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Sample records for bundles atomistic simulations

  1. Atomistic simulations, mesoscopic modeling, and theoretical analysis of thermal conductivity of bundles composed of carbon nanotubes

    Science.gov (United States)

    Volkov, Alexey N.; Salaway, Richard N.; Zhigilei, Leonid V.

    2013-09-01

    The propensity of carbon nanotubes (CNTs) to self-organize into continuous networks of bundles has direct implications for thermal transport properties of CNT network materials and defines the importance of clear understanding of the mechanisms and scaling laws governing the heat transfer within the primary building blocks of the network structures—close-packed bundles of CNTs. A comprehensive study of the thermal conductivity of CNT bundles is performed with a combination of non-equilibrium molecular dynamics (MD) simulations of heat transfer between adjacent CNTs and the intrinsic conductivity of CNTs in a bundle with a theoretical analysis that reveals the connections between the structure and thermal transport properties of CNT bundles. The results of MD simulations of heat transfer in CNT bundles consisting of up to 7 CNTs suggest that, contrary to the widespread notion of strongly reduced conductivity of CNTs in bundles, van der Waals interactions between defect-free well-aligned CNTs in a bundle have negligible effect on the intrinsic conductivity of the CNTs. The simulations of inter-tube heat conduction performed for partially overlapping parallel CNTs indicate that the conductance through the overlap region is proportional to the length of the overlap for CNTs and CNT-CNT overlaps longer than several tens of nm. Based on the predictions of the MD simulations, a mesoscopic-level model is developed and applied for theoretical analysis and numerical modeling of heat transfer in bundles consisting of CNTs with infinitely large and finite intrinsic thermal conductivities. The general scaling laws predicting the quadratic dependence of the bundle conductivity on the length of individual CNTs in the case when the thermal transport is controlled by the inter-tube conductance and the independence of the CNT length in another limiting case when the intrinsic conductivity of CNTs plays the dominant role are derived. An application of the scaling laws to bundles of

  2. 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.

  3. Parallel Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    HEFFELFINGER,GRANT S.

    2000-01-18

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

  4. 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.

  5. Atomistic Simulations of Bicelle Mixtures

    OpenAIRE

    Jiang, Yong; Wang, Hao; Kindt, James T.

    2010-01-01

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironmen...

  6. 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.

  7. Atomistic simulations of bicelle mixtures.

    Science.gov (United States)

    Jiang, Yong; Wang, Hao; Kindt, James T

    2010-06-16

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets.

  8. 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...

  9. 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

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

    Science.gov (United States)

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

    2014-02-01

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

  11. Systematic evaluation of bundled SPC water for biomolecular simulations.

    Science.gov (United States)

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

    2015-04-07

    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

  12. Atomistic simulations of nanoscale electrokinetic transport

    Science.gov (United States)

    Liu, Jin; Wang, Moran; Chen, Shiyi; Robbins, Mark

    2011-11-01

    An efficient and accurate algorithm for atomistic simulations of nanoscale electrokinetic transport will be described. The long-range interactions between charged molecules are treated using the Particle-Particle Particle-Mesh method and the Poisson equation for the electric potential is solved using an efficient multi-grid method in physical space. Using this method, we investigate two important applications in electrokinetic transport: electroosmotic flow in rough channels and electowetting on dielectric (EWOD). Simulations of electroosmotic and pressure driven flow in exactly the same geometries show that surface roughness has a much more pronounced effect on electroosmotic flow. Analysis of local quantities shows that this is because the driving force in electroosmotic flow is localized near the wall where the charge density is high. In atomistic simulations of EWOD, we find the contact angle follows the continuum theory at low voltages and always saturates at high voltages. Based on our results, a new mechanism for saturation is identified and possible techniques for controlling saturation are proposed. This work is supported by the National Science Foundation under Grant No. CMMI 0709187.

  13. Atomistic Monte Carlo Simulation of Lipid Membranes

    Directory of Open Access Journals (Sweden)

    Daniel Wüstner

    2014-01-01

    Full Text Available Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. 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 of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.

  14. 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.

  15. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction......, 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...... of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol....

  16. NiTi superelasticity via atomistic simulations

    Science.gov (United States)

    Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin

    2015-12-01

    The NiTi shape memory alloys (SMAs) are promising candidates for the next-generation multifunctional materials. These materials are superelastic i.e. they can fully recover their original shape even after fairly large inelastic deformations once the mechanical forces are removed. The superelasticity reportedly stems from atomic scale crystal transformations. However, very few computer simulations have emerged, elucidating the transformation mechanisms at the discrete lattice level, which underlie the extraordinary strain recoverability. Here, we conduct breakthrough molecular dynamics modelling on the superelastic behaviour of the NiTi single crystals, and unravel the atomistic genesis thereof. The deformation recovery is clearly traced to the reversible transformation between austenite and martensite crystals through simulations. We examine the mechanistic origin of the tension-compression asymmetries and the effects of pressure/temperature/strain rate variation isolatedly. Hence, this work essentially brings a new dimension to probing the NiTi performance based on the mesoscale physics under more complicated thermo-mechanical loading scenarios.

  17. Atomistic simulation of Voronoi-based coated nanoporous metals

    Science.gov (United States)

    Onur Yildiz, Yunus; Kirca, Mesut

    2017-02-01

    In this study, a new method developed for the generation of periodic atomistic models of coated and uncoated nanoporous metals (NPMs) is presented by examining the thermodynamic stability of coated nanoporous structures. The proposed method is mainly based on the Voronoi tessellation technique, which provides the ability to control cross-sectional dimension and slenderness of ligaments as well as the thickness of coating. By the utilization of the method, molecular dynamic (MD) simulations of randomly structured NPMs with coating can be performed efficiently in order to investigate their physical characteristics. In this context, for the purpose of demonstrating the functionality of the method, sample atomistic models of Au/Pt NPMs are generated and the effects of coating and porosity on the thermodynamic stability are investigated by using MD simulations. In addition to that, uniaxial tensile loading simulations are performed via MD technique to validate the nanoporous models by comparing the effective Young’s modulus values with the results from literature. Based on the results, while it is demonstrated that coating the nanoporous structures slightly decreases the structural stability causing atomistic configurational changes, it is also shown that the stability of the atomistic models is higher at lower porosities. Furthermore, adaptive common neighbour analysis is also performed to identify the stabilized atomistic structure after the coating process, which provides direct foresights for the mechanical behaviour of coated nanoporous structures.

  18. 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.

  19. 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.

  20. 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,

  1. 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

  2. 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...

  3. The notion of a plastic material spin in atomistic simulations

    Science.gov (United States)

    Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

    2016-12-01

    A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

  4. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

    Science.gov (United States)

    Pande, Vijay S; Baker, Ian; Chapman, Jarrod; Elmer, Sidney P; Khaliq, Siraj; Larson, Stefan M; Rhee, Young Min; Shirts, Michael R; Snow, Christopher D; Sorin, Eric J; Zagrovic, Bojan

    2003-01-01

    Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.

  5. Predicting dislocation climb: Classical modeling versus atomistic simulations

    OpenAIRE

    Clouet, Emmanuel

    2011-01-01

    International audience; The classical modeling of dislocation climb based on a continuous description of vacancy diffusion is compared to recent atomistic simulations of dislocation climb in body-centered cubic iron under vacancy supersaturation [Phys. Rev. Lett. 105 095501 (2010)]. A quantitative agreement is obtained, showing the ability of the classical approach to describe dislocation climb. The analytical model is then used to extrapolate dislocation climb velocities to lower dislocation...

  6. Perspective: Machine learning potentials for atomistic simulations

    Science.gov (United States)

    Behler, Jörg

    2016-11-01

    Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of the investigated problems, there is a constantly increasing need for simulations of more realistic, i.e., larger, model systems with improved accuracy. In many cases, the availability of sufficiently efficient interatomic potentials providing reliable energies and forces has become a serious bottleneck for performing these simulations. To address this problem, currently a paradigm change is taking place in the development of interatomic potentials. Since the early days of computer simulations simplified potentials have been derived using physical approximations whenever the direct application of electronic structure methods has been too demanding. Recent advances in machine learning (ML) now offer an alternative approach for the representation of potential-energy surfaces by fitting large data sets from electronic structure calculations. In this perspective, the central ideas underlying these ML potentials, solved problems and remaining challenges are reviewed along with a discussion of their current applicability and limitations.

  7. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable...

  8. 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.

  9. Nuclear wasteform materials: Atomistic simulation case studies

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-15

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

  10. 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.

  11. 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.

  12. 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

    2016-08-09

    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.

  13. 3d visualization of atomistic simulations on every desktop

    Science.gov (United States)

    Peled, Dan; Silverman, Amihai; Adler, Joan

    2013-08-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

  15. 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

  16. 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.

  17. Shock Hugoniot behavior of single crystal titanium using atomistic simulations

    Science.gov (United States)

    Mackenchery, Karoon; Dongare, Avinash

    2017-01-01

    Atomistic shock simulations are performed for single crystal titanium using four different interatomic potentials at impact velocities ranging from 0.5 km/s to 2.0 km/s. These potentials comprise of three parameterizations in the formulation of the embedded atom method and one formulation of the modified embedded atom method. The capability of the potentials to model the shock deformation and failure behavior is investigated by computing the shock hugoniot response of titanium and comparing to existing experimental data. In addition, the capability to reproduce the shock induced alpha (α) to omega (ω) phase transformation seen in Ti is investigated. The shock wave structure is discussed and the velocities for the elastic, plastic and the α-ω phase transformation waves are calculated for all the interatomic potentials considered.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a co...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-05

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

  20. Scoring multipole electrostatics in condensed-phase atomistic simulations.

    Science.gov (United States)

    Bereau, Tristan; Kramer, Christian; Monnard, Fabien W; Nogueira, Elisa S; Ward, Thomas R; Meuwly, Markus

    2013-05-09

    Permanent multipoles (MTPs) embody a natural extension to common point-charge (PC) representations in atomistic simulations. In this work, we propose an alternative to the computationally expensive MTP molecular dynamics simulations by running a simple PC simulation and later reevaluate-"score''-all energies using the more detailed MTP force field. The method, which relies on the assumption that the PC and MTP force fields generate closely related phase spaces, is accomplished by enforcing identical sets of monopoles between the two force fields-effectively highlighting the higher MTP terms as a correction to the PC approximation. We first detail our consistent parametrization of the electrostatics and van der Waals interactions for the two force fields. We then validate the method by comparing the accuracy of protein-ligand binding free energies from both PC and MTP-scored representations with experimentally determined binding constants obtained by us. Specifically, we study the binding of several arylsulfonamide ligands to human carbonic anhydrase II. We find that both representations yield an accuracy of 1 kcal/mol with respect to experiment. Finally, we apply the method to rank the energetic contributions of individual atomic MTP coefficients for molecules solvated in water. All in all, MTP scoring is a computationally appealing method that can provide insight into the multipolar electrostatic interactions of condensed-phase systems.

  1. Atomistic Simulations of Uranium Incorporation into Iron (Hydr)Oxides

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Felmy, Andrew R.; Ilton, Eugene S.

    2011-04-29

    Atomistic simulations were carried out to characterize the coordination environments of U incorporated in three Fe-(hydr)oxide minerals: goethite, magnetite, and hematite. The simulations provided information on U-O and U-Fe distances, coordination numbers, and lattice distortion for U incorporated in different sites (e.g., unoccupied versus occupied sites, octahedral versus tetrahedral) as a function of the oxidation state of U and charge compensation mechanisms (i.e., deprotonation, vacancy formation, or reduction of Fe(III) to Fe(II)). For goethite, deprotonation of first shell hydroxyls enables substitution of U for Fe(III) with a minimal amount of lattice distortion, whereas substitution in unoccupied octahedral sites induced appreciable distortion to 7-fold coordination regardless of U oxidation states and charge compensation mechanisms. Importantly, U-Fe distances of ~3.6 Å were associated with structural incorporation of U and cannot be considered diagnostic of simple adsorption to goethite surfaces. For magnetite, the octahedral site accommodates U(V) or U(VI) with little lattice distortion. U substituted for Fe(III) in hematite maintained octahedral coordination in most cases. In general, comparison of the simulations with available experimental data provides further evidence for the structural incorporation of U in iron (hydr)oxide minerals.

  2. 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...

  3. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si{sub 3}N

    Energy Technology Data Exchange (ETDEWEB)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-20

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  4. Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann-Molecular Dynamics Simulations of Dense Fluids

    Science.gov (United States)

    Dupuis, A.; Koumoutsakos, P.

    We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.

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

    Energy Technology Data Exchange (ETDEWEB)

    Duspiva, J. [Nuclear Research Inst., Rez plc (Czech Republic)

    2011-07-01

    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 YU{sub 2}911 was used for the simulation with slightly modified ELHEAT package. Sensitivity studies on input parameters and oxidation kinetics were performed. (author)

  6. 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.

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

    Science.gov (United States)

    Kotsalis, E. M.; Walther, J. H.; Koumoutsakos, P.

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a 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 the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

  8. 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.

  9. Atomistic Simulation of Non-Equilibrium Phenomena in Hypersonic Flows

    Science.gov (United States)

    Norman, Paul Erik

    The goal of this work is to model the heterogeneous recombination of atomic oxygen on silica surfaces, which is of interest for accurately predicting the heating on vehicles traveling at hypersonic speeds. This is accomplished by creating a finite rate catalytic model, which describes recombination with a set of elementary gas-surface reactions. Fundamental to a description of surface catalytic reactions are the in situ chemical structures on the surface where recombination can occur. Using molecular dynamics simulations with the Reax GSISiO potential, we find that the chemical sites active in direct gas-phase reactions on silica surfaces consist of a small number of specific structures (or defects). The existence of these defects on real silica surfaces is supported by experimental results and the structure and energetics of these defects have been verified with quantum chemical calculations. The reactions in the finite rate catalytic model are based on the interaction of molecular and atomic oxygen with these defects. Trajectory calculations are used to find the parameters in the forward rate equations, while a combination of detailed balance and transition state theory are used to find the parameters in the reverse rate equations. The rate model predicts that the oxygen recombination coefficient is relatively constant at T (300-1000 K), in agreement with experimental results. At T > 1000 K the rate model predicts a drop off in the oxygen recombination coefficient, in disagreement with experimental results, which predict that the oxygen recombination coefficient increases with temperature. A discussion of the possible reasons for this disagreement, including non-adiabatic collision dynamics, variable surface site concentrations, and additional recombination mechanisms is presented. This thesis also describes atomistic simulations with Classical Trajectory Calculation Direction Simulation Monte Carlo (CTC-DSMC), a particle based method for modeling non

  10. 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....

  11. 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

  12. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-04-15

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

  14. 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 ...

  15. Origin of unrealistic blunting during atomistic fracture simulations based on MEAM potentials

    Science.gov (United States)

    Ko, Won-Seok; Lee, Byeong-Joo

    2014-06-01

    Atomistic simulations based on interatomic potentials have frequently failed to correctly reproduce the brittle fracture of materials, showing an unrealistic blunting. We analyse the origin of the unrealistic blunting during atomistic simulations by modified embedded-atom method (MEAM) potentials for experimentally well-known brittle materials such as bcc tungsten and diamond silicon. The radial cut-off which has been thought to give no influence on MEAM calculations is found to have a decisive effect on the crack propagation behaviour. Extending both cut-off distance and truncation range can prevent the unrealistic blunting, reproducing many well-known fracture behaviour which have been difficult to reproduce. The result provides a guideline for future atomistic simulations that focus on various fracture-related phenomena including the failure of metallic-covalent bonding material systems using MEAM potentials.

  16. Atomistic simulation of laser ablation of gold : Effect of pressure relaxation

    NARCIS (Netherlands)

    Norman, G. E.; Starikov, S. V.; Stegailov, V. V.

