GBs) are common in methylammonium lead iodine CH3NH3PbI3 (MAPbI3) perovskite polycrystalline films. First-principles calculations have suggested that GBs have little effect on the recombination; however, experiments defy this prediction. Using nonadiabatic (NA) molecular dynamics combined with time-domain density functional theory, we show that GBs notably accelerate the electron-hole recombination in MAPbI3. First, GBs enhance the electron-phonon NA coupling by localizing and contributing to the electron and hole wave functions and by creating additional phonon modes that couple to the electronic degrees of freedom. Second, GBs decrease the MAPbI3 bandgap, reducing the number of vibrational quanta needed to accommodate the electronic energy loss. Third, the phonon-induced loss of electronic coherence remains largely unchanged and not accelerated, as one may expect from increased electron-phonon coupling. Further, replacing iodines by chlorines at GBs reduces the electron-hole recombination. By pushing the highest occupied molecular orbital (HOMO) density away from the boundary, chlorines restore the NA coupling close to the value observed in pristine MAPbI3. By introducing higher-frequency phonons and increasing fluctuation of the electronic gap, chlorines shorten electronic coherence. Both factors compete successfully with the reduced bandgap relative to pristine MAPbI3 and favor long excited-state lifetimes. The simulations show excellent agreement with experiment and characterize how GBs and chlorine dopants affect electron-hole recombination in perovskite solar cells. The simulations suggest a route to increased photon-to-electron conversion efficiencies through rational GB passivation. PMID:26930494

  6. Atomistic study of the buckling of gold nanowires

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-06-15

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

  7. Prioritary omalous bundles on Hirzebruch surfaces

    Science.gov (United States)

    Aprodu, Marian; Marchitan, Marius

    2016-01-01

    An irreducible algebraic stack is called unirational if there exists a surjective morphism, representable by algebraic spaces, from a rational variety to an open substack. We prove unirationality of the stack of prioritary omalous bundles on Hirzebruch surfaces, which implies also the unirationality of the moduli space of omalous H-stable bundles for any ample line bundle H on a Hirzebruch surface (compare with Costa and Miro-Ŕoig, 2002). To this end, we find an explicit description of the duals of omalous rank-two bundles with a vanishing condition in terms of monads. Since these bundles are prioritary, we conclude that the stack of prioritary omalous bundles on a Hirzebruch surface different from P1 ×P1 is dominated by an irreducible section of a Segre variety, and this linear section is rational (Ionescu, 2015). In the case of the space quadric, the stack has been explicitly described by N. Buchdahl. As a main tool we use Buchdahl's Beilinson-type spectral sequence. Monad descriptions of omalous bundles on hypersurfaces in P4, Calabi-Yau complete intersection, blowups of the projective plane and Segre varieties have been recently obtained by A.A. Henni and M. Jardim (Henni and Jardim, 2013), and monads on Hirzebruch surfaces have been applied in a different context in Bartocci et al. (2015).

  8. Singular hermitian metrics on vector bundles

    CERN Document Server

    De Cataldo, M A A

    1997-01-01

    We introduce a notion of singular hermitian metrics (s.h.m.) for holomorphic vector bundles and define positivity in view of $L^2$-estimates. Associated with a suitably positive s.h.m. there is a (coherent) sheaf 0-th kernel of a certain $d''$-complex. We prove a vanishing theorem for the cohomology of this sheaf. All this generalizes to the case of higher rank known results of Nadel for the case of line bundles. We introduce a new semi-positivity notion, $t$-nefness, for vector bundles, establish some of its basic properties and prove that on curves it coincides with ordinary nefness. We particularize the results on s.h.m. to the case of vector bundles of the form $E=F \\otimes L$, where $F$ is a $t$-nef vector bundle and $L$ is a positive (in the sense of currents) line bundle. As applications we generalize to the higher rank case 1) Kawamata-Viehweg Vanishing Theorem, 2) the effective results concerning the global generation of jets for the adjoint to powers of ample line bundles, and 3) Matsusaka Big Theor...

  9. Deformations of the generalised Picard bundle

    International Nuclear Information System (INIS)

    Let X be a nonsingular algebraic curve of genus g ≥ 3, and let Mξ denote the moduli space of stable vector bundles of rank n ≥ 2 and degree d with fixed determinant ξ over X such that n and d are coprime. We assume that if g = 3 then n ≥ 4 and if g = 4 then n ≥ 3, and suppose further that n0, d0 are integers such that n0 ≥ 1 and nd0 + n0d > nn0(2g - 2). Let E be a semistable vector bundle over X of rank n0 and degree d0. The generalised Picard bundle Wξ(E) is by definition the vector bundle over Mξ defined by the direct image pMξ *(Uξ x pX*E) where Uξ is a universal vector bundle over X x Mξ. We obtain an inversion formula allowing us to recover E from Wξ(E) and show that the space of infinitesimal deformations of Wξ(E) is isomorphic to H1(X, End(E)). This construction gives a locally complete family of vector bundles over Mξ parametrised by the moduli space M(n0,d0) of stable bundles of rank n0 and degree d0 over X. If (n0,d0) = 1 and Wξ(E) is stable for all E is an element of M(n0,d0), the construction determines an isomorphism from M(n0,d0) to a connected component M0 of a moduli space of stable sheaves over Mξ. This applies in particular when n0 = 1, in which case M0 is isomorphic to the Jacobian J of X as a polarised variety. The paper as a whole is a generalisation of results of Kempf and Mukai on Picard bundles over J, and is also related to a paper of Tyurin on the geometry of moduli of vector bundles. (author)

  10. Geometry of quantum principal bundles, 1

    CERN Document Server

    Durdevic, M

    1995-01-01

    A theory of principal bundles possessing quantum structure groups and classical base manifolds is presented. Structural analysis of such quantum principal bundles is performed. A differential calculus is constructed, combining differential forms on the base manifold with an appropriate differential calculus on the structure quantum group. Relations between the calculus on the group and the calculus on the bundle are investigated. A concept of (pseudo)tensoriality is formulated. The formalism of connections is developed. In particular, operators of horizontal projection, covariant derivative and curvature are constructed and analyzed. Generalizations of the first structure equation and of the Bianchi identity are found. Illustrative examples are presented.

  11. Weak equivalence classes of complex vector bundles

    OpenAIRE

    Hông-Vân Lê

    2006-01-01

    For any complex vector bundle Ek of rank k over a manifold Mm with Chern classes ci Î H2i(Mm, Z) and any non-negative integers l1, . . ., lk we show the existence of a positive number p(m, k) and the existence of a complex vector bundle Êk over Mm whose Chern classes are p(m, k) × li × ci Î H2i(Mm, Z). We also discuss a version of this statement for holomorphic vector bundles over projective algebraic manifolds.

  12. Vector supersymmetry in the universal bundle

    International Nuclear Information System (INIS)

    We present a vector supersymmetry for Witten-type topological gauge theories, and examine its algebra in terms of a superconnection formalism. When covariant constraints on the supercurvature are chosen, a correspondence is established with the universal bundle construction of Atiyah and Singer. The vector supersymmetry represents a certain shift operator in the curvature of the universal bundle, and can be used to generate the hierarchy of observables in these theories. This formalism should lead to the construction of vector supergravity theories, and perhaps to the gravitational analogue of the universal bundle. (orig.)

  13. Atomistic Method Applied to Computational Modeling of Surface Alloys

    Science.gov (United States)

    Bozzolo, Guillermo H.; Abel, Phillip B.

    2000-01-01

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

  14. Continuum simulations of water flow past fullerene molecules

    DEFF Research Database (Denmark)

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

    2015-01-01

    as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow...

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

    Directory of Open Access Journals (Sweden)

    M. W. Roberts

    2010-01-01

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

  16. Effect of Testing Conditions on Fibre-Bundle Tensile Properties Part Ⅰ: Sample Preparation, Bundle Mass and Fibre Alignment of Wool Bundles

    Institute of Scientific and Technical Information of China (English)

    YU Wei-dong; YAN Hao-jing; Ron Postle; Yang Shouren

    2002-01-01

    Due to the effects of samples and testing conditions on fibre-bundle tensile behaviour, it is necessary to investigate the relationships between experimental factors and tensile properties for the fibre-bumdle tensile tester (TENSOR). The effects of bundle sample preparation, fibre bundle mass and fibre alignment have been tested. The experimental results indicated that (1) the low damage in combing and no free-end fibres in the cut bundle are most important for the sample preparation; (2) the reasonable bundle mass is 400- 700tex, but the tensile properties measured should bemodified with the bundle mass because a small amount of bundle mass causes the scatter results, while the larger is the bundle mass, the more difficult to comb fibres parallel and to clamp fibre evenly; and (3) the fibre irregular arrangement forms a slack bundle resulting in interaction between fibres, which will affect the reproducibility and accuracy of the tensile testing.

  17. Mobility of Taxol in Microtubule Bundles

    Science.gov (United States)

    Ross, J.

    2003-06-01

    Mobility of taxol inside microtubules was investigated using fluorescence recovery after photobleaching (FRAP) on flow-aligned bundles. Bundles were made of microtubules with either GMPCPP or GTP at the exchangeable site on the tubulin dimer. Recovery times were sensitive to bundle thickness and packing, indicating that taxol molecules are able to move laterally through the bundle. The density of open binding sites along a microtubule was varied by controlling the concentration of taxol in solution for GMPCPP samples. With > 63% sites occupied, recovery times were independent of taxol concentration and, therefore, inversely proportional to the microscopic dissociation rate, k_{off}. It was found that 10*k_{off} (GMPCPP) ~ k_{off} (GTP), consistent with, but not fully accounting for, the difference in equilibrium constants for taxol on GMPCPP and GTP microtubules. With taxol along the microtubule interior is hindered by rebinding events when open sites are within ~7 nm of each other.

  18. Quantum Bundle Description of Quantum Projective Spaces

    Science.gov (United States)

    Ó Buachalla, Réamonn

    2012-12-01

    We realise Heckenberger and Kolb's canonical calculus on quantum projective ( N - 1)-space C q [ C p N-1] as the restriction of a distinguished quotient of the standard bicovariant calculus for the quantum special unitary group C q [ SU N ]. We introduce a calculus on the quantum sphere C q [ S 2 N-1] in the same way. With respect to these choices of calculi, we present C q [ C p N-1] as the base space of two different quantum principal bundles, one with total space C q [ SU N ], and the other with total space C q [ S 2 N-1]. We go on to give C q [ C p N-1] the structure of a quantum framed manifold. More specifically, we describe the module of one-forms of Heckenberger and Kolb's calculus as an associated vector bundle to the principal bundle with total space C q [ SU N ]. Finally, we construct strong connections for both bundles.

  19. A Geometric Approach to Noncommutative Principal Bundles

    CERN Document Server

    Wagner, Stefan

    2011-01-01

    From a geometrical point of view it is, so far, not sufficiently well understood what should be a "noncommutative principal bundle". Still, there is a well-developed abstract algebraic approach using the theory of Hopf algebras. An important handicap of this approach is the ignorance of topological and geometrical aspects. The aim of this thesis is to develop a geometrically oriented approach to the noncommutative geometry of principal bundles based on dynamical systems and the representation theory of the corresponding transformation group.

  20. Parahoric bundles on a compact Riemann surface

    CERN Document Server

    Balaji, V

    2010-01-01

    Let $X$ be a compact Riemann surface of genus $g \\geq 2$. The aim of this paper is to study homomorphisms of certain discrete subgroups of $PSL(2, {\\mathbb R})$ into maximal compact subgroups of semisimple simply connected algebraic groups and relate them to torsors under a Bruhat-Tits group scheme. We also construct the moduli spaces of semistable parahoric bundles. These results generalize the theorem of Mehta and Seshadri on parabolic vector bundles.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-10-15

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

  2. Comparison of atomistic and elasticity approaches for carbon diffusion near line defects in α-iron

    International Nuclear Information System (INIS)

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

  3. Annular burnout data from rod bundle experiments

    International Nuclear Information System (INIS)

    Burnout data for annular flow in a rod bundle are presented for both transient and steady-state conditions. Tests were performed at the Oak Ridge National Laboratory in the Thermal Hydraulic Test Facility (THTF), a pressurized-water loop containing an electrically heated 64-rod bundle. The bundle configuration is typical of later generation pressurized-water reactors with 17 x 17 fuel arrays. Both axial and radial power profiles are flat. All experiments were carried out in upflow with subcooled inlet conditions, insuring accurate flow measurement. Conditions within the bundle were typical of those which could be encountered during a nuclear reactor loss-of-coolant accident. Level average fluid conditions within the test section were calculated using steady-state mass and energy conservation considerations for the steady-state tests and a transient, homogeneous, equilibrium computer code for the transient tests. Unlike tube dryout, burnout within a rod bundle does not necessarily occur at one distinct axial level. The location of individual rod dryout was determined by scanning rods axially and locating the position where rod superheat increased from approx. =0 to 30 K or greater. Thermocouple instrumentation within the bundle allows the location of dryout to be determined to within approximately +.5 cm for many of the tests

  4. HLM fuel pin bundle experiments in the CIRCE pool facility

    Energy Technology Data Exchange (ETDEWEB)

    Martelli, Daniele, E-mail: daniele.martelli@ing.unipi.it [University of Pisa, Department of Civil and Industrial Engineering, Pisa (Italy); Forgione, Nicola [University of Pisa, Department of Civil and Industrial Engineering, Pisa (Italy); Di Piazza, Ivan; Tarantino, Mariano [Italian National Agency for New Technologies, Energy and Sustainable Economic Development, C.R. ENEA Brasimone (Italy)

    2015-10-15

    Highlights: • The experimental results represent the first set of values for LBE pool facility. • Heat transfer is investigated for a 37-pin electrical bundle cooled by LBE. • Experimental data are presented together with a detailed error analysis. • Nu is computed as a function of the Pe and compared with correlations. • Experimental Nu is about 25% lower than Nu derived from correlations. - Abstract: Since Lead-cooled Fast Reactors (LFR) have been conceptualized in the frame of GEN IV International Forum (GIF), great interest has focused on the development and testing of new technologies related to HLM nuclear reactors. In this frame the Integral Circulation Experiment (ICE) test section has been installed into the CIRCE pool facility and suitable experiments have been carried out aiming to fully investigate the heat transfer phenomena in grid spaced fuel pin bundles providing experimental data in support of European fast reactor development. In particular, the fuel pin bundle simulator (FPS) cooled by lead bismuth eutectic (LBE), has been conceived with a thermal power of about 1 MW and a uniform linear power up to 25 kW/m, relevant values for a LFR. It consists of 37 fuel pins (electrically simulated) placed on a hexagonal lattice with a pitch to diameter ratio of 1.8. The FPS was deeply instrumented by several thermocouples. In particular, two sections of the FPS were instrumented in order to evaluate the heat transfer coefficient along the bundle as well as the cladding temperature in different ranks of sub-channels. Nusselt number in the central sub-channel was therefore calculated as a function of the Peclet number and the obtained results were compared to Nusselt numbers obtained from convective heat transfer correlations available in literature on Heavy Liquid Metals (HLM). Results reported in the present work, represent the first set of experimental data concerning fuel pin bundle behaviour in a heavy liquid metal pool, both in forced and