    2012-01-01

    The process of ablation of a gold target by femto- and picosecond laser radiation pulses has been studied by numerical simulations using an atomistic model with allowance for the electron subsystem and the dependence of the ion-ion interaction potential on the electron temperature. Using this potent

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

    NARCIS (Netherlands)

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

    2011-01-01

    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. I

  18. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. I. Structural modeling

    Science.gov (United States)

    Kim, Nayong; Kim, Yongman; Tsotsis, Theodore T.; Sahimi, Muhammad

    2005-06-01

    An atomistic model of layered double hydroxides, an important class of nanoporous materials, is presented. These materials have wide applications, ranging from adsorbents for gases and liquid ions to nanoporous membranes and catalysts. They consist of two types of metallic cations that are accommodated by a close-packed configuration of OH- and other anions in a positively charged brucitelike layer. Water and various anions are distributed in the interlayer space for charge compensation. A modified form of the consistent-valence force field, together with energy minimization and molecular dynamics simulations, is utilized for developing an atomistic model of the materials. To test the accuracy of the model, we compare the vibrational frequencies, x-ray diffraction patterns, and the basal spacing of the material, computed using the atomistic model, with our experimental data over a wide range of temperature. Good agreement is found between the computed and measured quantities.

  19. Understanding materials behavior from atomistic simulations: Case study of al-containing high entropy alloys and thermally grown aluminum oxide

    Science.gov (United States)

    Yinkai Lei

    Atomistic simulation refers to a set of simulation methods that model the materials on the atomistic scale. These simulation methods are faster and cheaper alternative approaches to investigate thermodynamics and kinetics of materials compared to experiments. In this dissertation, atomistic simulation methods have been used to study the thermodynamic and kinetic properties of two material systems, i.e. the entropy of Al-containing high entropy alloys (HEAs) and the vacancy migration energy of thermally grown aluminum oxide. (Abstract shortened by ProQuest.).

  20. 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.

  1. Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

    Science.gov (United States)

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

    Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

  2. Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures

    Directory of Open Access Journals (Sweden)

    Aruna Prakash

    2017-01-01

    Full Text Available Single-crystal Ni-base superalloys, consisting of a two-phase γ/ γ ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/ γ ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ ′ particles with planar γ/ γ ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions.

  3. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Liedke, Bartosz

    2011-03-24

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

  5. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics.

    OpenAIRE

    Kerr, I. D.; Sankararamakrishnan, R; Smart, O.S.; Sansom, M S

    1994-01-01

    A parallel bundle of transmembrane (TM) alpha-helices surrounding a central pore is present in several classes of ion channel, including the nicotinic acetylcholine receptor (nAChR). We have modeled bundles of hydrophobic and of amphipathic helices using simulated annealing via restrained molecular dynamics. Bundles of Ala20 helices, with N = 4, 5, or 6 helices/bundle were generated. For all three N values the helices formed left-handed coiled coils, with pitches ranging from 160 A (N = 4) to...

  6. 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.

  7. 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

  8. 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.

  9. Towards Novel Energy Solutions - an Electronic/Atomistic Simulation Approach

    Science.gov (United States)

    Dong, Rui

    This thesis focuses on computer modeling and multi-scale simulations of new materials that can potentially be used in novel energy applications, i.e., the dye molecules in dye-sensitizedsolar- cells and polymers for the capacitive energy storage. The aim is to understand physical properties of existing materials and then to find ways to improve them. (Abstract shortened by ProQuest.).

  10. A fast mollified impulse method for biomolecular atomistic simulations

    Science.gov (United States)

    Fath, L.; Hochbruck, M.; Singh, C. V.

    2017-03-01

    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice-ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  11. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si3N4 Nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-01

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  12. Methods for atomistic abrasion simulations of laterally periodic polycrystalline substrates with fractal surfaces

    Science.gov (United States)

    Eder, S. J.; Bianchi, D.; Cihak-Bayr, U.; Gkagkas, K.

    2017-03-01

    In this work we discuss a method to generate laterally periodic polycrystalline samples with fractal surfaces for use in molecular dynamics simulations of abrasion. We also describe a workflow that allows us to produce random lateral distributions of simple but realistically shaped hard abrasive particles with Gaussian size distribution and random particle orientations. We evaluate some on-the-fly analysis and visualization possibilities that may be applied during a molecular dynamics simulation to considerably reduce the post-processing effort. Finally, we elaborate on a parallelizable post-processing approach to evaluating and visualizing the surface topography, the grain structure and orientation, as well as the temperature distribution in large atomistic systems.

  13. 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.

  14. Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

    Science.gov (United States)

    Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

    2006-01-01

    A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

  15. 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.

  16. Analysis of Boundary Conditions for Crystal Defect Atomistic Simulations

    Science.gov (United States)

    Ehrlacher, V.; Ortner, C.; Shapeev, A. V.

    2016-12-01

    Numerical simulations of crystal defects are necessarily restricted to finite computational domains, supplying artificial boundary conditions that emulate the effect of embedding the defect in an effectively infinite crystalline environment. This work develops a rigorous framework within which the accuracy of different types of boundary conditions can be precisely assessed. We formulate the equilibration of crystal defects as variational problems in a discrete energy space and establish qualitatively sharp regularity estimates for minimisers. Using this foundation we then present rigorous error estimates for (i) a truncation method (Dirichlet boundary conditions), (ii) periodic boundary conditions, (iii) boundary conditions from linear elasticity, and (iv) boundary conditions from nonlinear elasticity. Numerical results confirm the sharpness of the analysis.

  17. Atomistic simulation of helium bubble nucleation in palladium

    Energy Technology Data Exchange (ETDEWEB)

    Wang Liang [Department of Applied Physics, Hunan University, Changsha 410082 (China); Hu, Wangyu [Department of Applied Physics, Hunan University, Changsha 410082 (China)], E-mail: wangyuhu2001cn@yahoo.com.cn; Xiao Shifang [Department of Applied Physics, Hunan University, Changsha 410082 (China)], E-mail: sfxiao@yahoo.com.cn; Yang Jianyu [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China); Deng Huiqiu [Department of Applied Physics, Hunan University, Changsha 410082 (China)

    2009-09-15

    A palladium crystal has been constructed with 11808 atoms. 55 helium atoms occupied the octahedral position of palladium crystal are introduced and retained in a spherical region. Molecular dynamic simulations are performed in a constant temperature and constant volume ensemble (NVT) with temperature controlled by Nose-Hoover thermostat. The interactions between palladium atoms are described with modified analytic embedded atom method (MAEAM), the interactions between palladium atom and helium atom are in the form of Morse potential, and the interactions between helium atoms are in the form of L-J potential function. With the analysis of the radial distribution function (RDF) and microstructure, it reveals that some of helium atoms form a series of clusters with different size, and the nucleation core is random at low temperature, and which is the embryo of helium bubble. Increasing temperature can accelerate the process of bubble nucleation, and the clusters will aggregate and coalesce into a bigger one in which there are no palladium atoms, and it is considered as a helium bubble.

  18. Atomistic Molecular Dynamics Simulations of the Electrical Double

    Science.gov (United States)

    Li, Zifeng; Milner, Scott; Fichthorn, Kristen

    2015-03-01

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

  19. Dynamic Deformation of Thermosetting Polymers---All Atomistic Simulations

    Science.gov (United States)

    Tsige, Mesfin; Shenogina, Natalia; Mukhopadhyay, Sharmila; Patnaik, Soumya

    2013-03-01

    We are using all-atom molecular dynamics simulations to investigate the interconnection between structural and mechanical properties of highly cross-linked polymer networks. In this study we focused on the widely used resin-hardener system composed of DGEBA epoxy oligomers and aromatic amine hardener DETDA. Accurate cross-linked models were developed using the effective cross-linking procedure that enables to generate thermoset structures with realistic structural characteristics. These models were used to examine the elastic properties of thermosetting networks with various degrees of curing and length of resin strands both in glassy and rubbery states. In our recent study we employed static deformation approach to estimate potential energy contribution to the mechanical response. In the present work we are using dynamic deformation approach which takes into account both potential energy and thermal motions in the structure. Uniaxial, volumetric and shear dynamic deformation modes were used to obtain Young's, bulk, shear moduli and Poisson's ratio directly. We also calculated elastic constants using formulae of linear elasticity and analyzed the results obtained by direct deformation and interconversion methods. The elastic properties determined from these two approaches are in good agreement with each other and also with experimental data.

  20. 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

  1. Coupling-of-length-scale approach for multiscale atomistic-continuum simulations: Atomistically-induced stress distributions in Si/Si_3N4 nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George; Madhukar, Anupam

    2001-03-01

    A hybrid molecular-dynamics and finite-element simulation approach has been used to investigate stress distributions in Si(111) nanopixels covered with both crystalline and amorphous Si_3N4 thin films. Surfaces, lattice-mismatched interfaces, edges, and corners create stress fields on the order of 1 GPa inside the Si substrate with patterns that cannot be reproduced by a continuum approach alone. For these atomistically-induced inhomogeneouse stresses, the hybrid simulation approach provides an excellent agreement with the standard molecular dynamics, with considerably less computational costs.

  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. 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.

  4. 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.

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

    DEFF Research Database (Denmark)

    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 pos......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...... 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...... 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....

  7. 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.

  8. 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.

  9. 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.

  10. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    Science.gov (United States)

    Seppä, Jeremias; Reischl, Bernhard; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Raiteri, Paolo; Rohl, Andrew L.; Nordlund, Kai; Lassila, Antti

    2017-03-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation.

  11. Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code

    Energy Technology Data Exchange (ETDEWEB)

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

    1980-04-01

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

  12. 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.

  13. 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.)

  14. Predictive atomistic simulations of electronic properties of realistic nanoscale devices: A multiscale modeling approach

    Science.gov (United States)

    Vedula, Ravi Pramod Kumar

    Scaling of CMOS towards its ultimate limits, where quantum effects and atomistic variability due to fabrication, along with recent emphasis on heterogeneous integration of non-digital devices for increasing the functional diversification presents us with fundamentally new challenges. A comprehensive understanding of design and operation of these nanoscale transistors, and other electronic devices like RF-MEMS, requires an insight into their electronic and mechanical properties that are strongly influenced by underlying atomic structure. Hence, continuum descriptions of materials and use of empirical models at these scales become questionable. This increase in complexity of electronic devices necessitates an understanding at a more fundamental level to accurately predict the performance and reliability of these devices. The objective of this thesis is to outline the application of multiscale predictive modeling methods, ranging from atoms to devices, for addressing these challenges. This capability is demonstrated using two examples: characterization of (i) dielectric charging in RF-MEMS, and (ii) transport properties of Ge-nanofins. For characterizing the dielectric charging phenomenon, a continuum dielectric charging model, augmented by first principles informed trap distributions, is used to predict current transient measurements across a broad range of voltages and temperatures. These simulations demonstrate using ab initio informed model not only reduces the empiricism (number of adjustable parameters) in the model but also leads to a more accurate model over a broad range of operating conditions, and enable the precise determination of additional material parameters. These atomistic calculations also provide detailed information about the nature of charge traps and their trapping mechanisms that are not accessible experimentally; such information could prove invaluable in defect engineering. The second problem addresses the effect of the in-homogeneous strain

  15. 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.

  16. 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

  17. 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.

  18. A dynamic atomistic-continuum method for the simulation of crystalline materials

    CERN Document Server

    Huang Zhon Gy

    2002-01-01

    We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics in crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away from defects and interfaces. We propose a new class of matching conditions between the atomistic and the continuum regions. These conditions ensure the accurate passage of large-scale information between the atomistic and the continuum regions and at the same time minimize the reflection of phonons at the atomistic-continuum interface. They can be made adaptive by choosing appropriate weight functions. We present applications to dislocation dynamics, friction between two-dimensional crystal surfaces, and fracture dynamics. We compare results of the coupled method and of the detailed atomistic model.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  20. 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.

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

    CERN Document Server

    Patra, Amit K; Ganguli, Ranjan

    2014-01-01

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

  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. 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.

  4. Identifying early stage precipitation in large-scale atomistic simulations of superalloys

    Science.gov (United States)

    Schmidt, Eric; Bristowe, Paul D.

    2017-04-01

    A method for identifying and classifying ordered phases in large chemically and thermally disordered atomistic models is presented. The method uses Steinhardt parameters to represent local atomic configurations and develops probability density functions to classify individual atoms using naïve Bayes. The method is applied to large molecular dynamics simulations of supersaturated Ni-20 at% Al solid solutions in order to identify the formation of embryonic γ‧-Ni3Al. The composition and temperatures are chosen to promote precipitation, which is observed in the form of ordering and is found to occur more likely in regions with above average Al concentration producing ‘clusters’ of increasing size. The results are interpreted in terms of a precipitation mechanism in which the solid solution is unstable with respect to ordering and potentially followed by either spinodal decomposition or nucleation and growth.

  5. Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface

    Science.gov (United States)

    He, Xibing; Guvench, Olgun; MacKerell, Alexander D.; Klein, Michael L.

    2010-01-01

    Molecular Dynamics simulations with the CHARMM atomistic force field have been used to study monolayers of a series of linear alkylbenzene sulfonates (LAS) at the water/air interface. Both the numbers of carbon atoms in the LAS alkyl tail (1 to 11), and the position of attachment of the benzene ring on the alkyl chain have been varied. Totally 36 LAS homologues and isomers have been investigated. The surface tensions of the systems and the average tilt angles of the LAS molecules are found to be related to both the length and the degree of branching of the alkyl tails, whereas the solubility and mobility are mostly determined by the tail length. PMID:20614916

  6. 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.

  7. Parallel CFD simulations of turbulent flows inside a CANDU fuel bundle

    Energy Technology Data Exchange (ETDEWEB)

    Abbasian, F.; Yu, S.D.; Cao, J. [Ryerson Univ., Dept. of Mechanical and Industrial Engineering, Toronto, Ontario (Canada)], E-mail: fabbasia@ryerson.ca

    2008-07-01

    Large Eddy Simulation (LES) is used to study the turbulent flow inside a 43-rod bundle. The two LES models developed in this paper are of dynamic Smagorinsky type, featuring a satisfactory prediction of anisotropic turbulence intensity and frequency. The first model, by taking advantage of the geometric periodicity, deals with one seventh of a rod bundle; it is developed for studying the axial, lateral turbulence intensities and frequencies in the centers of subchannels and narrow-gap regions. The second model, dealing with the full rod bundle inside a pressure tube with nominal eccentricity, is developed for studying the turbulent fluid forces acting on the bundle. In order to accelerate the solution process for the two large CFD models, the parallelized CFD technique is utilized in connection with 24 processors. The numerical results, obtained for a test case (an eight-rod bundle), are in good agreement with those experimental data available in the literature. Numerical simulations of turbulent flow phenomena within subchannels are advantageous since true flow features are difficult or costly to reveal by experiments. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    Abbasian, F.; Hadaller, G.I.; Fortman, R.A., E-mail: fabbasian@sternlab.com [Stern Laboratories Inc., Hamilton, Ontario (Canada)

    2013-07-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  10. Atomistic simulation for deforming complex alloys with application toward TWIP steel and associated physical insights

    Science.gov (United States)

    Wang, Peng; Xu, Shaofeng; Liu, Jiabin; Li, Xiaoyan; Wei, Yujie; Wang, Hongtao; Gao, Huajian; Yang, Wei

    2017-01-01

    The interest in promoting deformation twinning for plasticity is mounting for advanced materials. In contrast to disordered grain boundaries, highly organized twin boundaries are beneficial to promoting strength-ductility combination. Twinning deformation typically involves the kinetics of stacking faults, its interplay with dislocations, as well as the interactions between dislocations and twin boundaries. While the latter has been intensively studied, the dynamics of stacking faults has been rarely touched upon. In this work, we report new physical insights on the stacking fault dynamics in twin induced plasticity (TWIP) steels. The atomistic simulation is made possible by a newly introduced approach: meta-atom molecular dynamics simulation. The simulation suggests that the stacking fault interactions are dominated by dislocation reactions that take place spontaneously, different from the existing mechanisms. Whether to generate a single stacking fault, or a twinning partial and a trailing partial dislocation, depends upon a unique parameter, namely the stacking fault energy. The latter in turn determines the deformation twinning characteristics. The complex twin-slip and twin-dislocation interactions demonstrate the dual role of deformation twins as both the dislocation barrier and dislocation storage. This duality contributes to the high strength and high ductility of TWIP steels.