  5. Total evaluation of in bundle void fraction measurement test of PWR fuel assembly

    International Nuclear Information System (INIS)

    Nuclear Power Engineering Corporation is performing the various proof or verification tests on safety and reliability of nuclear power plants under the sponsorship of the Ministry of International Trade and Industry. As one program of these Japanese national projects, an in bundle void fraction measurement test of a pressurized water reactor (PWR) fuel assembly was started in 1987 and finished at the end of 1994. The experiments were performed using the 5 x 5 square array rod bundle test sections. The rod bundle test section simulates the partial section and full length of a 17 x 17 type Japanese PWR fuel assembly. A distribution of subchannel averaged void fraction in a rod bundle test section was measured by the gamma-ray attenuation method using the stationary multi beam systems. The additional single channel test was performed to obtain the required information for the calibration of the rod bundle test data and the assessment of the void prediction method. Three test rod bundles were prepared to analyze an axial power distribution effect, an unheated rod effect, and a grid spacer effect. And, the obtained data were used for the assessment of the void prediction method relevant to the subchannel averaged void fraction of PWR fuel assemblies. This paper describes the outline of the experiments, the evaluation of the experimental data and the assessment of void prediction method

  6. Design and fabrication of remote welding system for the fuel bundle assembly

    Energy Technology Data Exchange (ETDEWEB)

    Kim, S.S.; Lee, J.W.; Park, G.I. [Korea Atomic Energy Research Inst., Daejeon (Korea, Republic of)

    2011-07-01

    Remote fuel bundle welding equipment in a hot-cell was designed and fabricated. To achieve this, a preliminary investigation of hands-on fuel fabrication outside a hot-cell was conducted with a consideration of the constraints caused by welding in a hot-cell. Some basic experiments were also carried out to improve the end-plate welding process for fuel bundle fabrication. The resistance welding equipment using end-plate welding was also improved. It was found that resistance welding was more suitable for joining an end-plate to end caps in a 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 fabrication. The greatest advantage of fuel bundle welding equipment would be a commercialized welding process in which there is extensive production experience. This paper presents an outline of the developed welding equipment for a fuel bundle fabrication and reviews the conceptual design of remote welding equipment using a master-slave manipulator. The design of the remote welding equipment using the Pro-Engineer method was also reviewed. Furthermore the mechanical considerations and a mock-up simulation test were described. Finally, its performance test results were presented for a mock-up of remote fuel bundle welding equipment. (author)

  7. Study on galloping behavior of iced eight bundle conductor transmission lines

    Science.gov (United States)

    Zhou, Linshu; Yan, Bo; Zhang, Liang; Zhou, Song

    2016-02-01

    Wind tunnel test was carried out to obtain the aerodynamic coefficients of an eight bundle conductor accreted with crescent-shaped ice. A user-defined cable element with torsional degree of freedom is developed in ABAQUS software to capture the torsional deformation of the iced conductors during galloping. By means of the user-defined cable element, different damping ratios in in-plane, out-of-plane and torsional directions of the conductors can be defined and the aerodynamic forces varying with their motion status can be exerted on the conductors conveniently when ABAQUS is used to simulate galloping of transmission lines. A wind tunnel test to model galloping of an iced eight bundle conductor segment was carried out, and the validity of the numerical simulation method is demonstrated by the agreement of the galloping orbit of the bundle conductor segment model recorded in the test and that by the numerical simulation. Furthermore, galloping behavior, including dynamic responses, galloping orbits, frequencies, vibration modes and amplitudes, of typical iced eight bundle conductor transmission lines in the cases of different span lengths, initial tensions in sub-conductors, wind velocities, angles of wind attack and damping ratios is studied, and the galloping behavior of the lines with internal resonance conditions is discussed. The obtained results may provide a fundamental tool for the development of anti-galloping techniques of eight bundle conductor transmission lines.

  8. From NEMO1D and NEMO3D to OMEN: Moving Towards Atomistic 3-D Quantum Transport in Nano-scale Semiconductors

    OpenAIRE

    Klimeck, Gerhard; Luisier, Mathieu

    2008-01-01

    Lessons learned in 15 years of NEMO development starting from quantitative and predictive resonant tunneling diode (RTD) to multi-million atom electronic structure modeling and the path for OMEN are laid out. The recent OMEN capabilities enable realistically large 3D atomistic nano-scale device simulation.

  9. K-Theories for Certain Infinite Rank Bundles

    OpenAIRE

    Larrain-Hubach, Andres

    2011-01-01

    Several authors have recently constructed characteristic classes for classes of infinite rank vector bundles appearing in topology and physics. These include the tangent bundle to the space of maps between closed manifolds, the infinite rank bundles in the families index theorem, and bundles with pseudodifferential operators as structure group. In this paper, we construct the corresponding K-theories for these types of bundles. We develop the formalism of these theories and use their Chern ch...

  10. Effect of left bundle branch block on TIMI frame count

    OpenAIRE

    Hatice Tolunay; Ahmet Kasapkara; İsa Öner Yüksel; Nurcan Başar; Ayşe Saatcı Yaşar; Mehmet Bilge

    2010-01-01

    Aim: Left bundle branch block is an independent risk factorfor cardiac mortality. In this study we aimed to evaluatecoronary blood flow with TIMI frame count in patients with left bundle branch block and angiographically proven normal coronary arteries.Materials and methods: We retrospectively studied 17 patients with left bundle branch block and as a control group 16 patients without left bundle branch block. All patientshad angiographically proven normal coronary arteries.Left bundle branch...

  11. Atomistic Simulation of He Clustering and Defects Produced in Ni

    Institute of Scientific and Technical Information of China (English)

    LIU Ti-Jiang; WANG Yue-Xia; PAN Zheng-Ying; JIANG Xiao-Mei; ZHOU Liang; ZHU Jing

    2006-01-01

    @@ Using the molecular dynamics method, the stability of small He-vacancy clusters is studied under the condition of the high He and low vacancy densities. The result shows that there is a competition between He atoms detrapped and self-interstitial atoms (SIAs) emitted during the clustering of He atoms. When the He number is above a critical value of 9, the SIA emission is predominant. The SIA emission can result in deep capture of He atoms since the binding energy of He to a He-vacancy cluster is increased with the number of SIAs created. The cluster thus grows up. In addition, more SIAs are created when the temperature is elevated. The average volume of a He atom is increased. The cluster expansion takes place at high temperature.

  12. Quantum chemistry and atomistic simulations of solid nitrides

    OpenAIRE

    Eck, Bernhard

    2000-01-01

    The present thesis covers, at first, the binary nitrides of the the 3d transition metals. Based on their electronic band structures and bonding analyses for the sodium chloride as well as the zinc blend structure type it is then determined why the early nitrides crystallize in the NaCl structure while Fe- and Co-nitride adopt the ZnS structure. Thereafter all stoichiometrically well-defined iron nitrides are theoretically investigated, in particular with respect to the influence of the nitrog...

  13. Atomistic simulation of defect structure in ternary intermetallics

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-08-01

    Interatomic potentials of the Embedded Atom type were used to study defect structure in ternary intermetallics. Interatomic potentials with appropriate inner consistency were developed for the modeling of ternary systems. Alloys were considered in the Nb-Al-Ti and in the Ni-Al-Ti systems. The stability of ternary phases in these systems was studied, particularly the B2 phase in Nb rich alloys of the Nb-Al-Ti system. The effects of increasing Ti additions in these alloys were studied, as well as the APB energies in these ternary alloys.

  14. Atomistic simulations of methane interactions with an atmospheric moisture.

    Science.gov (United States)

    Galashev, Alexander Y

    2013-09-28

    Methane is an extremely effective absorber of radiation, i.e., it is a relatively potent greenhouse gas, and the increased concentration of methane in the atmosphere must influence earth's radiation balance. The adsorption of one to six methane molecules by water clusters is studied by the method of molecular dynamics under near-atmospheric conditions. The capture of methane molecules by water clusters produces an increase in the integrated intensity of IR absorbance and the reflection coefficient. The Raman spectrum of the system is considerably depleted due to the addition of methane molecules to the disperse water system. The observed emission power of a dispersed aqueous system with adsorbed methane molecules has appreciably increased relative to the analogous characteristics of the pure water cluster system. The Voronoi polyhedra and simplified ones constructed within the framework of molecular-dynamic model of clusters are used for the analysis of the structure changes occurring with increasing the number of adsorbed CH4 molecules. PMID:24089763

  15. Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks.

    Science.gov (United States)

    Zhang, Haiyang; Lv, Yongqin; Tan, Tianwei; van der Spoel, David

    2016-01-28

    Fabrication of metal-organic frameworks (MOFs) with large apertures triggers a brand-new research area for selective encapsulation of biomolecules within MOF nanopores. The underlying inclusion mechanism is yet to be clarified however. Here we report a molecular dynamics study on the mechanism of protein encapsulation in MOFs. Evaluation for the binding of amino acid side chain analogues reveals that van der Waals interaction is the main driving force for the binding and that guest size acts as a key factor predicting protein binding with MOFs. Analysis on the conformation and thermodynamic stability of the miniprotein Trp-cage encapsulated in a series of MOFs with varying pore apertures and surface chemistries indicates that protein encapsulation can be achieved via maintaining a polar/nonpolar balance in the MOF surface through tunable modification of organic linkers and Mg-O chelating moieties. Such modifications endow MOFs with a more biocompatible confinement. This work provides guidelines for selective inclusion of biomolecules within MOFs and facilitates MOF functions as a new class of host materials and molecular chaperones. PMID:26730607

  16. Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks.

    Science.gov (United States)

    Zhang, Haiyang; Lv, Yongqin; Tan, Tianwei; van der Spoel, David

    2016-01-28

    Fabrication of metal-organic frameworks (MOFs) with large apertures triggers a brand-new research area for selective encapsulation of biomolecules within MOF nanopores. The underlying inclusion mechanism is yet to be clarified however. Here we report a molecular dynamics study on the mechanism of protein encapsulation in MOFs. Evaluation for the binding of amino acid side chain analogues reveals that van der Waals interaction is the main driving force for the binding and that guest size acts as a key factor predicting protein binding with MOFs. Analysis on the conformation and thermodynamic stability of the miniprotein Trp-cage encapsulated in a series of MOFs with varying pore apertures and surface chemistries indicates that protein encapsulation can be achieved via maintaining a polar/nonpolar balance in the MOF surface through tunable modification of organic linkers and Mg-O chelating moieties. Such modifications endow MOFs with a more biocompatible confinement. This work provides guidelines for selective inclusion of biomolecules within MOFs and facilitates MOF functions as a new class of host materials and molecular chaperones.

  17. Nonlinear dynamics of bi-layered graphene sheet, double-walled carbon nanotube and nanotube bundle

    Science.gov (United States)

    Gajbhiye, Sachin O.; Singh, S. P.

    2016-05-01

    Due to strong van der Waals (vdW) interactions, the graphene sheets and nanotubes stick to each other and form clusters of these corresponding nanostructures, viz. bi-layered graphene sheet (BLGS), double-walled carbon nanotube (DWCNT) and nanotube bundle (NB) or ropes. This research work is concerned with the study of nonlinear dynamics of BLGS, DWCNT and NB due to nonlinear interlayer vdW forces using multiscale atomistic finite element method. The energy between two adjacent carbon atoms is represented by the multibody interatomic Tersoff-Brenner potential, whereas the nonlinear interlayer vdW forces are represented by Lennard-Jones 6-12 potential function. The equivalent nonlinear material model of carbon-carbon bond is used to model it based on its force-deflection relation. Newmark's algorithm is used to solve the nonlinear matrix equation governing the motion of the BLGS, DWCNT and NB. An impulse and harmonic excitations are used to excite these nanostructures under cantilevered, bridged and clamped boundary conditions. The frequency responses of these nanostructures are computed, and the dominant resonant frequencies are identified. Along with the forced vibration of these structures, the eigenvalue extraction problem of armchair and zigzag NB is also considered. The natural frequencies and corresponding mode shapes are extracted for the different length and boundary conditions of the nanotube bundle.

  18. Atomistic theory of transport in organic and inorganic nanostructures

    International Nuclear Information System (INIS)

    As the size of modern electronic and optoelectronic devices is scaling down at a steady pace, atomistic simulations become necessary for an accurate modelling of their structural, electronic, optical and transport properties. Such microscopic approaches are important in order to account correctly for quantum-mechanical phenomena affecting both electronic and transport properties of nanodevices. Effective bulk parameters cannot be used for the description of the electronic states since interfacial properties play a crucial role and semiclassical methods for transport calculations are not suitable at the typical scales where the device behaviour is characterized by coherent tunnelling. Quantum-mechanical computations with atomic resolution can be achieved using localized basis sets for the description of the system Hamiltonian. Such methods have been extensively used to predict optical and electronic properties of molecules and mesoscopic systems. The most important approaches formulated in terms of localized basis sets, from empirical tight-binding (TB) to first principles methods, are here reviewed. Being a full band approach, even the simplest TB overcomes the limitations of envelope function approximations, such as the well-known k · p, and allows to retain atomic details and realistic band structures. First principles calculations, on the other hand, can give a very accurate description of the electronic and structural properties. Transport in nanoscale devices cannot neglect quantum effects such as coherent tunnelling. In this context, localized basis sets are well-suited for the formal treatment of quantum transport since they provide a simple mathematical framework to treat open-boundary conditions, typically encountered when the system eigenstates carry a steady-state current. We review the principal methods used to formulate quantum transport based on local orbital sets via transfer matrix and Green's function (GF) techniques. We start from a general

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

    Directory of Open Access Journals (Sweden)

    Ramon Reigada

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2014-04-15

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

  2. Electrostatically actuated oscillator of bundle and double-walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Jeong Won; Song, Ki Oh; Hwang, Ho Jung [Chung-Ang University, Seoul (Korea, Republic of); Lee, Jun Ha; Lee, Hoong Joo [Sangmyung University, Chonan (Korea, Republic of); Kwon, Oh Keun [Semyung University, Jecheon (Korea, Republic of); Yoon, Young Sik; Song, Young Jin [Konyang University, Nonsan (Korea, Republic of)

    2006-03-15

    Schematics of capacitively driven carbon nanotube (CNT) oscillators were presented and investigated by using classical molecular dynamics simulations. While the capacitive force acting on a CNT oscillator extruded it, the force exerted by the excess van der Waals energy sucked the CNT oscillator into the bundle or outer shell. The CNT oscillator could be oscillated by using both the Coulomb and the van der Waals interactions. The van der Waals force of the bundle-type CNT oscillator was less than the van der Waals force of the double-walled CNT oscillator. Molecular dynamics simulation results showed that double-walled CNT oscillators were better than bundle-type CNT oscillators in the aspects of both energy dissipation and stable operation.