  11. 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).

  12. 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.

  13. 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

  14. Atomistic simulation of the structure and elastic properties of gold nanowires

    Science.gov (United States)

    Diao, Jiankuai; Gall, Ken; Dunn, Martin L.

    2004-09-01

    We performed atomistic simulations to study the effect of free surfaces on the structure and elastic properties of gold nanowires aligned in the and crystallographic directions. Computationally, we formed a nanowire by assembling gold atoms into a long wire with free sides by putting them in their bulk fcc lattice positions. We then performed a static relaxation on the assemblage. The tensile surface stresses on the sides of the wire cause the wire to contract along the length with respect to the original fcc lattice, and we characterize this deformation in terms of an equilibrium strain versus the cross-sectional area. While the surface stress causes wires of both orientations and all sizes to increasingly contract with decreasing cross-sectional area, when the cross-sectional area of a nanowire is less than 1.83 nm×1.83 nm, the wire undergoes a phase transformation from fcc to bct, and the equilibrium strain increases by an order of magnitude. We then applied a uniform uniaxial strain incrementally to 1.2% to the relaxed nanowires in a molecular statics framework. From the simulation results we computed the effective axial Young's modulus and Poisson's ratios of the nanowire as a function of cross-sectional area. We used two approaches to compute the effective elastic moduli, one based on a definition in terms of the strain derivative of the total energy and another in terms of the virial stress often used in atomistic simulations. Both give quantitatively similar results, showing an increase in Young's modulus with a decrease of cross-sectional area in the nanowires that do not undergo a phase transformation. Those that undergo a phase transformation experience an increase of about a factor of three of Young's modulus. The Poisson's ratio of the wires that do not undergo a phase transformation show little change with the cross-sectional area. Those wires that undergo a phase transformation experience an increase of about 10% in Poisson's ratio. The wires show

  15. Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

    Science.gov (United States)

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

    2012-01-01

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

  16. Molecular dynamics simulation of doxorubicin adsorption on a bundle of functionalized CNT.

    Science.gov (United States)

    Izadyar, Akram; Farhadian, Nafiseh; Chenarani, Naser

    2016-08-01

    In this study, molecular dynamics simulation is used to investigate the adsorption of an anticancer drug, doxorubicin, on bundles of functionalized single-walled carbon nanotubes (SWNTs) in an aqueous solution. Carboxylic group has been selected as the functional group. Molecular dynamics (MD) simulations are performed for both separated systems containing a SWNT bundle and a functionalized carbon nanotube bundle, and results are compared with existing experimental data. MD results show that doxorubicin can be adsorbed on CNTs using different methods such as entrapment within CNT bundle, attachment to the side wall of the CNT, and adsorption on the CNT inner cavity. For functionalized CNT, the adsorption of drugs on the functional groups is essential for predicting the enhancement of drug loading on the functionalized nanotubes. Furthermore, the adsorption behavior of doxorubicin on CNTs is fitted with Langmuir and Freundlich isotherm models. The results show that Langmuir model can predict the adsorption behavior of doxorubicin on CNTs more accurately than Freundlich model does. As predicted by this isotherm model, the adsorption process of doxorubicin on CNTs is relatively difficult, but it can be improved by increasing the functional groups on the CNTs surface.

  17. 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.

  18. Features of structure and phase transitions in pure uranium and U-Mo alloys: atomistic simulation

    Science.gov (United States)

    Kolotova, L. N.; Kuksin, A. Yu; Smirnova, D. E.; Starikov, S. V.; Tseplyaev, V. I.

    2016-11-01

    We study structural properties of cubic and tetragonal phases of U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. For pure uranium and U-Mo alloys at low temperatures we observe body-centered tetragonal (bct) structure, which is similar to the metastable γ°-phase found in the experiments. At higher temperatures bct structure transforms to a quasi body-centered cubic (q-bcc) phase that exhibits cubic symmetry just on the scale of several interatomic spacings or when averaged over time. Instantaneous pair distribution function (PDF) differs from PDF for the time-averaged atomic coordinates corresponding to the bcc lattice. The local positions of uranium atoms in q-bcc lattice correspond to the bct structure, which is energetically favourable due to formation of short U-U bonds. Transition from bct to q-bcc could be considered as ferro-to paraelastic transition of order-disorder type. The temperature of transition depends on Mo concentration. For pure uranium it is equal to about 700 K, which is well below than the upper boundary of the stability region of the α-U phase. Due to this reason, bct phase is observed only in uranium alloys containing metals with low solubility in α-U.

  19. 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.

  20. Atomistic simulations of CO2 and N2 within cage-type silica zeolites.

    Science.gov (United States)

    Madison, Lindsey; Heitzer, Henry; Russell, Colin; Kohen, Daniela

    2011-03-01

    The behavior of CO(2) and N(2), both as single components and as binary mixtures, in two cage-type silica zeolites was studied using atomistic simulations. The zeolites considered, ITQ-3 and paradigm cage-type zeolite ZK4 (the all-silica analog of LTA), were chosen so that the principles illustrated can be generalized to other adsorbent/adsorbate systems with similar topology and types of interactions. N(2) was chosen both because of the potential uses of N(2)/CO(2) separations and because it differs from CO(2) most significantly in the magnitude of its Coulombic interactions with zeolites. Despite similarities between N(2) and CO(2) diffusion in other materials, we show here that the diffusion of CO(2) within cage-type zeolites is dominated by an energy barrier to diffusion located at the entrance to the narrow channels connecting larger cages. This barrier originates in Coulombic interactions between zeolites and CO(2)'s quadrupole and results in well-defined orientations for the diffusing molecules. Furthermore, CO(2)'s favorable electrostatic interactions with the zeolite framework result in preferential binding in the windows between cages. N(2)'s behavior, in contrast, is more consistent with that of molecules previously studied. Our analysis suggests that CO(2)'s behavior might be common for adsorbates with quadrupoles that interact strongly with a material that has narrow windows between cages.

  1. 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.

  2. Atomistic-Scale Simulations of Defect Formation in Graphene under Noble Gas Ion Irradiation.

    Science.gov (United States)

    Yoon, Kichul; Rahnamoun, Ali; Swett, Jacob L; Iberi, Vighter; Cullen, David A; Vlassiouk, Ivan V; Belianinov, Alex; Jesse, Stephen; Sang, Xiahan; Ovchinnikova, Olga S; Rondinone, Adam J; Unocic, Raymond R; van Duin, Adri C T

    2016-09-27

    Despite the frequent use of noble gas ion irradiation of graphene, the atomistic-scale details, including the effects of dose, energy, and ion bombardment species on defect formation, and the associated dynamic processes involved in the irradiations and subsequent relaxation have not yet been thoroughly studied. Here, we simulated the irradiation of graphene with noble gas ions and the subsequent effects of annealing. Lattice defects, including nanopores, were generated after the annealing of the irradiated graphene, which was the result of structural relaxation that allowed the vacancy-type defects to coalesce into a larger defect. Larger nanopores were generated by irradiation with a series of heavier noble gas ions, due to a larger collision cross section that led to more detrimental effects in the graphene, and by a higher ion dose that increased the chance of displacing the carbon atoms from graphene. Overall trends in the evolution of defects with respect to a dose, as well as the defect characteristics, were in good agreement with experimental results. Additionally, the statistics in the defect types generated by different irradiating ions suggested that the most frequently observed defect types were Stone-Thrower-Wales (STW) defects for He(+) irradiation and monovacancy (MV) defects for all other ion irradiations.

  3. 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.

  4. 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.

  5. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. II. Adsorption and diffusion

    Science.gov (United States)

    Kim, Nayong; Harale, Aadesh; Tsotsis, Theodore T.; Sahimi, Muhammad

    2007-12-01

    Nanoporous layered double hydroxide (LDH) materials have wide applications, ranging from being good adsorbents for gases (particularly CO2) and liquid ions to membranes and catalysts. They also have applications in medicine, environmental remediation, and electrochemistry. Their general chemical composition is [M1-xIIMxIII(OH-)2]x+[Xn/mm -•nH2O], where M represents a metallic cation (of valence II or III), and Xn/mm - is an m-valence inorganic, or heteropolyacid, or organic anion. We study diffusion and adsorption of CO2 in a particular LDH with MII=Mg, MIII=Al, and x ≃0.71, using an atomistic model developed based on energy minimization and molecular dynamics simulations, together with a modified form of the consistent-valence force field. The adsorption isotherms and self-diffusivity of CO2 in the material are computed over a range of temperature, using molecular simulations. The computed diffusivities are within one order of magnitude of the measured ones at lower temperatures, while agreeing well with the data at high temperatures. The measured and computed adsorption isotherms agree at low loadings, but differ by about 25% at high loadings. Possible reasons for the differences between the computed properties and the experimental data are discussed, and a model for improving the accuracy of the computed properties is suggested. Also studied are the material's hydration and swelling properties. As water molecules are added to the pore space, the LDH material swells to some extent, with the hydration energy exhibiting interesting variations with the number of the water molecules added. The implications of the results are discussed.

  6. 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

  7. Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

    Science.gov (United States)

    2017-01-01

    Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor–acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)–phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device. PMID:28209056

  8. 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.

  9. 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

  10. Role of Ionic Clusters in Dynamics of Ionomer Melts: From Atomistic to Coarse Grained Simulations

    Science.gov (United States)

    Agrawal, Anupriya

    Ionomers, polymers decorated with ionizable groups, have found application in numerous technologies where ionic transport is required. The ionic groups associate into random clusters resulting in substantial effect on structure, dynamics and transport of these materials. The effects of topology, size and dynamics of these aggregates however remain an open question. Here we probe cluster formation correlated with polymer dynamics through a model system of randomly sulfonated polystyrene (SPS) melts with molecular dynamics (MD) simulations over a broad time and length scales ranging from that within the ionic clusters through polymer segmental dynamics to the motion of the entire molecules. The cluster evolution was probed by fully atomistic studies. We find ladder-like aggregates that transform to globule-like with increasing the dielectric constant of media for sodium neutralized SPS. With increasing dielectric constant, the size of the aggregates decrease and their number increases. Concurrently, the mobility of the polymer increases. The counterion radius and valency affect both morphology and dynamics as is evident in the calculated static and dynamic structure factors. It is further manifested in the results of viscosity obtained through non-equilibrium molecular dynamics technique. Finally, to access larger length scales a three bead coarse-grained model to describe sulfonated styrene that we have developed will be discussed in view of the outstanding challenges in ionic polymers. Supported in part by DOE Grant No. DE-SC007908. This work was carried out in collaboration with Dvora Perahia and Gary Grest while I was a postdoc at Clemson University. I gratefully acknowledge both of them for their support and encouragement.

  11. Atomistic Simulations of Chemical Reactivity of TATB Under Thermal and Shock Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Manaa, M R; Reed, E J; Fried, L E

    2009-09-23

    The study of chemical transformations that occur at the reactive shock front of energetic materials provides important information for the development of predictive models at the grain-and continuum scales. A major shortcoming of current high explosives models is the lack of chemical kinetics data of the reacting explosive in the high pressure and temperature regimes. In the absence of experimental data, long-time scale atomistic molecular dynamics simulations with reactive chemistry become a viable recourse to provide an insight into the decomposition mechanism of explosives, and to obtain effective reaction rate laws. These rates can then be incorporated into thermo-chemical-hydro codes (such as Cheetah linked to ALE3D) for accurate description of the grain and macro scales dynamics of reacting explosives. In this talk, I will present quantum simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystals under thermal decomposition (high density and temperature) and shock compression conditions. This is the first time that condensed phase quantum methods have been used to study the chemistry of insensitive high explosives. We used the quantum-based, self-consistent charge density functional tight binding method (SCC{_}DFTB) to calculate the interatomic forces for reliable predictions of chemical reactions, and to examine electronic properties at detonation conditions for a relatively long time-scale on the order of several hundreds of picoseconds. For thermal decomposition of TATB, we conducted constant volume-temperature simulations, ranging from 0.35 to 2 nanoseconds, at {rho} = 2.87 g/cm{sup 3} at T = 3500, 3000, 2500, and 1500 K, and {rho} = 2.9 g/cm{sup 3} and 2.72 g/cm{sup 3}, at T = 3000 K. We also simulated crystal TATB's reactivity under steady overdriven shock compression using the multi-scale shock technique. We conducted shock simulations with specified shock speeds of 8, 9, and 10 km/s for up to 0.43 ns duration, enabling us to track the

  12. 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.

  13. Simulations and measurements of adiabatic annular flows in triangular, tight lattice nuclear fuel bundle model

    Energy Technology Data Exchange (ETDEWEB)

    Saxena, Abhishek, E-mail: asaxena@lke.mavt.ethz.ch [ETH Zurich, Laboratory for Nuclear Energy Systems, Department of Mechanical and Process Engineering, Sonneggstrasse 3, 8092 Zürich (Switzerland); Zboray, Robert [Laboratory for Thermal-hydraulics, Nuclear Energy and Safety Department, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Prasser, Horst-Michael [ETH Zurich, Laboratory for Nuclear Energy Systems, Department of Mechanical and Process Engineering, Sonneggstrasse 3, 8092 Zürich (Switzerland); Laboratory for Thermal-hydraulics, Nuclear Energy and Safety Department, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland)

    2016-04-01

    High conversion light water reactors (HCLWR) having triangular, tight-lattice fuels bundles could enable improved fuel utilization compared to present day LWRs. However, the efficient cooling of a tight lattice bundle has to be still proven. Major concern is the avoidance of high-quality boiling crisis (film dry-out) by the use of efficient functional spacers. For this reason, we have carried out experiments on adiabatic, air-water annular two-phase flows in a tight-lattice, triangular fuel bundle model using generic spacers. A high-spatial-resolution, non-intrusive measurement technology, cold neutron tomography, has been utilized to resolve the distribution of the liquid film thickness on the virtual fuel pin surfaces. Unsteady CFD simulations have also been performed to replicate and compare with the experiments using the commercial code STAR-CCM+. Large eddies have been resolved on the grid level to capture the dominant unsteady flow features expected to drive the liquid film thickness distribution downstream of a spacer while the subgrid scales have been modeled using the Wall Adapting Local Eddy (WALE) subgrid model. A Volume of Fluid (VOF) method, which directly tracks the interface and does away with closure relationship models for interfacial exchange terms, has also been employed. The present paper shows first comparison of the measurement with the simulation results.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Measurements of turbulent pressures of flow in a water-conveying pipe containing a simulation fuel bundle

    Energy Technology Data Exchange (ETDEWEB)

    Abbasian, F.; Cao, J.; Yu, S.D. [Ryerson Univ., Dept. of Mechanical and Industrial Engineering, Toronto, Ontario (Canada)

    2008-07-01

    A test apparatus was set up to investigate the turbulent flows and flow induced vibrations in a fluid-conveying pipe containing a CANDU 43-element simulation fuel bundle. The fuel bundle is immersed in test pipe of 4-inch in diameter. A centrifugal pump circulates fresh water with a maximum velocity of 9 m/s at full pump power. The pressure fluctuation near the inner surface of the flow channel was measured at various locations using a pressure transducer and a data acquisition system. It was found that the turbulence away from the test section containing the simulation fuel bundle is largely caused by the pipe flow of high Reynolds number; the turbulence near and inside the bundle structures is the result of pipe flow and fluid-solid interactions. The measurements of pressures near the fuel bundle structure showed that the power spectral density (PSD) of pressure fluctuation has a frequency range of 1-300 Hz, and a normalized maximum pressure range of 0.04 to 0.05 times dynamic pressure. The effects of bundle angular alignments and subchannels on the pressure spectra, Strouhal number range, and streamwise pressure drop are also investigated in this paper. Results presented in this paper are useful in validating the computational models for flow-induced fluid forces that cause the fuel bundle structure to rock and fret. (author)

  19. 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.