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

    CERN Document Server

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

    2015-01-01

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

  4. Twistor bundle theory and its application

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    Over an oriented even dimensional Riemannian manifold (M2m, ds2), in terms of the Levi-Civita connection form Ω and the canonical form Θ on the bundle of positive or→ J+(M, ds2) → M. The integrability on an almost complex structure J compatible with the metric and the orientation, is shown to be equivalent to the fact that the corresponding cross section of the twistor bundle is holomorphic with respect to J and the canonical almost complex structure J1 on J+(M, ds2), by using moving frame theory. Moreover, for various metrics and a fixed orientation on M, a canonical bundle isomorphism is established. As a consequence, we generalize a celebrated theorem of LeBrun.

  5. Tangent bundle formulation of a charged gas

    CERN Document Server

    Sarbach, Olivier

    2013-01-01

    We discuss the relativistic kinetic theory for a simple, collisionless, charged gas propagating on an arbitrary curved spacetime geometry. Our general relativistic treatment is formulated on the tangent bundle of the spacetime manifold and takes advantage of its rich geometric structure. In particular, we point out the existence of a natural metric on the tangent bundle and illustrate its role for the development of the relativistic kinetic theory. This metric, combined with the electromagnetic field of the spacetime, yields an appropriate symplectic form on the tangent bundle. The Liouville vector field arises as the Hamiltonian vector field of a natural Hamiltonian. The latter also defines natural energy surfaces, called mass shells, which turn out to be smooth Lorentzian submanifolds. A simple, collisionless, charged gas is described by a distribution function which is defined on the mass shell and satisfies the Liouville equation. Suitable fibre integrals of the distribution function define observable fie...

  6. Porous Silicon and Denim Fiber Bundle Characterization

    Science.gov (United States)

    Deuro, Randi Ellen

    My thesis research aims to characterize and exploit materials in an efficient, rapid, non-destructive manner. Part I of this document summarizes my research on porous silicon (pSi) design, fabrication, and surface modification for use as a novel chemical sensor. The optimization of fabrication process parameters (etching time, etching solution, electrode shape, and the fixing process) on pSi photoluminescence (PL) is presented. I have also investigated the effects of analyte vapors (acetonitrile, toluene, methanol, acetone) on the pSi PL and surface chemistry using luminescence and Fourier-transform infrared (FT-IR) spectroscopy and microscopy methods. The mechanism and benefits of one method of pSi surface modification and protection (ultraviolet (UV) hydrosilylation) will also be presented. Finally, high thorough-put methods of pSi sensor production are described. In Part II of this document, I introduce a novel technique for analyzing and discriminating among denim fiber bundles. An investigation into the benefits of luminescence-based multispectral imaging (LMSI) for denim fiber bundle identification has been conducted. I explore the power of nitromethane (CH 3NO2) based quenching in fiber bundle classification and identify the quenching mechanism. The luminescence spectra (450 - 850 nm) and images from the denim fiber bundles were obtained while exciting at 325 nm or 405 nm. Here, LMSI data were recorded in < 10 s and subsequently assessed by principal component analysis (PCA) and rendered red, green, blue (RGB) component histograms. The results show that LMSI data can be used to rapidly and uniquely classify all the fiber bundle types studied in this research. These non-destructive techniques eliminate extensive sample preparation and allow for rapid multispectral image collection, analysis, and assessment. The quenching data also revealed that the dye molecules within the individual fiber bundles exhibited dramatically different accessibilities to CH 3NO2.

  7. Characteristic classes of quantum principal bundles

    CERN Document Server

    Durdevic, M

    1995-01-01

    A noncommutative-geometric generalization of classical Weil theory of characteristic classes is presented, in the conceptual framework of quantum principal bundles. A particular care is given to the case when the bundle does not admit regular connections. A cohomological description of the domain of the Weil homomorphism is given. Relations between universal characteristic classes for the regular and the general case are analyzed. In analogy with classical geometry, a natural spectral sequence is introduced and investigated. The appropriate counterpart of the Chern character is constructed, for structures admitting regular connections. Illustrative examples and constructions are presented.

  8. Are Medicare bundles in your future?

    Science.gov (United States)

    Mulvany, Chad

    2015-08-01

    To ensure they are well-positioned for an expansion by the Centers for Medicare & Medicaid Services of bundled payment, hospitals that are not participants in the Bundled Payments for Care Improvement initiative should take the following steps: Understand which organizations in their markets are already participating and which might participate. Understand care utilization patterns within their care delivery networks and how those patterns affect cost per episode. Identify high-quality, cost-efficient postacute care providers and begin collaborating with them to further improve outcomes. Educate discharging physicians about the impact that choices related to postacute settings have on both beneficiary out-of-pocket obligations and overall cost of care.

  9. A bundle of sticks in my garden

    OpenAIRE

    Farran, Sue

    2012-01-01

    The English law of property is often described as a ‘bundle of sticks’ in which each ‘stick’ represents a particular right. Gardens challenge these rights and wreak havoc on the ‘bundle of sticks’. This paper looks at the twenty-first century manifestations of community engagement with ground and explores how ‘gardening’ is undermining concepts of ownership, possession and management of land and how the fence between what is private and what is public is being encroached and challenged by com...

  10. Bundling in semiflexible polymers: A theoretical overview.

    Science.gov (United States)

    Benetatos, Panayotis; Jho, YongSeok

    2016-06-01

    Supramolecular assemblies of polymers are key modules to sustain the structure of cells and their function. The main elements of these assemblies are charged semiflexible polymers (polyelectrolytes) generally interacting via a long(er)-range repulsion and a short(er)-range attraction. The most common supramolecular structure formed by these polymers is the bundle. In the present paper, we critically review some recent theoretical and computational advances on the problem of bundle formation, and point a few promising directions for future work. PMID:26813628

  11. TRIGA spent fuel bundles safe storage

    International Nuclear Information System (INIS)

    TRIGA-SSR is a steady state research and material test reactor that has been in operation since 1980. The original TRIGA fuel was HEU (highly enriched uranium) with a U235 enrichment of 93 per cent. Almost all TRIGA HEU fuel bundles are now burned-up. Part of the spent fuel was loaded and transferred to US, in a Romania - DOE arrangement. The rest of the TRIGA fuel bundles have to be temporarily stored in the TRIGA facility. As the storage conditions had to be established with caution, neutron and thermal hydraulic evaluations of the storage conditions were required. Some criticality evaluations were made based on the SAR (Safety Analysis Report) data. Fuel constant axial temperature approximation effect is usual for criticality computations. TRIGA-SSR fuel bundle geometry and materials model for SCALE5-CSAS module allows the introduction of a fuel temperature dependency for the entire fuel active height, using different materials for each fuel bundle region. Previous RELAP5 thermal hydraulic computations for an axial and radial power distribution in the TRIGA fuel pin were done. Fuel constant temperature approximation overestimates pin factors for every core operating at high temperatures. From the thermal hydraulic point of view the worst condition of the storage grid occurs when the transfer channel is accidentally emptied of water from the pool, or the bundle is handled accidentally to remain in air. All the residual heat from the bundles has to be removed without fuel overheating and clad failure. RELAP5 computer code for residual heat removal was used in the assessment of residual heat removal. We made a couple of evaluations of TRIGA bundle clad temperatures in air cooling conditions, with different residual heat levels. The criticality computations have shown that the spent TRIGA fuel bundles storage grid is strongly sub-critical with k(eff) = 0.5951. So, there is no danger for a criticality accident for this storage grid type. The assessment is done for

  12. A Comparison between Clinical Results of Selective Bundle and Double Bundle Anterior Cruciate Ligament Reconstruction

    Science.gov (United States)

    Yoo, Yon-Sik; Song, Si Young; Yang, Cheol Jung; Ha, Jong Mun; Kim, Yoon Sang

    2016-01-01

    Purpose The purpose of this study was to compare the clinical outcomes of arthroscopic anatomical double bundle (DB) anterior cruciate ligament (ACL) reconstruction with either selective anteromedial (AM) or posterolateral (PL) bundle reconstruction while preserving a relatively healthy ACL bundle. Materials and Methods The authors evaluated 98 patients with a mean follow-up of 30.8±4.0 months who had undergone DB or selective bundle ACL reconstructions. Of these, 34 cases underwent DB ACL reconstruction (group A), 34 underwent selective AM bundle reconstruction (group B), and 30 underwent selective PL bundle reconstructions (group C). These groups were compared with respect to Lysholm and International Knee Documentation Committee (IKDC) score, side-to-side differences of anterior laxity measured by KT-2000 arthrometer at 30 lbs, and stress radiography and Lachman and pivot shift test results. Pre- and post-operative data were objectively evaluated using a statistical approach. Results The preoperative anterior instability measured by manual stress radiography at 90° of knee flexion in group A was significantly greater than that in groups B and C (all panterior instability measured by KT-2000 arthrometer, pivot shift, or functional scores. Conclusion Selective bundle reconstruction in partial ACL tears offers comparable clinical results to DB reconstruction in complete ACL tears. PMID:27401652

  13. Adsorption site analysis of impurity embedded single-walled carbon nanotube bundles

    Science.gov (United States)

    Agnihotri, S.; Mota, J.P.B.; Rostam-Abadi, M.; Rood, M.J.

    2006-01-01

    Bundle morphology and adsorptive contributions from nanotubes and impurities are studied both experimentally and by simulation using a computer-aided methodology, which employs a small physisorbed probe molecule to explore the porosity of nanotube samples. Grand canonical Monte Carlo simulation of nitrogen adsorption on localized sites of a bundle is carried out to predict adsorption in its accessible internal pore volume and on its external surface as a function of tube diameter. External adsorption is split into the contributions from the clean surface of the outermost nanotubes of the bundle and from the surface of the impurities. The site-specific isotherms are then combined into a global isotherm for a given sample using knowledge of its tube-diameter distribution obtained by Raman spectroscopy. The structural parameters of the sample, such as the fraction of open-ended nanotubes and the contributions from impurities and nanotube bundles to total external surface area, are determined by fitting the experimental nitrogen adsorption data to the simulated isotherm. The degree of closure between experimental and calculated adsorption isotherms for samples manufactured by two different methods, to provide different nanotube morphology and contamination level, further strengthens the validity and resulting interpretations based on the proposed approach. The average number of nanotubes per bundle and average bundle size, within a sample, are also quantified. The proposed method allows for extrapolation of adsorption properties to conditions where the purification process is 100% effective at removing all impurities and opening access to all intrabundle adsorption sites. ?? 2006 Elsevier Ltd. All rights reserved.

  14. The Stochastic Grid Bundling Method :Efficient pricing of Bermudan options and their Greeks

    NARCIS (Netherlands)

    Jain, S.; Oosterlee, C.W.

    2015-01-01

    This paper describes a practical simulation-based algorithm, which we call the Stochastic Grid Bundling Metho d(SGBM) for pricing multdimensional Bermudan (i.e.discretely exercisable) options. The method generates a direct estimator of the option price, an optimal early-exercise policy as well as a

  15. Capillary Micro-flow Through a Fiber Bundle(Part 2)

    Institute of Scientific and Technical Information of China (English)

    ZHU Yingdan; WANG Jihui; TAN Hua; GAO Guoqiang

    2005-01-01

    A numerical model was proposed to simulate the capillary micro-flow through a fiber bundle.The capillary pressure was predicted by the Young-Laplace equation and the corresponding optimal values of permeability were found by a trial-and-error method. The empirical Kozeny constants which are dependent on fiber volume fraction were recommended for the prediction of permeability.

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

    Science.gov (United States)

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

    2013-05-01

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

  17. Impact of bundle deformation on CHF: ASSERT-PV assessment of extended burnup Bruce B bundle G85159W

    International Nuclear Information System (INIS)

    This paper presents a subchannel thermalhydraulic analysis of the effect on critical heat flux (CHF) of bundle deformation such as element bow and diametral creep. The bundle geometry is based on the post-irradiation examination (PIE) data of a single bundle from the Bruce B Nuclear Generating Station, Bruce B bundle G85159W, which was irradiated for more than two years in the core during reactor commissioning. The subchannel code ASSERT-PV IST is used to assess changes in CHF and dryout power due to bundle deformation, compared to the reference, undeformed bundle. (author)

  18. Pool boiling and condensation analysis for a vertical tube bundle condenser

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, W.; Wolf, B., E-mail: zhouw@purdue.edu [Purdue Univ., West Lafayette, Indiana (United States); Revankar, S.T., E-mail: shripad@ecn.purdue.edu [Purdue Univ., West Lafayette, Indiana (United States); POSTECH, Pohang (Korea, Republic of)

    2011-07-01

    An experimental and theoretical study is performed for the steam condensation in a vertical tube bundle passive condenser simulating PCCS condenser in the ESBWR. Four condenser tubes are submerged in a water pool where the heat from the condenser tube is removed through boiling heat transfer. Condenser tubes with a full length/diameter scale are used to obtain the condensation data with various process parameters. The comparison of tube bundle experimental data with the single tube data by both the experiments and models shows that the single tube secondary heat transfer coefficient (HTC) is between 25% - 35% less than what was recorded for the tube bundle, and the tube bundle condensation rates are slightly higher than the data from the single tube test sections due to turbulent mixing effect which increases the condensation heat removal. The turbulent mixing on the secondary side decreases the DT between pool water and condenser tube outer wall, causing an increase in secondary HTC. This increase in secondary HTC thus results in higher condensate mass flow rates. Tube bundle boundary layer model and heat and mass analogy model were then developed for the prediction of the filmwise steam condensation with noncondensable (NC) gas in a vertical tube bundle. The predictions from the models are compared with the experimental data for various complete condensation and through flow conditions and the agreement is satisfactory. The local parameters predicted by the boundary layer model and heat and mass analogy model with tube bundle pool boiling can also be predicted with the axial distance from entrance for different NC gas fractions and system pressures. (author)

  19. Pool boiling and condensation analysis for a vertical tube bundle condenser

    International Nuclear Information System (INIS)

    An experimental and theoretical study is performed for the steam condensation in a vertical tube bundle passive condenser simulating PCCS condenser in the ESBWR. Four condenser tubes are submerged in a water pool where the heat from the condenser tube is removed through boiling heat transfer. Condenser tubes with a full length/diameter scale are used to obtain the condensation data with various process parameters. The comparison of tube bundle experimental data with the single tube data by both the experiments and models shows that the single tube secondary heat transfer coefficient (HTC) is between 25% - 35% less than what was recorded for the tube bundle, and the tube bundle condensation rates are slightly higher than the data from the single tube test sections due to turbulent mixing effect which increases the condensation heat removal. The turbulent mixing on the secondary side decreases the DT between pool water and condenser tube outer wall, causing an increase in secondary HTC. This increase in secondary HTC thus results in higher condensate mass flow rates. Tube bundle boundary layer model and heat and mass analogy model were then developed for the prediction of the filmwise steam condensation with noncondensable (NC) gas in a vertical tube bundle. The predictions from the models are compared with the experimental data for various complete condensation and through flow conditions and the agreement is satisfactory. The local parameters predicted by the boundary layer model and heat and mass analogy model with tube bundle pool boiling can also be predicted with the axial distance from entrance for different NC gas fractions and system pressures. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-13