  20. 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.)

  1. 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.

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

    Science.gov (United States)

    Rao, Satish

    2015-03-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Pavel V. Komarov

    2013-09-01

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

  6. Atomistic Monte Carlo simulations of the diffusion of P and C near grain boundaries in BCC iron

    Energy Technology Data Exchange (ETDEWEB)

    Binkele, P.; Kizler, P. [MPA, Univ. Stuttgart, Stuttgart (Germany); Schmauder, S. [IMWF, Univ. Stuttgart, Stuttgart (Germany)

    2004-07-01

    It is well known that thermal ageing of steels can be caused by the segregation of phosphorus (P) and carbon (C) to grain boundaries. Atomistic Monte Carlo simulations of the diffusion of P and C to grain boundaries in bcc iron will allow, if validated, predictions of the time-dependent segregation. Simulations of the Fe-P-C system are presented, where the diffusion of Fe and P is realized via a vacancy mechanism and the diffusion of C is realized via an interstitial mechanism. Time-dependent segregations have been simulated for different temperatures and start conditions and are found to follow Johnson-Mehl-Avrami laws. A comparison of the simulation results with available AES (Auger Electron Spectroscopy) data shows close agreement with respect to P segregation. In simulations starting with a pre-filled grain boundary in increase of P and a decrease of C in the grain boundary are found where the decrease of C proceeds significantly faster than the increase of P for any temperature. The temperature-dependent ratios of the different speeds of P- and C-segregation, due to their different diffusion mechanisms, are calculated as a result of the simulations. (orig.)

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Judith C. [Univ. of Pittsburgh, Pittsburgh, PA (United States)

    2015-01-09

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

  8. 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.

  9. 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.

  10. 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

  11. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-12-01

    Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations.

  12. Laminar simulation of intersubchannel mixing in a triangular nuclear fuel bundle geometry

    Energy Technology Data Exchange (ETDEWEB)

    Zaretsky, A.; Lightstone, M.F., E-mail: lightsm@mcmaster.ca; Tullis, S.

    2015-12-15

    Highlights: • Quasi-periodic flow was observed through rod-to-wall gaps. • Triangular subchannel flows were fundamentally irregular. • Cross-gap flow was influenced both by local and adjacent cross-gap intensity. • Phase-linking between gaps induced cross-plane peripheral circulation through rod–wall gaps. • Cross-gap flow structure was dependent on subchannel geometry. - Abstract: Predicting temperature distributions in fuel rod bundles is an important component of nuclear reactor safety analysis. Intersubchannel mixing acts to homogenize coolant temperatures thus reducing the likelihood of localized regions of high fuel temperature. Previous research has shown that intersubchannel mixing in nuclear fuel rod bundles is enhanced by a large-scale quasi-periodic energetic fluid motion, which transports fluid on the cross-plane between the narrow gaps connecting subchannels. This phenomenon has also been observed in laminar flows. Unsteady laminar flow simulations were performed in a simplified bundle of three rods with a pipe. Three similar geometries of varying gap width were examined, and a thermal trace was implemented on the first geometry. Thermal mixing was driven by the advection of energy between subchannels by the cross-plane flow. Flow through the rod-to-wall gaps in the wall subchannels alternated with a dominant frequency, particularly when rod-to-wall gaps were smaller than rod-to-rod gaps. Significant phase-linking between rod-to-wall gaps was also observed such that a peripheral circulation occurred through each gap simultaneously. Cross-plane flow through the rod-to-rod gaps in the triangular subchannel was irregular in each case. This was due to the fundamental irregularity of the triangular subchannel geometry. Vortices were continually broken up by cross-plane flow from other gaps due to the odd number of fluid pathways within the central subchannel. Cross-plane flow in subchannel geometries is highly interconnected between gaps. The

  13. Numerical simulation of liquid metal turbulent heat transfer from an inline tube bundle in cross-flow

    Directory of Open Access Journals (Sweden)

    Alexey G. Abramov

    2015-12-01

    Full Text Available Results of the numerical simulation of turbulent flow field and heat transfer of liquid metal in cross-flow over inline tube bundles consisting of smooth round tubes are presented. Computations have been performed with CFD-code ANSYS Fluent on the base of a two-dimensional unsteady RANS formulation using the SST turbulence model by Menter and assuming constant physical properties of a fluid with the Prandtl number equal to 0.023. The Reynolds number ranged from 26,200 to 52,400. Instantaneous and time-averaged velocity and temperature fields obtained for bundles of different intertube spacing with a variation of the bundle width (number of tube rows in the cross direction were analyzed. Integral characteristics of heat transfer were compared with the experimental data.

  14. 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.

  15. 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.

  16. 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.

  17. Towards understanding photomigration: Insights from atomistic simulations of azopolymer films explicitly including light-induced isomerization dynamics

    Science.gov (United States)

    Böckmann, Marcus; Doltsinis, Nikos L.

    2016-10-01

    The light-induced surface modification of a thin film of poly-(disperse orange-3-methylmethacrylate) is investigated computationally using atomistic molecular dynamics simulations specifically tailored to include photoisomerization dynamics. For a model surface consisting of a periodic pattern of alternating irradiated and dark spots, it is shown that repeated photoisomerization in the irradiated areas initially leads to a local temperature increase and a raised surface profile accompanied by a migration of molecules away from the bright spots. After switching off the light source and letting the system cool down, this leads to an inversion of the surface profile, i.e., dips in the bright spots and bumps in the dark spots. To separate the effect of photoisomerization from the pure heating effect, a second simulation is performed in which no photoisomerization is allowed to occur in the bright spots, but the equivalent amount of energy is introduced there locally in the form of heat. This also leads to a raised surface in these areas; however, no outward migration of molecules is observed and the surface pattern practically vanishes when the system is subsequently cooled back to room temperature.

  18. 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.

  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 (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.

  20. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

    Science.gov (United States)

    Reif, Maria M; Oostenbrink, Chris

    2014-01-30

    The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.

  1. 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.

  2. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing.

    Science.gov (United States)

    Zagrovic, Bojan; Snow, Christopher D; Shirts, Michael R; Pande, Vijay S

    2002-11-08

    By employing thousands of PCs and new worldwide-distributed computing techniques, we have simulated in atomistic detail the folding of a fast-folding 36-residue alpha-helical protein from the villin headpiece. The total simulated time exceeds 300 micros, orders of magnitude more than previous simulations of a molecule of this size. Starting from an extended state, we obtained an ensemble of folded structures, which is on average 1.7A and 1.9A away from the native state in C(alpha) distance-based root-mean-square deviation (dRMS) and C(beta) dRMS sense, respectively. The folding mechanism of villin is most consistent with the hydrophobic collapse view of folding: the molecule collapses non-specifically very quickly ( approximately 20ns), which greatly reduces the size of the conformational space that needs to be explored in search of the native state. The conformational search in the collapsed state appears to be rate-limited by the formation of the aromatic core: in a significant fraction of our simulations, the C-terminal phenylalanine residue packs improperly with the rest of the hydrophobic core. We suggest that the breaking of this interaction may be the rate-determining step in the course of folding. On the basis of our simulations we estimate the folding rate of villin to be approximately 5micros. By analyzing the average features of the folded ensemble obtained by simulation, we see that the mean folded structure is more similar to the native fold than any individual folded structure. This finding highlights the need for simulating ensembles of molecules and averaging the results in an experiment-like fashion if meaningful comparison between simulation and experiment is to be attempted. Moreover, our results demonstrate that (1) the computational methodology exists to simulate the multi-microsecond regime using distributed computing and (2) that potential sets used to describe interatomic interactions may be sufficiently accurate to reach the folded state

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

    Science.gov (United States)

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

    2016-05-25

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

  4. Symmetry Breaking and Fine Structure Splitting in Zincblende Quantum Dots: Atomistic Simulations of Long-Range Strain and Piezoelectric Field

    Science.gov (United States)

    Ahmed, Shaikh; Usman, Muhammad; Heitzinger, Clemens; Rahman, Rajib; Schliwa, Andrei; Klimeck, Gerhard

    2007-04-01

    Electrons and holes captured in self-assembled quantum dots (QDs) are subject to symmetry breaking that cannot be represented in with continuum material representations. Atomistic calculations reveal symmetry lowering due to effects of strain and piezo-electric fields. These effects are fundamentally based on the crystal topology in the quantum dots. This work studies these two competing effects and demonstrates the fine structure splitting that has been demonstrated experimentally can be attributed to the underlying atomistic structure of the quantum dots.

  5. 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.

  6. Phase separation in H2O:N2 mixture - molecular dynamics simulations using atomistic force fields

    Energy Technology Data Exchange (ETDEWEB)

    Maiti, A; Gee, R; Bastea, S; Fried, L

    2006-09-25

    A class II atomistic force field with Lennard-Jones 6-9 nonbond interactions is used to investigate equations of state (EOS) for important high explosive detonation products N{sub 2} and H{sub 2}O in the temperature range 700-2500 K and pressure range 0.1-10 GPa. A standard 6th order parameter-mixing scheme is then employed to study a 2:1 (molar) H{sub 2}O:N{sub 2} mixture, to investigate in particular the possibility of phase-separation under detonation conditions. The simulations demonstrate several important results, including: (1) the accuracy of computed EOS for both N{sub 2} and H{sub 2}O over the entire range of temperature and pressure considered; (2) accurate mixing-demixing phase boundary as compared to experimental data; and (3) the departure of mixing free energy from that predicted by ideal mixing law. The results provide comparison and guidance to state-of-the-art chemical kinetic models.

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

    Science.gov (United States)

    Nagata, Yuki; Lennartz, Christian

    2008-07-21

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

  10. Fluid Simulations with Atomistic Resolution: Multiscale Model with Account of Nonlocal Momentum Transfer

    NARCIS (Netherlands)

    Svitenkov, A.I.; Chivilikhin, S.A.; Hoekstra, A.G.; Boukhanovsky, A.V.

    2015-01-01

    Nano- and microscale flow phenomena turn out to be highly non-trivial for simulation and require the use of heterogeneous modeling approaches. While the continuum Navier-Stokes equations and related boundary conditions quickly break down at those scales, various direct simulation methods and hybrid

  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. Atomistic Simulation and Electronic Structure of Lithium Doped Ionic Liquids: Structure, Transport, and Electrochemical Stability

    Science.gov (United States)

    Haskins, Justin B.; Bauschlicher, Charles W.; Lawson, John W.

    2015-01-01

    Zero-temperature density functional theory (DFT), density functional theory molecular dynamics (DFT-MD), and classical molecular dynamics using polarizable force fields (PFF-MD) are employed to evaluate the influence of Lithium ion on the structure, transport, and electrochemical stability of three potential ionic liquid electrolytes: N--methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([pyr14][TFSI]), N--methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide ([pyr13][FSI]), and 1-ethyl-3--methylimidazolium boron tetrafluoride ([EMIM][BF4]). We characterize the Lithium ion solvation shell through zero-temperature DFT simulations of [Li(Anion)sub n](exp n-1) -clusters, DFT-MD simulations of isolated lithium ions in small ionic liquid systems, and PFF-MD simulations with high Li-doping levels in large ionic liquid systems. At low levels of Li-salt doping, highly stable solvation shells having 2-3 anions are seen in both [pyr14][TFSI] and [pyr13][FSI], while solvation shells with 4 anions dominate in [EMIM][BF sub 4]. At higher levels of doping, we find the formation of complex Li-network structures that increase the frequency of 4 anion-coordinated solvation shells. A comparison of computational and experimental Raman spectra for a wide range of [Li(Anion) sub n](exp n -1) - clusters shows that our proposed structures are consistent with experiment. We estimate the ion diffusion coefficients and quantify both size and simulation time effects. We find estimates of lithium ion diffusion are a reasonable order of magnitude and can be corrected for simulation time effects. Simulation size, on the other hand, is also important, with diffusion coefficients from long PFF-MD simulations of small cells having 20-40% error compared to large-cell values. Finally, we compute the electrochemical window using differences in electronic energy levels of both isolated cation/anion pairs and small ionic liquid systems with Li-salt doping. The single pair and liquid

  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...... observe a slight decrease in density, up to 1%, within the shear band, which is consistent with notions of increased free volume or disorder within a plastically deforming amorphous material....

  16. 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.

  17. 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.

  18. 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.

  19. 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...

  20. 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...

  1. 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.

  2. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.

    Science.gov (United States)

    Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R; Shalashilin, Dmitrii V

    2014-08-06

    In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Cholesteryl ester transfer protein (CETP) mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides) and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity...... 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...

  8. Superlattice of stress domains in nanometer-size semiconductor devices predicted from atomistic simulations

    Science.gov (United States)

    Bachlechner, Martina E.; Ebbsjö, Ingvar; Kalia, Rajiv K.; Kodiyalam, Sanjay; Madhukar, Anupam; Nakano, Aiichiro; Omeltchenko, Andrey; Walsh, Phillip; Vashishta, Priya

    2001-03-01

    Semiconductor industry association estimates pixel sizes in next generation devices to be on the order of 70 nm by the year of 2008. Although recent measurements of local strain distributions2 and strain relaxation in nano wires have reached 100-nm spatial resolution, experimental tools for determining stresses for sub 100 nm, feature sizes are still to be developed4. On the other hand, recent developments in efficient simulation algorithms on state-of-the-art parallel computers5 enable us to gain valuable information on interface structure and atomic level stresses in nanopixels of < 100 nm size. Here, we present results for a 27.5-million atom molecular-dynamics simulations of a 70 nm x 70 nm crystalline silicon nanopixel covered with amorphous silicon nitride and placed on a 140 nm x 140 nm crystalline silicon substrate. The stresses parallel to the silicon/silicon nitride interface exhibit a hexagonal superlattice of stress domains with a lattice constant of 12.8 (±1.8) nm. From our analysis of the 70 nm x 70 nm pixel and on comparing with a smaller 25 nm x 25 nm nanopixel, we conclude that for square pixels the superlattice constant is independent of the pixel size and is entirely determined by the mismatch between silicon and silicon nitride. Such stress inhomogeneity with values of up to ±2 GPa will have a significant impact on the performance of semiconductor devices with sub 100 nm features.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    Science.gov (United States)

    Uhl, Felix; Marx, Dominik; Ceriotti, Michele

    2016-08-07

    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.

  15. 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.

  16. Atomistic simulations of calcium uranyl(VI) carbonate adsorption on calcite and stepped-calcite surfaces.

    Science.gov (United States)

    Doudou, Slimane; Vaughan, David J; Livens, Francis R; Burton, Neil A

    2012-07-17

    Adsorption of actinyl ions onto mineral surfaces is one of the main mechanisms that control the migration of these ions in environmental systems. Here, we present computational classical molecular dynamics (MD) simulations to investigate the behavior of U(VI) in contact with different calcite surfaces. The calcium-uranyl-carbonate [Ca(2)UO(2)(CO(3))(3)] species is shown to display both inner- and outer-sphere adsorption to the flat {101̅4} and the stepped {314̅8} and {31̅2̅16} planes of calcite. Free energy calculations, using the umbrella sampling method, are employed to simulate adsorption paths of the same uranyl species on the different calcite surfaces under aqueous condition. Outer-sphere adsorption is found to dominate over inner-sphere adsorption because of the high free energy barrier of removing a uranyl-carbonate interaction and replacing it with a new uranyl-surface interaction. An important binding mode is proposed involving a single vicinal water monolayer between the surface and the sorbed complex. From the free energy profiles of the different calcite surfaces, the uranyl complex was also found to adsorb preferentially on the acute-stepped {314̅8} face of calcite, in agreement with experiment.

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev

    2014-05-01

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

  19. 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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Science.gov (United States)

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

    2015-09-01

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

  2. Atomistic simulation of He bubble in Fe as obstacle to dislocation

    Science.gov (United States)

    Hafez Haghighat, S. M.; Lucas, G.; Schäublin, R.

    2009-07-01

    Degradation of mechanical properties due to nanometric irradiation induced defects is one of the challenging issues in designing materials for future fusion reactors. Various types of defects such as voids and He bubbles may be produced due to high dose of neutron irradiation due to fusion reaction. We study the influence of He bubble on the mobility of an edge dislocation in pure bcc-Fe using molecular dynamics simulation as a function of bubble size, He density and temperature. It appears that low contents He bubbles are penetrable defects, which size and temperature rise make them harder and softer, respectively. At high He contents a size dependent loop punching is observed, which at larger bubble sizes leads to a multistep dislocation-defect interaction. It also appears that the bubble surface curvature and temperature are the main parameters in the screw segments annihilation needed for the release of the dislocation from the bubble.

  3. 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.

  4. 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.

  5. Atomistic simulation of fcc-bcc phase transition in single crystal A1 under uniform compression

    Institute of Scientific and Technical Information of China (English)

    Li Li; Shao Jian-Li; Li Yan-Fang; Duan Su-Qing; [ Liang Jiu-Qing

    2012-01-01

    By molecular dynamics simulations employing an embedded atom model potential,we investigate the fcc-to-bcc phase transition in single crystal Al,caused by uniform compression.Results show that the fec structure is unstable when the pressure is over 250 GPa,in reasonable agreement with the calculated value through the density functional theory.The morphology evolution of the structural transition and the corresponding transition mechanism are analysed in detail.The bec (011) planes are transited from the fcc (11(1)) plane and the (1(1)1) plane.We suggest that the transition mechanism consists mainly of compression,shear,slid and rotation of the lattice.In addition,our radial distribution function analysis explicitly indicates the phase transition of A1 from fcc phase to bcc structure.

  6. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-15

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

  8. 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.

  9. Experimental and numerical investigations of three-dimensional turbulent flow of water surrounding a CANDU simulation fuel bundle structure inside a channel

    Energy Technology Data Exchange (ETDEWEB)

    Abbasian, F.; Yu, S.D. [Department of Mechanical and Industrial Engineering, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3 (Canada); Cao, J. [Department of Mechanical and Industrial Engineering, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3 (Canada)], E-mail: jcao@ryerson.ca

    2009-11-15

    Computational fluid dynamics (CFD) is used to simulate highly turbulent coolant flows surrounding a simulation CANDU fuel bundle structure inside a flow channel. Three CFD methods are used: large eddy simulation (LES), detached eddy simulation (DES), and Reynolds stress model (RSM). The outcome of the simulations is compared with the experimental pressure data measured using an in-water microphone and a miniature pressure transducer placed at various locations in the vicinity of the bundle structure. Among all the three methods employed in developing computational models, LES provides the most accurate results for turbulent pressures.

  10. 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.

  11. 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.

  12. Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Wei Ye

    Full Text Available MicroRNAs are endogenous 23-25 nt RNAs that play important gene-regulatory roles in animals and plants. Recently, miR369-3 was found to upregulate translation of TNFα mRNA in quiescent (G0 mammalian cell lines. Knock down and immunofluorescence experiments suggest that microRNA-protein complexes (with FXR1 and AGO2 are necessary for the translation upregulation. However the molecular mechanism of microRNA translation activation is poorly understood. In this study we constructed the microRNA-mRNA-AGO2-FXR1 quadruple complex by bioinformatics and molecular modeling, followed with all atom molecular dynamics simulations in explicit solvent to investigate the interaction mechanisms for the complex. A combined analysis of experimental and computational data suggests that AGO2-FXR1 complex relocalize microRNA:mRNA duplex to polysomes in G0. The two strands of dsRNA are then separated upon binding of AGO2 and FXR1. Finally, polysomes may improve the translation efficiency of mRNA. The mutation research confirms the stability of microRNA-mRNA-FXR1 and illustrates importance of key residue of Ile304. This possible mechanism can shed more light on the microRNA-dependent upregulation of translation.

  13. 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.

  14. Structures of the Alzheimer's Wild-Type Aβ1-40 Dimer from Atomistic Simulations.

    Science.gov (United States)

    Tarus, Bogdan; Tran, Thanh T; Nasica-Labouze, Jessica; Sterpone, Fabio; Nguyen, Phuong H; Derreumaux, Philippe

    2015-08-20

    We have studied the dimer of amyloid beta peptide Aβ of 40 residues by means of all-atom replica exchange molecular dynamics. The Aβ-dimers have been found to be the smallest toxic species in Alzheimer's disease, but their inherent flexibilities have precluded structural characterization by experimental methods. Though the 24-μs-scale simulation reveals a mean secondary structure of 18% β-strand and 10% α helix, we find transient configurations with an unstructured N-terminus and multiple β-hairpins spanning residues 17-21 and 30-36, but the antiparallel and perpendicular peptide orientations are preferred over the parallel organization. Short-lived conformational states also consist of all α topologies, and one compact peptide with β-sheet structure stabilized by a rather extended peptide with α-helical content. Overall, this first all-atom study provides insights into the equilibrium structure of the Aβ1-40 dimer in aqueous solution, opening a new avenue for a comprehensive understanding of the impact of pathogenic and protective mutations in early-stage Alzheimer's disease on a molecular level.

  15. 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.

  16. Orientation dependence of structural transition in fcc Al driven under uniaxial compression by atomistic simulations

    Institute of Scientific and Technical Information of China (English)

    Li Li; Shao Jian-Li; Duan Su-Qing; Liang Jiu-Qing

    2011-01-01

    By molecular dynamics simulations employing an embedded atom method potential, we have investigated structural transformations in single crystal Al caused by uniaxial strain loading along the[001],[011]and[111]directions.We find that the structural transition is strongly dependent on the crystal orientations. The entire structure phase transition only occurs when loading along the[001]direction, and the increased amplitude of temperature for[001]loading is evidently lower than that for other orientations. The morphology evolutions of the structural transition for [011]and[111]loadings are analysed in detail. The results indicate that only 20% of atoms transit to the hcp phase for[011]and[111]loadings, and the appearance of the hcp phase is due to the partial dislocation moving forward on {111}fcc family. For[011]loading, the hcp phase grows to form laminar morphology in four planes, which belong to the{111}fcc family;while for[111]loading, the hcp phase grows into a laminar structure in three planes, which belong to the {111}fcc family except for the(111)plane. In addition, the phase transition is evaluated by using the radial distribution functions.

  17. Atomistic Simulations of Helium Clustering and Grain Boundary Reconstruction in Alpha-Iron

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Li; Gao, Fei; Kurtz, Richard J.; Zu, Xiaotao

    2015-01-01

    The accumulation and clustering of He atoms at Σ3 <110> {112} and Σ73b<110>{661} grain boundaries (GBs) in bcc Fe, as well as their effects on GB reconstruction, have been investigated using atomic-level computer simulations. The accumulation of He atoms and the evolution of the GB structure all depend on local He concentration, temperature and the original GB structure. At a local He concentration of 1%, small He clusters are formed in the Σ3 GB, accompanied by the emission of single self-interstitial Fe atoms (SIAs). At a He concentration of 5%, a large number of SIAs are emitted from He clusters in the Σ3 GB and collect at the periphery of these clusters. The SIAs eventually form <100> dislocation loops between two He clusters. It is likely that impurities may promote the formation of <100> loops and enhance their stabilities in α-Fe. At a He concentration of 10%, the large number of emitted SIAs are able to rearrange themselves, forming a new GB plane within the Σ3 GB, which results in self-healing of the GB and leads to GB migration. In contrast to the Σ3 GB, He clusters are mainly formed along the GB dislocation lines in the Σ73b, and the emitted SIAs accumulate at the cores of the GB dislocations, leading to the climb of the dislocations within the GB plane. As compared to bulk Fe, a higher number density of clusters form at GBs, but the average cluster size is smaller. The product of cluster density and average cluster size is roughly constant at a given He level, and is about the same in bulk and GB regions and varies linearly with the He concentration.

  18. 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

  19. Coupling atomistic and continuum length scales in heteroepitaxial systems: Multiscale molecular-dynamics/finite-element simulations of strain relaxation in Si/ Si3 N4 nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2005-09-01

    A hybrid atomistic-continuum simulation approach has been implemented to study strain relaxation in lattice-mismatched Si/Si3N4 nanopixels on a Si(111) substrate. We couple the molecular-dynamics (MD) and finite-element simulation approaches to provide an atomistic description near the interface and a continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are validated against full multimillion-atom MD simulations. We find that strain relaxation in Si/Si3N4 nanopixels may occur through the formation of a network of interfacial domain boundaries reminiscent of interfacial misfit dislocations. They result from the nucleation of domains of different interfacial bonding at the free edges and corners of the nanopixel, and subsequent to their creation they propagate inwards. We follow the motion of the domain boundaries and estimate a propagation speed of about ˜2.5×103m/s . The effects of temperature, nanopixel architecture, and film structure on strain relaxation are also investigated. We find: (i) elevated temperature increases the interfacial domain nucleation rates; (ii) a thin compliant Si layer between the film and the substrate plays a beneficial role in partially suppressing strain relaxation; and (iii) additional control over the interface morphology may be achieved by varying the film structure.

  20. 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.

  1. 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.

  2. Model simulation of the SPOC wave in a bundle of striated myofibrils.

    Science.gov (United States)

    Nakagome, Koutaro; Sato, Katsuhiko; Shintani, Seine A; Ishiwata, Shin'ichi

    2016-01-01

    SPOC (spontaneous oscillatory contraction) is a phenomenon observed in striated muscle under intermediate activation conditions. Recently, we constructed a theoretical model of SPOC for a sarcomere, a unit sarcomere model, which explains the behavior of SPOC at each sarcomere level. We also constructed a single myofibril model, which visco-elastically connects the unit model in series, and explains the behaviors of SPOC at the myofibril level. In the present study, to understand the SPOC properties in a bundle of myofibrils, we extended the single myofibril model to a two-dimensional (2D) model and a three-dimensional (3D) model, in which myofibrils were elastically connected side-by-side through cross-linkers between the Z-lines and M-lines. These 2D and 3D myofibril models could reproduce various patterns of SPOC waves experimentally observed in a 2D sheet and a 3D bundle of myofibrils only by choosing different values of elastic constants of the cross-linkers and the external spring. The results of these 2D and 3D myofibril models provide insight into the SPOC properties of the higher-ordered assembly of myofibrils.

  3. 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.

    2011-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 are candidate materials for applications in extreme environments because of their high melting point, good mechanical properties and reasonable oxidation resistance. Unlike many ceramics, these materials have high thermal conductivity which can be advantageous, for example, to reduce thermal shock. Recently, we developed Tersoff style interatomic 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. Results at room temperature and at elevated temperatures will be reported.

  4. 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.

  5. 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.

  6. Characterization and quantification of the role of coherence in ultrafast quantum biological experiments using quantum master equations, atomistic simulations, and quantum process tomography

    CERN Document Server

    Rebentrost, Patrick; Yuen-Zhou, Joel; Aspuru-Guzik, Alán

    2010-01-01

    Long-lived electronic coherences in various photosynthetic complexes at cryogenic and room temperature have generated vigorous efforts both in theory and experiment to understand their origins and explore their potential role to biological function. The ultrafast signals resulting from the experiments that show evidence for these coherences result from many contributions to the molecular polarization. Quantum process tomography (QPT) was conceived in the context of quantum information processing to characterize and understand general quantum evolution of controllable quantum systems, for example while carrying out quantum computational tasks. We introduce our QPT method for ultrafast experiments, and as an illustrative example, apply it to a simulation of a two-chromophore subsystem of the Fenna-Matthews-Olson photosynthetic complex, which was recently shown to have long-lived quantum coherences. Our Fenna-Matthews-Olson model is constructed using an atomistic approach to extract relevant parameters for the s...

  7. 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.

  8. Combined atomistic-continuum model for simulation of laser interaction with metals: application in the calculation of melting thresholds in Ni targets of varying thickness

    Science.gov (United States)

    Ivanov, D. S.; Zhigilei, L. V.

    The threshold laser fluence for the onset of surface melting is calculated for Ni films of different thicknesses and for a bulk Ni target using a combined atomistic-continuum computational model. The model combines the classical molecular dynamics (MD) method for simulation of non-equilibrium processes of lattice superheating and fast phase transformations with a continuum description of the laser excitation and subsequent relaxation of the conduction band electrons based on the two-temperature model (TTM). In the hybrid TTM-MD method, MD substitutes the TTM equation for the lattice temperature, and the diffusion equation for the electron temperature is solved simultaneously with MD integration of the equations of motion of atoms. The dependence of the threshold fluence on the film thickness predicted in TTM-MD simulations qualitatively agrees with TTM calculations, while the values of the thresholds for thick films and bulk targets are 10% higher in TTM-MD. The quantitative differences between the predictions of TTM and TTM-MD demonstrate that the kinetics of laser melting as well as the energy partitioning between the thermal energy of atomic vibrations and energy of the collective atomic motion driven by the relaxation of the laser-induced pressure should be taken into account in interpretation of experimental results on surface melting.

  9. 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.

  10. 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.

  11. Effect of point and grain boundary defects on the mechanical behavior of monolayer MoS{sub 2} under tension via atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Dang, Khanh Q. [Department of Mechanical Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States); Spearot, Douglas E., E-mail: dspearot@uark.edu [Department of Mechanical Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States); Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States)

    2014-07-07

    Atomistic simulation is used to study the structure and energy of defects in monolayer MoS{sub 2} and the role of defects on the mechanical properties of monolayer MoS{sub 2}. First, energy minimization is used to study the structure and energy of monosulfur vacancies positioned within the bottom S layer of the MoS{sub 2} lattice, and 60° symmetric tilt grain boundaries along the zigzag and armchair directions, with comparison to experimental observations and density functional theory calculations. Second, molecular dynamics simulations are used to subject suspended defect-containing MoS{sub 2} membranes to a state of multiaxial tension. A phase transformation is observed in the defect-containing membranes, similar to prior work in the literature. For monolayer MoS{sub 2} membranes with point defects, groups of monosulfur vacancies promote stress-concentration points, allowing failure to initiate away from the center of the membrane. For monolayer MoS{sub 2} membranes with grain boundaries, failure initiates at the grain boundary and it is found that the breaking force for the membrane is independent of grain boundary energy.

  12. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-11-01

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

  14. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

    DEFF Research Database (Denmark)

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia

    2016-01-01

    In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present ...... (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3]....

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2014-11-07

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

  18. 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.