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

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

    Science.gov (United States)

    Wang, Yong-Lei; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N; Laaksonen, Aatto

    2014-07-24

    We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions. PMID:25020237

  2. Quantum Thermodynamics: Non-equilibrium 3D Description of an Unbounded System at an Atomistic Level

    Directory of Open Access Journals (Sweden)

    Vittorio Verda

    2010-03-01

    Full Text Available Quantum thermodynamics (QT provides a general framework for the description of non-equilibrium phenomena at any level, particularly the atomistic one. This theory and its dynamical postulate are used here to extend the work reported in previous papers of modeling the storage of hydrogen in an isolated system, by extending the modeling to 3D. The system is prepared in a state with the hydrogen molecules initially far from stable equilibrium after which the system is allowed to relax (evolve to a state of stable equilibrium. The so-called energy eigenvalue problem, which entails a many-body problem that for dilute and moderately dense gases can be solved using virial expansion theory, is used to determine the energy eigenvalues and eigenstates of the system. This information is then used in the nonlinear Beretta equation of motion of QT to determine the evolution of the thermodynamic state of the system as well as the spatial distributions of the hydrogen molecules in time. The results of our simulations provide a quantification of the entropy generated due to irreversibilities at an atomistic level and show in detail the trajectory of the state of the system as the hydrogen molecules, which are initially arranged to be far from the carbon nanotube, spread out in the system and eventually become more concentrated near the carbon atoms which make up the nanotube.

  3. Bundle structures of stretching-energy and nonlinear interactions among modes in elastic wave turbulence

    International Nuclear Information System (INIS)

    The real-space dynamics and the nonlinear interactions among Fourier modes in elastic wave turbulence are investigated by simulating the Foppl-von Karman equation. We find that the bundle structures of ridges appear intermittently in the time evolution of the stretching energy field. The time-evolution of the nonlinearity indicates the existence of active and moderate phases in turbulent state. Conditional sampling analysis reveals that the bundle structure, which is the embodiment of the strong nonlinear interactions among modes, induces the energy supply from an external force to the system

  4. The unintended consequences of bundled payments.

    Science.gov (United States)

    Weeks, William B; Rauh, Stephen S; Wadsworth, Eric B; Weinstein, James N

    2013-01-01

    Consensus is building that episode-based bundled payments can produce substantial Medicare savings, and the Center for Medicare & Medicaid Innovation's Bundled Payment Initiative endorses this concept. The program generates potential cost savings by reducing the historic cost of time-defined episodes of care, provided through a discount. Although bundled payments can reduce waste primarily in the postacute care setting, concerns arise that, in an effort to maintain income levels that are necessary to cover fixed costs, providers may change their behaviors to increase the volume of episodes. Such actions would mitigate the savings that Medicare might have accrued and may perpetuate the fee-for-service payment mechanism, with episodes of care becoming the new service. Although bundled payments have some advantages over the current reimbursement system, true cost-savings to Medicare will be realized only when the federal government addresses the use issue that underlies much of the waste inherent in the system and provides ample incentives to eliminate capacity and move toward capitation.

  5. Graph Bundling by Kernel Density Estimation

    NARCIS (Netherlands)

    Hurter, C.; Ersoy, O.; Telea, A.

    2012-01-01

    We present a fast and simple method to compute bundled layouts of general graphs. For this, we first transform a given graph drawing into a density map using kernel density estimation. Next, we apply an image sharpening technique which progressively merges local height maxima by moving the convolved

  6. Optimization of a bundle divertor for FED

    International Nuclear Information System (INIS)

    Optimal double-T bundle divertor configurations have been obtained for the Fusion Engineering Device (FED). On-axis ripple is minimized, while satisfying a series of engineering constraints. The ensuing non-linear optimization problem is solved via a sequence of quadratic programming subproblems, using the VMCON algorithm. The resulting divertor designs are substantially improved over previous configurations

  7. η-Invariant and Flat Vector Bundles

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    We present an alternate definition of the mod Z component of the AtiyahPatodi-Singer η invariant associated to (not necessary unitary) fiat vector bundles, which identifies explicitly its real and imaginary parts. This is done by combining a deformation of flat connections introduced in a previous paper with the analytic continuation procedure appearing in the original article of Atiyah, Parodi and Singer.

  8. Computations in intersection rings of flag bundles

    CERN Document Server

    Grayson, Daniel R; Stillman, Michael E

    2012-01-01

    Intersection rings of flag varieties and of isotropic flag varieties are generated by Chern classes of the tautological bundles modulo the relations coming from multiplicativity of total Chern classes. In this paper we describe the Groebner bases of the ideals of relations and give applications to computation of intersections, as implemented in Macaulay2.

  9. Hydrodynamic behavior of a bare rod bundle. [LMFBR

    Energy Technology Data Exchange (ETDEWEB)

    Bartzis, J.G.; Todreas, N.E.

    1977-06-01

    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.

  10. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    NARCIS (Netherlands)

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

    2015-01-01

    Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that

  11. Interplanetary Overlay Network Bundle Protocol Implementation

    Science.gov (United States)

    Burleigh, Scott C.

    2011-01-01

    The Interplanetary Overlay Network (ION) system's BP package, an implementation of the Delay-Tolerant Networking (DTN) Bundle Protocol (BP) and supporting services, has been specifically designed to be suitable for use on deep-space robotic vehicles. Although the ION BP implementation is unique in its use of zero-copy objects for high performance, and in its use of resource-sensitive rate control, it is fully interoperable with other implementations of the BP specification (Internet RFC 5050). The ION BP implementation is built using the same software infrastructure that underlies the implementation of the CCSDS (Consultative Committee for Space Data Systems) File Delivery Protocol (CFDP) built into the flight software of Deep Impact. It is designed to minimize resource consumption, while maximizing operational robustness. For example, no dynamic allocation of system memory is required. Like all the other ION packages, ION's BP implementation is designed to port readily between Linux and Solaris (for easy development and for ground system operations) and VxWorks (for flight systems operations). The exact same source code is exercised in both environments. Initially included in the ION BP implementations are the following: libraries of functions used in constructing bundle forwarders and convergence-layer (CL) input and output adapters; a simple prototype bundle forwarder and associated CL adapters designed to run over an IPbased local area network; administrative tools for managing a simple DTN infrastructure built from these components; a background daemon process that silently destroys bundles whose time-to-live intervals have expired; a library of functions exposed to applications, enabling them to issue and receive data encapsulated in DTN bundles; and some simple applications that can be used for system checkout and benchmarking.

  12. CFD analysis of turbulent cross-flow in a staggered tube bundle equipped with grooved cylinders

    Directory of Open Access Journals (Sweden)

    Imine O.