  19. 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

  20. Heat transfer on HLM cooled wire-spaced fuel pin bundle simulator in the NACIE-UP facility

    Energy Technology Data Exchange (ETDEWEB)

    Di Piazza, Ivan, E-mail: ivan.dipiazza@enea.it [Italian National Agency for New Technologies, Energy and Sustainable Economic Development, C.R. ENEA Brasimone, Camugnano (Italy); Angelucci, Morena; Marinari, Ranieri [University of Pisa, Dipartimento di Ingegneria Civile e Industriale, Pisa (Italy); Tarantino, Mariano [Italian National Agency for New Technologies, Energy and Sustainable Economic Development, C.R. ENEA Brasimone, Camugnano (Italy); Forgione, Nicola [University of Pisa, Dipartimento di Ingegneria Civile e Industriale, Pisa (Italy)

    2016-04-15

    Highlights: • Experiments with a wire-wrapped 19-pin fuel bundle cooled by LBE. • Wall and bulk temperature measurements at three axial positions. • Heat transfer and error analysis in the range of low mass flow rates and Péclet number. • Comparison of local and section-averaged Nusselt number with correlations. - Abstract: The NACIE-UP experimental facility at the ENEA Brasimone Research Centre (Italy) allowed to evaluate the heat transfer coefficient of a wire-spaced fuel bundle cooled by lead-bismuth eutectic (LBE). Lead or lead-bismuth eutectic are very attractive as coolants for the GEN-IV fast reactors due to the good thermo-physical properties and the capability to fulfil the GEN-IV goals. Nevertheless, few experimental data on heat transfer with heavy liquid metals (HLM) are available in literature. Furthermore, just a few data can be identified on the specific topic of wire-spaced fuel bundle cooled by HLM. Additional analysis on thermo-fluid dynamic behaviour of the HLM inside the subchannels of a rod bundle is necessary to support the design and safety assessment of GEN. IV/ADS reactors. In this context, a wire-spaced 19-pin fuel bundle was installed inside the NACIE-UP facility. The pin bundle is equipped with 67 thermocouples to monitor temperatures and analyse the heat transfer behaviour in different sub-channels and axial positions. The experimental campaign was part of the SEARCH FP7 EU project to support the development of the MYRRHA irradiation facility (SCK-CEN). Natural and mixed circulation flow regimes were investigated, with subchannel Reynolds number in the range Re = 1000–10,000 and heat flux in the range q″ = 50–500 kW/m{sup 2}. Local Nusselt numbers were calculated for five sub-channels in different ranks at three axial positions. Section-averaged Nusselt number was also defined and calculated. Local Nusselt data showed good consistency with some of the correlation existing in literature for heat transfer in liquid metals

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

    Science.gov (United States)

    Karim, Eaman T.; Shugaev, Maxim; Wu, Chengping; Lin, Zhibin; Hainsey, Robert F.; Zhigilei, Leonid V.

    2014-05-01

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

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    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...

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

    DEFF Research Database (Denmark)

    Orlowski, A.; St-Pierre, J. F.; Magarkar, A.

    2011-01-01

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

  4. Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

    Science.gov (United States)

    Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

    2017-01-01

    This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

  5. 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...

  6. 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.

  7. Atomistic comparative study of VUV photodeposited silicon nitride on InP(100) by simulation and atomic force microscopy

    Science.gov (United States)

    Flicstein, J.; Guillonneau, E.; Marquez, J.; How Kee Chun, L. S.; Maisonneuve, D.; David, C.; Wang, Zh.; Palmier, J. F.; Courant, J. L.

    2000-02-01

    We report on an accurate validation of a new Monte Carlo three-dimensional model. Simulations up to 1200 Å layer thickness have been carried out for amorphous thin film layers of SiN:H deposited at low temperature (400-650 K) on (100) InP, by vacuum ultraviolet (VUV, ˜185 nm)-induced chemical vapor deposition (CVD). The computer simulations in the mesoscopic-submicronic range are compared with atomic force microscopy and index of refraction measurements. The reconstituted surface roughness and the voids discrete representations of the bulk are found to be in good agreement with these measurements. Simultaneously at around 450 K (at ˜175°C), thermal characteristic evolution of the both surface roughness and bulk porosity showed a transition from rough to smooth deposition and from low to high density.

  8. The alloying processes in solid–solid and liquid–solid Li–Pb interfaces with atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gan, Xianglai [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Deng, Huiqiu; Xiao, Shifang; Li, Xiaofan [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Hu, Wangyu, E-mail: wyuhu@hnu.edu.cn [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China)

    2015-05-25

    Highlights: • B2-LiPb forms in these three kinds of Li–Pb interfaces. • The nucleation of the B2-LiPb at the solid–solid Li–Pb interface is the earliest. • The B2-LiPb acts as a diffusion barrier. • The block Li in the critical interface sample collapses from distortion. • The interface width growth rate of the liquid–solid interface is the largest. - Abstract: The alloying processes of solid–solid (at 400 K) and liquid–solid (at 500 K) Li–Pb interfaces are investigated by molecular dynamics simulations with embedded-atom method (EAM) potentials. As a comparison, a critical Li–Pb interface at 450 K near the melting point of Li is also studied. Three-stage feature, including the interface disordering, nucleation and growth of an intermetallic phase (B2-LiPb), has been clearly observed in these three cases. It is found that the alloying products are the same, however, the nucleation of the intermetallic phase at the solid–solid Li–Pb interface is earlier than that in the other two cases. The block Li in the solid–solid interface sample keeps the body-centered cubic structure during the course of simulation, while in the critical Li–Pb interface sample, it collapses from the excessive lattice distortion. As simulation time increasing, the interface widths increase gradually with decreasing growth rates, and the growth rate is the largest for the liquid–solid interface and the smallest for the solid–solid interface. The interface width of the solid–solid Li–Pb interface saturates at about 0.3 ns for the diffusion barrier—B2-LiPb almost traversed across the entire interface plane at that time.

  9. Atomistic simulation study of the effect of martensitic transformation volume change on crack-tip material evolution and fracture toughness

    Energy Technology Data Exchange (ETDEWEB)

    Grujicic, M. [Clemson Univ., SC (United States). Dept. of Mechanical Engineering; Lai, S.G. [Clemson Univ., SC (United States). Dept. of Mechanical Engineering; Gumbsch, P. [Max Planck-Institut fur Metallforshung Institut fuer Werstoffwissenshaft, Seestrasse 92, D-7000 Stuttgart I (Germany)

    1997-07-15

    The effect of the sign of the F.C.C.{yields}B.C.C. martensitic transformation volume change in Fe-20Ni on material evolution in a region surrounding the crack tip and the accompanying change in the fracture resistance of the material have been investigated using molecular dynamics simulations. The interaction between atoms has been modeled using the embedded atom method (EAM) interatomic potentials. To obtain both the positive and the negative values of the transformation volume change, small adjustments had to be made in the EAM functions. These changes did not significantly affect of the key materials properties, such as the relative thermodynamic stability of the F.C.C. and B.C.C. structures, elastic constants, (11 anti 2){sub bcc} twin boundary energy, (10 anti 1){sub fcc}/(1 anti 21){sub bcc} interfacial energy, etc. The simulation results show that the sign of the transformation volume change has a profound effect on the material evolution and the path of the advancing crack. When the volume change is negative, the region ahead of the crack tip undergoes the transformation only after the other regions around the crack tip have already transformed. The crack tip undergoes a significant blunting and tends to stay on the original crack plane. In sharp contrast, when the volume change is positive, the region ahead of the crack tip transforms first and significant decohesion along the F.C.C./B.C.C. interfaces takes place. Consequently the crack tends to branch out. The effect of material evolution at the crack tip on the ability of the material to withstand further fracture has been quantified by calculating the Eshelby`s F{sub 1} conservation integral. The sign of the transformation volume change is found to have a major effect on the change of the F{sub 1} integral with the simulation time. (orig.)

  10. 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.

  11. Direct dynamics simulations of the product channels and atomistic mechanisms for the OH(-) + CH3I reaction. Comparison with experiment.

    Science.gov (United States)

    Xie, Jing; Sun, Rui; Siebert, Matthew R; Otto, Rico; Wester, Roland; Hase, William L

    2013-08-15

    Electronic structure and direct dynamics calculations were used to study the potential energy surface and atomic-level dynamics for the OH(-) + CH3I reactions. The results are compared with crossed molecular beam, ion imaging experiments. The DFT/B97-1/ECP/d level of theory gives reaction energetics in good agreement with experiment and higher level calculations, and it was used for the direct dynamics simulations that were performed for reactant collision energies of 2.0, 1.0, 0.5, and 0.05 eV. Five different pathways are observed in the simulations, forming CH3OH + I(-), CH2I(-) + H2O, CH2 + I(-) + H2O, IOH(-) + CH3, and [CH3--I--OH](-). The SN2 first pathway and the proton-transfer second pathway dominate the reaction dynamics. Though the reaction energetics favor the SN2 pathway, the proton-transfer pathway is more important except for the lowest collision energy. The relative ion yield determined from the simulations is in overall good agreement with experiment. Both the SN2 and proton-transfer pathways occur via direct rebound, direct stripping, and indirect mechanisms. Except for the highest collision energy, 70-90% of the indirect reaction for the SN2 pathway occurs via formation of the hydrogen-bonded OH(-)---HCH2I prereaction complex. For the proton-transfer pathway the indirect reaction is more complex with the roundabout mechanism and formation of the OH(-)---HCH2I and CH2I(-)---HOH complexes contributing to the reaction. The majority of the SN2 reaction is direct at 2.0, 1.0, and 0.5 eV, dominated by stripping. At 0.05 eV the two direct mechanisms and the indirect mechanisms have nearly equal contributions. The majority of the proton-transfer pathway is direct stripping at 2.0, 1.0, and 0.5 eV, but the majority of the reaction is indirect at 0.05 eV. The product relative translational energy distributions are in good agreement with experiment for both the SN2 and proton-transfer pathways. For both, direct reaction preferentially transfers the product

  12. Comparison of the Solid Solution Properties of Mg-RE (Gd, Dy, Y Alloys with Atomistic Simulation

    Directory of Open Access Journals (Sweden)

    Yurong Wu

    2008-01-01

    Full Text Available Molecular dynamic simulations have been performed to study the solid solution mechanism of Mg100-xREx (RE=Gd,Dy,Y, x=0.5,1,2,3,4  at.%. The obtained results reveal that the additions of Gd, Dy and Y increase the lattice constants of Mg-RE alloys. Also the axis ratio c/a remains unchanged with increase in temperature, restraining the occurrence of nonbasal slip and twinning. Furthermore, it is confirmed that bulk modulus of Mg alloys can be increased remarkably by adding the Gd, Dy, Y, especially Gd, because the solid solubility of Gd in Mg decrease sharply with temperature in comparison with Dy and Y. Consequently, the addition of the RE can enhance the strength of Mg-based alloys, which is in agreement with the experimental results.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    -molecular interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic......Cytochrome (cyt) bc(1) is a multi-subunit membrane protein complex that is a vital component of the respiratory and photosynthetic electron transfer chains both in bacteria and eukaryotes. Although the complex's dimer structure has been solved using X-ray crystallography, it has not yet been...... 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...

  14. Atomistic simulations of the effect of embedded hydrogen and helium on the tensile properties of monocrystalline and nanocrystalline tungsten

    Science.gov (United States)

    Chen, Zhe; Kecskes, Laszlo J.; Zhu, Kaigui; Wei, Qiuming

    2016-12-01

    Uniaxial tensile properties of monocrystalline tungsten (MC-W) and nanocrystalline tungsten (NC-W) with embedded hydrogen and helium atoms have been investigated using molecular dynamics (MD) simulations in the context of radiation damage evolution. Different strain rates have been imposed to investigate the strain rate sensitivity (SRS) of the samples. Results show that the plastic deformation processes of MC-W and NC-W are dominated by different mechanisms, namely dislocation-based for MC-W and grain boundary-based activities for NC-W, respectively. For MC-W, the SRS increases and a transition appears in the deformation mechanism with increasing embedded atom concentration. However, no obvious embedded atom concentration dependence of the SRS has been observed for NC-W. Instead, in the latter case, the embedded atoms facilitate GB sliding and intergranular fracture. Additionally, a strong strain enhanced He cluster growth has been observed. The corresponding underlying mechanisms are discussed.

  15. 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...

  16. Mathematical modelling for nanotube bundle oscillators

    Science.gov (United States)

    Thamwattana, Ngamta; Cox, Barry J.; Hill, James M.

    2009-07-01

    This paper investigates the mechanics of a gigahertz oscillator comprising a nanotube oscillating within the centre of a uniform concentric ring or bundle of nanotubes. The study is also extended to the oscillation of a fullerene inside a nanotube bundle. In particular, certain fullerene-nanotube bundle oscillators are studied, namely C60-carbon nanotube bundle, C60-boron nitride nanotube bundle, B36N36-carbon nanotube bundle and B36N36-boron nitride nanotube bundle. Using the Lennard-Jones potential and the continuum approach, we obtain a relation between the bundle radius and the radii of the nanotubes forming the bundle, as well as the optimum bundle size which gives rise to the maximum oscillatory frequency for both the fullerene and the nanotube bundle oscillators. While previous studies in this area have been undertaken through molecular dynamics simulations, this paper emphasizes the use of applied mathematical modelling techniques which provides considerable insight into the underlying mechanisms. The paper presents a synopsis of the major results derived in detail by the present authors in [1, 2].

  17. Atomistic properties of γ uranium.

    Science.gov (United States)

    Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

    2012-02-22

    The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

  18. Experimental and atomistic simulation studies of corrosion inhibition of copper by a new benzotriazole derivative in acid medium

    Energy Technology Data Exchange (ETDEWEB)

    Khaled, K.F. [Electrochemistry Research Laboratory, Chemistry Department, Ain Shams University, Roxy, Cairo 11711 (Egypt)], E-mail: khaledrice2003@yahoo.com

    2009-07-15

    The efficiency of N-(2-thiazolyl)-1H-benzotriazole-1-carbothioamide (TBC) as a non-toxic corrosion inhibitor for copper in 0.5 M HCl has been tested by weight loss and electrochemical techniques. Electrochemical techniques show that TBC is a mixed-type inhibitor and its inhibition mechanism on copper surface is adsorption assisted by H-bond formation. Impedance measurements show a wide peak presumably given by more than one time constant in the presence of TBC. Also, impedance results show that the values of CPEs (constant phase elements) tend to decrease and both polarization resistance and inhibition efficiency tend to increase with increasing of TBC concentration due to an increase in the electric double layer. Monte Carlo simulations incorporating molecular mechanics and molecular dynamics show that the TBC adsorb on the copper surface firmly through the thiazolyl and carbothioamide groups, the adsorption energy as well as hydrogen bond length have been calculated for both TBC and benzotriazole (BTA) for comparison. Quantum chemical calculations reveal that TBC has higher HOMO, lower LUMO, lower energy gap and lower dipole moment ({mu}) than BTA, which proves that TBC is better copper corrosion inhibitor compared with BTA in 0.5 M HCl.

  19. Atomistic simulations of P(NDI2OD-T2) morphologies: from single chain to condensed phases.

    Science.gov (United States)

    Caddeo, Claudia; Fazzi, Daniele; Caironi, Mario; Mattoni, Alessandro

    2014-10-30

    We investigate theoretically the structure, crystallinity, and solubility of a high-mobility n-type semiconducting copolymer, P(NDI2OD-T2), and we propose a set of new force field parameters. The force field is reparametrized against density functional theory (DFT) calculations, with the aim to reproduce the correct torsional angles that govern the polymer chain flexibility and morphology. We simulate P(NDI2OD-T2) oligomers in different environments, namely, in vacuo, in the bulk phase, and in liquid toluene and chloronaphthalene solution. The choice of these solvents is motivated by the fact that they induce different kinds of molecular preaggregates during the casting procedures, resulting in variable device performances. Our results are in good agreement with the available experimental data; the polymer bulk structure, in which the chains are quite planar, is correcly reproduced, yet the isolated chains are flexible enough to fold in vacuo. We also calculate the solubility of P(NDI2OD-T2) in toluene and chloronaphthalene, predicting a much better solubility of the polymer in the latter, also in accordance to experimental observations. Different morphologies and dynamics of the oligomers in the two solvents have been observed. The proposed parameters make it possible to obtain the description of P(NDI2OD-T2) in different environments and can serve as a basis for extensive studies of this polymer semiconductor, such as, for example, the dynamics of aggregation in solvent.