    2013-04-01

    Full Text Available This study describes the Computational Fluid Dynamics (CFD analysis of the turbulent cross-flow in a staggered tube bundle with transverse and longitudinal pitch-to-diameter ratio of 3.8 and 2.1 respectively. Two Longitudinal grooves are placed on the external surface at 90° and 270° degrees. Each cylinder has two grooves on the external surface of the cylinder. The Navier-Stokes equations of the turbulent flow are solved using Spalart almaras, k-ε realizable and k-ω SST, turbulence models provided by Fluent CFD code. The staggered tube bundle geometry simulations were performed at steady conditions. An adapted grid using static pressure, pressure coefficient and velocity gradient, furthermore, a second order upwind scheme were used. The CFD results were in agreement with the experimental data. The study demonstrates the capability of the CFD calculations in predicting flow characteristics around the bundle

  13. Study of matrix crack-tilted fiber bundle interaction using caustics and finite element method

    Science.gov (United States)

    Hao, Wenfeng; Zhu, Jianguo; Zhu, Qi; Yuan, Yanan

    2016-02-01

    In this work, the interaction between the matrix crack and a tilted fiber bundle was investigated via caustics and the finite element method (FEM). First, the caustic patterns at the crack tip with different distances from the tilted fiber were obtained and the stress intensity factors were extracted from the geometry of the caustic patterns. Subsequently, the shielding effect of the fiber bundle in front of the crack tip was analyzed. Furthermore, the interaction between the matrix crack and the broken fiber bundle was discussed. Finally, a finite element simulation was carried out using ABAQUS to verify the experimental results. The results demonstrate that the stress intensity factors extracted from caustic experiments are in excellent agreement with the data calculated by FEM.

  14. Holomorphic Vector Bundle on Hopf Manifolds with Abelian Fundamental Groups

    Institute of Scientific and Technical Information of China (English)

    Xiang Yu ZHOU; Wei Ming LIU

    2004-01-01

    Let X be a Hopf manifolds with an Abelian fundamental group. E is a holomorphic vector bundle of rank r with trivial pull-back to W = Cn - {0}. We prove the existence of a non-vanishing section of L(×) E for some line bundle on X and study the vector bundles filtration structure of E. These generalize the results of D. Mall about structure theorem of such a vector bundle E.

  15. In-pile test of Qinshan PWR fuel bundle

    International Nuclear Information System (INIS)

    In-pile test of Qinshan Nuclear Power Plant PWR fuel bundle has been conducted in HWRR HTHP Test loop at CIAE. The test fuel bundle was irradiated to an average burnup of 25000 Mwd/tU. The authors describe the structure of (3 x 3-2) test fuel bundle, structure of irradiation rig, fuel fabrication, irradiation conditions, power and fuel burnup. Some comments on the in-pile performance for fuel bundle, fuel rod and irradiation rig were made

  16. Anatomic Double-Bundle Posterior Cruciate Ligament Reconstruction

    OpenAIRE

    Chahla, Jorge; Nitri, Marco; Civitarese, David; Dean, Chase S.; Moulton, Samuel G.; LaPrade, Robert F.

    2016-01-01

    The posterior cruciate ligament (PCL) is known to be the main posterior stabilizer of the knee. Anatomic single-bundle PCL reconstruction, focusing on reconstruction of the larger anterolateral bundle, is the most commonly performed procedure. Because of the residual posterior and rotational tibial instability after the single-bundle procedure and the inability to restore the normal knee kinematics, an anatomic double-bundle PCL reconstruction has been proposed in an effort to re-create the n...

  17. Geometrically frustrated filament assemblies: Unravelling the connection between bundle shape and inter-filament order

    Science.gov (United States)

    Grason, Gregory

    2014-03-01

    From steel cables and textile fibers to filamentous protein bundles in cells and tissues, densely-packed assemblies of filaments are vital structural elements of the worlds around us and inside of us. Despite the ubiquity and utility of dense-filament assemblies in such diverse materials (across 7 orders of magnitude in size!) surprisingly little is known about the fundamental rules that govern their structure. This talk will discuss recent progress in our understanding of the non-linear relationship between the geometry of a rope-like assembly and the structure and energetics of inter-filament packing. In particular, we focus on mathematical models of the geometric frustration between twist - as in macroscopic cables or chiral biofilament bundles - and the preference for isometric, or ``constant spacing,'' packing of filaments in the cross section. Any measure of twist makes it geometrically impossible to evenly space filaments in bundles, begging the question what is the optimal packing of a twisted bundle? We show that geometry of interfilament contact can be mapped formally onto a problem of packing on a 2D non-Euclidean surfaces, whose intrinsically-curved geometry points to the necessity of a complex spectrum defects in the ground-state packing. We confirm the existence of defects and their sensitivity to bundle twist and radius through simulations of energy-minimizing assemblies of cohesive filaments.

  18. Atomistic theory of transport in organic and inorganic nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Pecchia, Alessandro; Di Carlo, Aldo [INFM-Department of Electronic Engineering, University of Rome, Tor Vergata, Rome (Italy)

    2004-08-01

    As the size of modern electronic and optoelectronic devices is scaling down at a steady pace, atomistic simulations become necessary for an accurate modelling of their structural, electronic, optical and transport properties. Such microscopic approaches are important in order to account correctly for quantum-mechanical phenomena affecting both electronic and transport properties of nanodevices. Effective bulk parameters cannot be used for the description of the electronic states since interfacial properties play a crucial role and semiclassical methods for transport calculations are not suitable at the typical scales where the device behaviour is characterized by coherent tunnelling. Quantum-mechanical computations with atomic resolution can be achieved using localized basis sets for the description of the system Hamiltonian. Such methods have been extensively used to predict optical and electronic properties of molecules and mesoscopic systems. The most important approaches formulated in terms of localized basis sets, from empirical tight-binding (TB) to first principles methods, are here reviewed. Being a full band approach, even the simplest TB overcomes the limitations of envelope function approximations, such as the well-known k {center_dot} p, and allows to retain atomic details and realistic band structures. First principles calculations, on the other hand, can give a very accurate description of the electronic and structural properties. Transport in nanoscale devices cannot neglect quantum effects such as coherent tunnelling. In this context, localized basis sets are well-suited for the formal treatment of quantum transport since they provide a simple mathematical framework to treat open-boundary conditions, typically encountered when the system eigenstates carry a steady-state current. We review the principal methods used to formulate quantum transport based on local orbital sets via transfer matrix and Green's function (GF) techniques. We start from

  19. A Comparison between Clinical Results of Selective Bundle and Double Bundle Anterior Cruciate Ligament Reconstruction

    Science.gov (United States)

    Yoo, Yon-Sik; Song, Si Young; Yang, Cheol Jung; Ha, Jong Mun; Kim, Yoon Sang

    2016-01-01

    Purpose The purpose of this study was to compare the clinical outcomes of arthroscopic anatomical double bundle (DB) anterior cruciate ligament (ACL) reconstruction with either selective anteromedial (AM) or posterolateral (PL) bundle reconstruction while preserving a relatively healthy ACL bundle. Materials and Methods The authors evaluated 98 patients with a mean follow-up of 30.8±4.0 months who had undergone DB or selective bundle ACL reconstructions. Of these, 34 cases underwent DB ACL reconstruction (group A), 34 underwent selective AM bundle reconstruction (group B), and 30 underwent selective PL bundle reconstructions (group C). These groups were compared with respect to Lysholm and International Knee Documentation Committee (IKDC) score, side-to-side differences of anterior laxity measured by KT-2000 arthrometer at 30 lbs, and stress radiography and Lachman and pivot shift test results. Pre- and post-operative data were objectively evaluated using a statistical approach. Results The preoperative anterior instability measured by manual stress radiography at 90° of knee flexion in group A was significantly greater than that in groups B and C (all pACL tears offers comparable clinical results to DB reconstruction in complete ACL tears. PMID:27401652

  20. Geometry of torus bundles in integrable Hamiltonian systems

    NARCIS (Netherlands)

    Lukina, Olga

    2008-01-01

    Thesis is concerned with global properties of Lagrangian bundles, i.e. symplectic n-torus bundles, as these occur in integrable Hamiltonian systems. It treats obstructions to triviality and concerns with classification of such bundles, as well as with manifestations of global invariants in real-worl