  20. A numerical study of ultraprecision machining of monocrystalline silicon with laser nano-structured diamond tools by atomistic simulation

    Science.gov (United States)

    Dai, Houfu; Chen, Genyu; Zhou, Cong; Fang, Qihong; Fei, Xinjiang

    2017-01-01

    Three-dimension molecular dynamics (MD) simulations is employed to investigate the ultraprecision machining of single crystal silicon with structured nanoscale diamond tool fabricated by laser. The advantages and disadvantages of diamond machining using structured tools are discussed in comparison with those of using non-structured tools. The von Mises stress distribution, hydrostatic stress distribution, atomic displacement, stress, the radial distribution function, cutting forces, frictional coefficient, subsurface temperature and potential energy during the nanometric machining process are studied. A theoretical analysis model is also established to investigate the subsurface damage mechanism by analyzing the distribution of residual stress during the nanoscale machining process. The results show that a structured nanoscale tool in machining brittle material silicon causes a smaller hydrostatic stress, a less compressive normal stress σxx and σyy , a lower temperature and a smaller cutting force. However, the structured nanoscale tool machining results in smaller chip volume and more beta-silicon phase. Besides, the friction coefficient for tool with V-shape groove is smaller than those for non-structured tools and other structured nanoscale tools. This means that the tool with V-shape groove can reduce the resistance to cutting during the nanoscale machining process. In addition, the results also point out that the potential energy of subsurface atoms and the number of other atoms for pyramid-structured tool are much smaller than those of using non-structured tools and other structured nanoscale tools.

  1. Atomistic simulations on the axial nanowelding configuration and contact behavior between Ag nanowire and single-walled carbon nanotubes

    Science.gov (United States)

    Cui, Jianlei; Zhang, Jianwei; He, Xiaoqiao; Yang, Xinjun; Mei, Xuesong; Wang, Wenjun; Jiang, Gedong; Wang, Kedian; Yang, Lijun; Xie, Hui

    2017-03-01

    As for the interesting new building blocks, the Ag nanowires (AgNWs) and single-walled carbon nanotubes (SWNTs) as the interesting new building blocks are viewed as the promising candidates for the next-generation interconnects due to their most remarkable electrical, thermal, optical, mechanical, and other properties. The axial nanowelding of head-to-head style and side-to-side style is relatively simulated with the molecular dynamics method. As for the head-to-head structural style, SWNTs will move toward the AgNWs and contact with the head of AgNWs. And, the part of the Ag nanowire may be subsequently encapsulated in SWNT with the core-filling Ag atom chain as the final atomic contact configuration during nanowelding, which is related to the nanowelding temperature. When the SWNTs and AgNWs are arranged by the side-to-side contact style, the SWNTs will move along the SWNT surface and may eventually catch up with the AgNW being neck and neck. Aiming at the final axial atomic configurations and the contact behavior during nanowelding process, the related dominant mechanism is revealed in this paper.

  2. Boundary-dependent mechanical properties of graphene annular under in-plane circular shearing via atomistic simulations

    Science.gov (United States)

    Li, Yinfeng; Lin, Qianling; Cui, Daxiang

    2017-02-01

    Graphene annulus possesses special wrinkling phenomenon with wide range of potential applications. Using molecular dynamics simulation, this study concerns the effect of boundary on the mechanical properties of circular and elliptical graphene annuli under circular shearing at inner edge. Both the wrinkle characteristic and torque capacity of annular graphene can be effectively tuned by outer boundary radius and aspect ratio. For circular annulus with fixed inner radius, the critical angle of rotation can be increased by several times without sacrificing its torque capacity by increasing outer boundary radius. The wrinkle characteristic of graphene annulus with elliptical outer boundary differs markedly with that of circular annulus. Torque capacity anomalously decreases with the increase of aspect ratio, and a coupled effect of the boundary aspect ratio and the ratio of minor axis to inner radius on wrinkling are revealed. By studying the stress distribution and wrinkle characteristics, we find the decay of torque capacity is the result of circular stress concentration around the minor axis, while the nonuniform stress distribution is anomalously caused by the change of wrinkle profiles near the major axis. The specific mechanism of out-of-plane deformation on in-plane strength provides a straightforward means to develop novel graphene-based devices.

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

    Science.gov (United States)

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

    2015-09-29

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

  4. Boundary-dependent mechanical properties of graphene annular under in-plane circular shearing via atomistic simulations

    Science.gov (United States)

    Li, Yinfeng; Lin, Qianling; Cui, Daxiang

    2017-01-01

    Graphene annulus possesses special wrinkling phenomenon with wide range of potential applications. Using molecular dynamics simulation, this study concerns the effect of boundary on the mechanical properties of circular and elliptical graphene annuli under circular shearing at inner edge. Both the wrinkle characteristic and torque capacity of annular graphene can be effectively tuned by outer boundary radius and aspect ratio. For circular annulus with fixed inner radius, the critical angle of rotation can be increased by several times without sacrificing its torque capacity by increasing outer boundary radius. The wrinkle characteristic of graphene annulus with elliptical outer boundary differs markedly with that of circular annulus. Torque capacity anomalously decreases with the increase of aspect ratio, and a coupled effect of the boundary aspect ratio and the ratio of minor axis to inner radius on wrinkling are revealed. By studying the stress distribution and wrinkle characteristics, we find the decay of torque capacity is the result of circular stress concentration around the minor axis, while the nonuniform stress distribution is anomalously caused by the change of wrinkle profiles near the major axis. The specific mechanism of out-of-plane deformation on in-plane strength provides a straightforward means to develop novel graphene-based devices. PMID:28198805

  5. Atomistic simulation of charge effects: From tunable thin film growth to isolation of surface states with spin-orbit coupling

    Science.gov (United States)

    Ming, Wenmei

    This dissertation revitalizes the importance of surface charge effects in semiconductor nanostructures, in particular in the context of thin film growth and exotic electronic structures under delicate spin-orbit coupling. A combination of simulation techniques, including density functional theory calculation, kinetic Monte Carlo method, nonequilibrium Green's function method, and tight binding method, were employed to reveal the underlying physical mechanisms of four topics: (1) Effects of Li doping on H-diffusion in MgH 2 for hydrogen storage. It addresses both the effect of Fermi level tuning by charged dopant and the effect of dopant-defect interaction, and the latter was largely neglected in previous works; (2) Tuning nucleation density of the metal island with charge doping of the graphene substrate. It is the first time that the surface charge doping effect is proposed and studied as an effective approach to tune the kinetics of island nucleation at the early stage of thin film growth; (3) Complete isolation of Rashba surface states on the saturated semiconductor surface. It shows that the naturally saturated semiconductor surface of InSe(0001) with Au single layer film provides a mechanism for the formation of Rashba states with large spin splitting; it opens up an innovative route to obtaining ideal Rashba states without the overwhelming bulk spin-degenerate carriers in spin-dependent transport; (4) Formation of large band gap quantum spin Hall state on Si surface. This study reveals the importance of atomic orbital composition in the formation of a topological insulator, and shows promisingly the possible integration of topological insulator technology into Si-based modern electronic devices.

  6. Automatic and Systematic Atomistic Simulations in the MedeA® Software Environment: Application to EU-REACH

    Directory of Open Access Journals (Sweden)

    Rozanska Xavier

    2015-03-01

    Full Text Available This work demonstrates the systematic prediction of thermodynamic properties for batches of thousands of molecules using automated procedures. This is accomplished with newly developed tools and functions within the Material Exploration and Design Analysis (MedeA® software environment, which handle the automatic execution of sequences of tasks for large numbers of molecules including the creation of 3D molecular models from 1D representations, systematic exploration of possible conformers for each molecule, the creation and submission of computational tasks for property calculations on parallel computers, and the post-processing for comparison with available experimental properties. After the description of the different MedeA® functionalities and methods that make it easy to perform such large number of computations, we illustrate the strength and power of the approach with selected examples from molecular mechanics and quantum chemical simulations. Specifically, comparisons of thermochemical data with quantum-based heat capacities and standard energies of formation have been obtained for more than 2 000 compounds, yielding average deviations with experiments of less than 4% with the Design Institute for Physical PRoperties (DIPPR database. The automatic calculation of the density of molecular fluids is demonstrated for 192 systems. The relaxation to minimum-energy structures and the calculation of vibrational frequencies of 5 869 molecules are evaluated automatically using a semi-empirical quantum mechanical approach with a success rate of 99.9%. The present approach is scalable to large number of molecules, thus opening exciting possibilities with the advent of exascale computing.

  7. Effects of Zr doping on the surface energy and surface structure of UO{sub 2}: Atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Hongxing, E-mail: xiaohongxing2003@163.com [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China); Long, Chongsheng; Chen, Hongsheng [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China); Tian, Xiaofeng [The College of Nuclear Technology and Automation Engineering, Chengdu University of Technology, Chengdu (China); Wei, Tianguo; Zhao, Yi; Gao, Wen [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China)

    2015-10-01

    A shell-core model is applied to investigate the effects of Zr doping on the surface energies and surface structures of the three low Miller index surfaces in UO{sub 2} using the molecular dynamics (MD) technique. The surface energies and atomic structures of the Zr-doped and undoped UO{sub 2} (1 0 0), (1 1 0) and (1 1 1) surfaces are compared. Simulation results indicate that (i) the surface energy of (U{sub 1−y}Zr{sub y})O{sub 2} depend on the crystallographic orientation, as well as of undoped UO{sub 2}. The (1 0 0) surface exhibits the highest surface energy, followed by the (1 1 0) surface, and the (1 1 1) surface; (ii) Zr doping will significantly increase the surface energy of UO{sub 2} by approximately 20% on (1 0 0) surface, 10% on (1 1 0) surface and 15% on (1 1 1) surface with the ZrO{sub 2} contents ranging from 0 to 12.5 mol%, respectively; (iii) the surface energies of the three low Miller index surfaces decrease with increasing temperature both in undoped UO{sub 2} and in (U{sub 1−y}Zr{sub y})O{sub 2}; (iv) the addition of Zr induces a severe distortion of the (U{sub 1−y}Zr{sub y})O{sub 2} surface structure, and the outermost top layer exhibits the strongest rumpling; (v) the considerable reconstructions can be observed in the two top layers of Zr-doped and undoped UO{sub 2} surfaces when the temperature is elevated to 900–1500 K.

  8. On Double Vector Bundles

    Institute of Scientific and Technical Information of China (English)

    Zhuo CHEN; Zhang Ju LIU; Yun He SHENG

    2014-01-01

    In this paper, we construct a category of short exact sequences of vector bundles and prove that it is equivalent to the category of double vector bundles. Moreover, operations on double vector bundles can be transferred to operations on the corresponding short exact sequences. In particular, we study the duality theory of double vector bundles in term of the corresponding short exact sequences. Examples including the jet bundle and the Atiyah algebroid are discussed.

  9. On Double Vector Bundles

    OpenAIRE

    Chen, Zhuo; Liu, Zhangju; Sheng, Yunhe

    2011-01-01

    In this paper, we construct a category of short exact sequences of vector bundles and prove that it is equivalent to the category of double vector bundles. Moreover, operations on double vector bundles can be transferred to operations on the corresponding short exact sequences. In particular, we study the duality theory of double vector bundles in term of the corresponding short exact sequences. Examples including the jet bundle and the Atiyah algebroid are discussed.

  10. 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

    2012-05-01

    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.High-density carbon nanotube networks (CNNs) continue to attract interest as active elements in nanoelectronic devices, nanoelectromechanical systems

  11. Atomistic stimulation of defective oxides

    CERN Document Server

    Minervini, L

    2000-01-01

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

  12. Efficiency of various lattices from hard ball to soft ball: theoretical study of thermodynamic properties of dendrimer liquid crystal from atomistic simulation.

    Science.gov (United States)

    Li, Youyong; Lin, Shiang-Tai; Goddard, William A

    2004-02-18

    Self-assembled supramolecular organic liquid crystal structures at nanoscale have potential applications in molecular electronics, photonics, and porous nanomaterials. Most of these structures are formed by aggregation of soft spherical supramolecules, which have soft coronas and overlap each other in the packing process. Our main focus here is to study the possible packing mechanisms via molecular dynamics simulations at the atomistic level. We consider the relative stability of various lattices packed by the soft dendrimer balls, first synthesized and characterized by Percec et al. (J. Am. Chem. Soc. 1997, 119, 1539) with different packing methods. The dendrons, which form the soft dendrimer balls, have the character of a hard aromatic region from the point of the cone to the edge with C(12) alkane "hair". After the dendrons pack into a sphere, the core of the sphere has the hard aromatic groups, while the surface is covered with the C(12) alkane "hair". In our studies, we propose three ways to organize the hair on the balls, Smooth/Valentino balls, Sticky/Einstein balls, and Asymmetric/Punk balls, which lead to three different packing mechanisms, Slippery, Sticky, and Anisotropic, respectively. We carry out a series of molecular dynamics (MD) studies on three plausible crystal structures (A15, FCC, and BCC) as a function of density and analyze the MD based on the vibrational density of state (DoS) method to extract the enthalpy, entropy, and free energies of these systems. We find that anisotropic packed A15 is favored over FCC, BCC lattices. Our predicted X-ray intensities of the best structures are in excellent agreement with experiment. "Anisotropic ball packing" proposed here plays an intermediate role between the enthalpy-favored "disk packing" and entropy-favored "isotropic ball packing", which explains the phase transitions at different temperatures. Free energies of various lattices at different densities are essentially the same, indicating that the

  13. 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.

  14. Principal noncommutative torus bundles

    DEFF Research Database (Denmark)

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

    2008-01-01

    In this paper we study continuous bundles of C*-algebras which are non-commutative analogues of principal torus bundles. We show that all such bundles, although in general being very far away from being locally trivial bundles, are at least locally trivial with respect to a suitable bundle version...... of bivariant K-theory (denoted RKK-theory) due to Kasparov. Using earlier results of Echterhoff and Williams, we shall give a complete classification of principal non-commutative torus bundles up to equivariant Morita equivalence. We then study these bundles as topological fibrations (forgetting the group...... 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...

  15. Possibilités actuelles du calcul des constantes élastiques de polymères par des méthodes de simulation atomistique Current Possibilities of the Computation of Elastic Constants of Polymers Using Atomistic Simulations

    Directory of Open Access Journals (Sweden)

    Dal Maso F.

    2006-12-01

    Full Text Available Les propriétés élastiques des phases amorphe et cristalline pures de polymères semi-cristallins ne sont en général pas mesurables directement avec les moyens physiques habituels. Il est donc nécessaire de recourir à des méthodes de calcul numérique. Cet article décrit certaines de ces méthodes, fondées sur des modélisations atomistiques, ainsi qu'une évaluation des implémentations actuelles. Il est montré que la méthode proposée par Zehnder et al. (1996 fournit les meilleurs résultats, au prix d'un temps long de calcul, dû à la dynamique moléculaire. Néanmoins, aucune de ces méthodes n'est vraiment utilisable simplement au jour le jour, car elles requièrent des moyens importants de calcul. Elastic properties of pure crystalline and amorphous phases of a semicrystalline polymer are usually not directly measurable by usual physical means. It therefore is necessary to resort to numerical computing methods. This paper describes some of these methods, based on atomistic simulations, as well as an assessment of current implementations. It is shown that the method proposed by Zehnder et al. (1996 gives the best results, at the expense of long computing time, due to molecular dynamic simulation. Nevertheless none of these methods are really usable on a daily basis, since there are demanding important computing capabilities.

  16. 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.

  17. Going Backward : A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

    NARCIS (Netherlands)

    Wassenaar, Tsjerk A.; Pluhackova, Kristyna; Böckmann, Rainer A.; Marrink, Siewert J.; Tieleman, D. Peter

    2014-01-01

    The conversion of coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations. For this process, called backmapping or reverse transformation, several tools are available, but these commonly require libraries of molecul

  18. CFD simulations in heavy liquid metal flows for square lattice bare rod bundle geometries with a four parameter heat transfer turbulence model

    Energy Technology Data Exchange (ETDEWEB)

    Manservisi, Sandro, E-mail: sandro.manservisi@unibo.it; Menghini, Filippo, E-mail: filippo.menghini3@unibo.it

    2015-12-15

    Highlights: • Turbulent heat transfer with a κ–ϵ–κ{sub θ}–ϵ{sub θ} turbulence model is investigated. • Numerical simulations with different pitch-to-diameter ratios are performed. • The results are compared with SED model and a few available experimental correlations. - Abstract: The study of heat transfer in heavy liquid metals has gained more attention in the last several years due to their applications in new advanced nuclear reactors. These fluids are characterized by low Prandtl numbers and a peculiar heat transfer that cannot be accurately reproduced with standard turbulence approximations, such as the Simple Eddy Diffusivity model (SED), commonly used in commercial codes. In this paper we report the results obtained for the SED and a more advanced κ–ϵ–κ{sub θ}–ϵ{sub θ} four parameter turbulence model for simulations in square lattice bare rod bundle geometries with different pitch-to-diameter ratios. We compare these numerical results with the available experimental data and correlations for the prediction of the Nusselt number.

  19. Numerical Simulation of Galloping for Iced Quad-bundled Conductor%覆冰四分裂导线舞动数值模拟方法

    Institute of Scientific and Technical Information of China (English)

    秦力; 李亚南; 魏晓光

    2014-01-01

    The galloping for quad-bundled conductor serious threat to the safe operation of the issue of EHV lines,the theoretical study of galloping can effectively promote the development of anti-dance techniques. A two-node cable element with three translational and one torsional degree of freedom at each node is utilized to imitate the bundled conductor,and a two-node space beam elements are used to simulated the spacers,estab-lished galloping finite element analysis model which can consider sub-conductors wake interference. The finite element equation was solved by time integration method and the calculation program was compiled by MAT-LAB,the central difference method was used to deal with acceleration and the velocity was handled by back-ward difference method. Numerical simulation example was employed to demonstrate the reliable and efficient of the presented method and program.%覆冰四分裂导线舞动问题严重威胁超高压线路的安全运行,对舞动的理论研究可有效推动防舞技术的发展。采用具3个平动自由度和1个扭转自由度的两节点索单元模拟分裂导线各子导线,利用空间梁单元模拟间隔棒,建立可考虑子导线尾流效应的舞动分析有限元模型。采用对加速度中心差分、对速度向后差分的时间积分法对舞动进行非线性数值求解,利用MATLAB编制了相应的计算程序。运用该方法对典型算例的舞动进行数值模拟,结果表明:该方法可有效模拟覆冰四分裂导线的舞动特性,所编写的求解程序具有较高的计算精度和效率。

  20. 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.

  1. Atomistic deformation mechanisms in twinned copper nanospheres.

    Science.gov (United States)

    Bian, Jianjun; Niu, Xinrui; Zhang, Hao; Wang, Gangfeng

    2014-01-01

    In the present study, we perform molecular dynamic simulations to investigate the compression response and atomistic deformation mechanisms of twinned nanospheres. The relationship between load and compression depth is calculated for various twin spacing and loading directions. Then, the overall elastic properties and the underlying plastic deformation mechanisms are illuminated. Twin boundaries (TBs) act as obstacles to dislocation motion and lead to strengthening. As the loading direction varies, the plastic deformation transfers from dislocations intersecting with TBs, slipping parallel to TBs, and then to being restrained by TBs. The strengthening of TBs depends strongly on the twin spacing.

  2. 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.

  3. 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.

  4. Numerical Simulation on the Influence of Flow Direction for Mixed Convection Across a Tube Bundle%流向对管束外混合对流影响的数值模拟

    Institute of Scientific and Technical Information of China (English)

    王秋香; 戴传山; 李琪

    2011-01-01

    用格子玻尔兹曼方法对微圆管管束外混合对流的换热情况进行了数值模拟研究。在充分验证程序正确性的基础上,对混合流动绕流时不同壳侧进液角度,不同雷诺数Re以及瑞利数Ra等方面对传热的影响进行模拟研究,对衡量传热效果的Nu数及温度场进行了对比,总结出了换热规律。为高效微管换热器的开发提供了理论指导。%The influence of flow direction on heat transfer of mixed convection fluid flowing across a tube bundle was simulated using Lattice Boltzmann Method.The correctness of our program was fully verified firstly.Then several influential factors for the overall heat transfer of the tube bundle was investigated,such as the installation angles for the liquid pipe of MTHE shell side,Reynolds numbers and Rayleigh number.The averaged Nusselt numbers and temperature fields for various situations were compared.The effects of incoming direction of fluid flow across a tube bundle was summarized which is helpful for designing a efficient micro-tube bundle heat exchanger.

  5. 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...

  6. 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.

  7. 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.

  8. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    Science.gov (United States)

    2014-03-28

    Approved for Public Release; Distribution Unlimited Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic...non peer-reviewed journals: Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration" Report Title In... nanoscience of multifunctional materials: atomistic exploration” PI:Inna Ponomareva We have accomplished the following. 1. We have developed a set of

  9. 预应力对多晶铁冲击行为影响的微观模拟研究∗%Influence of prestress on sho ck b ehavior of p olycrystalline iron via atomistic simulations

    Institute of Scientific and Technical Information of China (English)

    任国武; 张世文; 范诚; 陈永涛

    2016-01-01

    冲击加载铁动力学响应是当前冲击波领域金属材料塑性和相变行为研究最为关注的焦点之一。本文采用分子动力学模拟方法开展预应力作用下冲击加载多晶铁的动力学行为研究。模拟结果表明,随着预应力的增加,导致弹塑转变应力(Hugoniot弹性极限)和冲击波速度提高,符合已有的理论分析结果。微观晶体结构表征则发现较大的预应力导致剪应力大于屈服应力,塑性弛豫时间缩短,加快多晶铁α→ε相转变。进一步通过与平面及柱壳纯铁冲击加载获得的自由面速度剖面对比分析,证实了模拟结果。%Plasticity behavior and phase transition of metal Fe subjected to shock loading have attracted considerable attention in shock physics community, in particular for underlying relationship between them. Experimental examinations and atomistic simulations on shocked Fe have displayed a three-wave structure: elastic wave, plastic wave and transformation wave. However, these studies are primarily limited to the one-dimensional planar case. Recently, owing to the rapid development of experimental techniques, investigating dynamic property of shocked metal has extended to the multi-dimensional loading conditions, such as cylindrical or spherical shocks. In this regard, fruitful findings are achieved, for example, twinning ratio in polycrystalline Fe under implosive compression is found to be much higher than that under planar shock, implying that the the complex stress state plays a critical role. In this paper, we explore the effects of prestress on plasticity and phase transition of shocked polycrystalline iron. The imposed presstress normal to the impact direction in one-dimensional planar shocking represents the varying deviatoric stress, and does not nearly affect the principal stress. The utilized empirical potential for iron could describe the plasticity dislocation and phase transition very well. The simulations

  10. 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...

  11. 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.

  12. The avalanche process of the fiber bundle model with defect

    Science.gov (United States)

    Hao, Da-Peng; Tang, Gang; Xia, Hui; Xun, Zhi-Peng; Han, Kui

    2017-04-01

    In order to explore the impacts of defect on the tensile fracture process of materials, the fiber bundle model with defect is constructed based on the classical fiber bundle model. In the fiber bundle model with defect, the two key parameters are the mean size and the density of defects. In both uniform and Weibull threshold distributions, the mean size and density all bring impacts on the threshold distribution of fibers. By means of analytical approximation and numerical simulation, we show that the two key parameters of the model have substantial effects on the failure process of the bundle. From macroscopic view, the defect described by the altering of threshold distribution of fibers will has a significant impact on the mechanical properties of the bundle. While in microscopic scale, the statistical properties of the model are still harmonious with the classical fiber bundle model.

  13. 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.......60-1.62). The presence of IRBBB was not associated with any adverse outcome.ConclusionIn this cohort study, RBBB and IRBBB were two to three times more common among men than women. Right bundle branch block was associated with increased cardiovascular risk and all-cause mortality, whereas IRBBB was not. Contrary...

  14. 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.

  15. 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 .

  16. 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.

  17. Dynamic Model and Simulation of Lifiing Log Bundle Deflection Systems for Cranes in Forestry%林用起重机起吊木捆偏摆系统的动力学模型与仿真

    Institute of Scientific and Technical Information of China (English)

    薛伟; 郭永娟

    2011-01-01

    A study was conducted to establish a dynamic model of log bundle deflection system for gantry crane in forestry. Relationships between swing angle of log bundle in the vertical direction and trolley' s acceleration, rope length and lifting speed of log bundle are obtained by linear simplification, while the horizontal swing angle is related with the torsion coefficient of wire rope and its inertia. Load shimmy differential equations of uniform descent of log bundle after the trolley brake are set up. Moreover, vibration differential equations are simulated by Simulink. Results show that rope length, rate of decline and material length have major impacts on the lifting log bundle deflection system. The simulation results further improve the previous achievements in theoretical research, which make the model more consistent with the actual system by considering the system damping%建立了林用起重机木捆偏摆系统的动力学模型,并经过线性简化得出木捆在垂直方向的摆角主要与其同向的小车加(减)速度和绳长,以及木捆升降速度有关,而水平摆角与自身的转动惯量和钢丝绳的扭转系数有关.建立了小车制动后木捆匀速下降过程的二自由度木捆摆振微分方程,最后采用Simulink对振动微分方程进行仿真,结果表明绳索长度、木捆下降速度以及木捆材长对木捆偏摆系统动力响应有重要影响.所得仿真结果进一步完善了先前理论分析研究成果,理论上考虑了系统阻尼,从而使模型更加与实际系统一致.

  18. 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...

  19. 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.

  20. The atomistic mechanism of hcp-to-bcc martensitic transformation in the Ti-Nb system revealed by molecular dynamics simulations.

    Science.gov (United States)

    Li, Yang; Li, JiaHao; Liu, BaiXin

    2015-02-14

    Applying the constructed Ti-Nb potentials, molecular dynamics simulations were conducted to investigate the martensitic transformation of Ti100-xNbx alloys (x = 5, 10…25) from the α' phase (hcp) to the β phase (bcc). It is found that the transformation involved four phases, i.e. α', α'', fco (face-centered orthorhombic), and β phases. The structures of the obtained phases exhibit consistency with experimental data, verifying the validity of atomic simulations. The simulations not only revealed the processes of atomic displacements during the transformation, but also elucidated the underlying mechanism of the martensitic transformation at the atomic level. The martensitic transformation incorporates three types of coinstantaneous deformations i.e. slide, shear as well as extension, and the subsequent lattice constant relaxation. Furthermore, according to the proposed mechanism, the crystallographic correlation between the initial α' phase and the final β phase has been deduced. The simulation results provide a clear landscape on the martensitic transformation mechanism, facilitating our comprehensive understanding on the phase transition in the Ti-Nb system.

  1. Influence of specific intermolecular interactions on the thermal and dielectric properties of bulk polymers: atomistic molecular dynamics simulations of Nylon 6.

    Science.gov (United States)

    Lukasheva, N V; Tolmachev, D A; Nazarychev, V M; Kenny, J M; Lyulin, S V

    2017-01-04

    Specific intermolecular interactions, in particular H-bonding, have a strong influence on the structural, thermal and relaxation characteristics of polymers. We report here the results of molecular dynamics simulations of Nylon 6 which provides an excellent example for the investigation of such an influence. To demonstrate the effect of proper accounting for H-bonding on bulk polymer properties, the AMBER99sb force field is used with two different parametrization approaches leading to two different sets of partial atomic charges. The simulations allowed the study of the thermal and dielectric properties in a wide range of temperatures and cooling rates. The feasibility of the use of the three methods for the estimation of the glass transition temperature not only from the temperature dependence of structural characteristics such as density, but also by using the electrostatic energy and dielectric constant is demonstrated. The values of glass transition temperatures obtained at different cooling rates are practically the same for the three methods. By proper accounting for partial charges in the simulations, a reasonable agreement between the results of our simulations and experimental data for the density, thermal expansion coefficient, static dielectric constant and activation energy of γ and β relaxations is obtained demonstrating the validity of the modeling approach reported.

  2. 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.

  3. Kernel bundle EPDiff

    DEFF Research Database (Denmark)

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

    2011-01-01

    In the LDDMM framework, optimal warps for image registration are found as end-points of critical paths for an energy functional, and the EPDiff equations describe the evolution along such paths. The Large Deformation Diffeomorphic Kernel Bundle Mapping (LDDKBM) extension of LDDMM allows scale space...

  4. 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

  5. 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.

  6. 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.

  7. Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations.

    Science.gov (United States)

    Dobrev, Plamen; Donnini, Serena; Groenhof, Gerrit; Grubmüller, Helmut

    2017-01-10

    Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a "water" molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing "water" molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH.

  8. 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.

  9. 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

  10. 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.

    2013-10-01

    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

  11. Coherent hollow-core waveguide bundles for thermal imaging.

    Science.gov (United States)

    Gal, Udi; Harrington, James; Ben-David, Moshe; Bledt, Carlos; Syzonenko, Nicholas; Gannot, Israel

    2010-09-01

    There has been very little work done in the past to extend the wavelength range of fiber image bundles to the IR range. This is due, in part, to the lack of IR transmissive fibers with optical and mechanical properties analogous to the oxide glass fibers currently employed in the visible fiber bundles. Our research is aimed at developing high-resolution hollow-core coherent IR fiber bundles for transendoscopic infrared imaging. We employ the hollow glass waveguide (HGW) technology that was used successfully to make single-HGWs with Ag/AgI thin film coatings to form coherent bundles for IR imaging. We examine the possibility of developing endoscopic systems to capture thermal images using hollow waveguide fiber bundles adjusted to the 8-10?mum spectral range and investigate the applicability of such systems. We carried out a series of measurements in order to characterize the optical properties of the fiber bundles. These included the attenuation, resolution, and temperature response. We developed theoretical models and simulation tools that calculate the light propagation through HGW bundles, and which can be used to calculate the optical properties of the fiber bundles. Finally, the HGW fiber bundles were used to transmit thermal images of various heated objects; the results were compared with simulation results. The experimental results are encouraging, show an improvement in the resolution and thermal response of the HGW fiber bundles, and are consistent with the theoretical results. Nonetheless, additional improvements in the attenuation of the bundles are required in order to be able to use this technology for medical applications.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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).

  17. 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

  18. Simulation of ablation and plume dynamics under femtosecond double-pulse laser irradiation of aluminum: Comparison of atomistic and continual approaches

    Science.gov (United States)

    Fokin, Vladimir B.; Povarnitsyn, Mikhail E.; Levashov, Pavel R.

    2017-02-01

    We elaborated two numerical methods, two-temperature hydrodynamics and hybrid two-temperature molecular dynamics, which take into account basic mechanisms of a metal target response to ultrashort laser irradiation. The model used for the description of the electronic subsystem is identical for both approaches, while the ionic part is defined by an equation of state in hydrodynamics and by an interatomic potential in molecular dynamics. Since the phase diagram of the equation of state and corresponding potential match reasonably well, the dynamics of laser ablation obtained by both methods is quite similar. This correspondence can be considered as a first step towards the development of a self-consistent combined model. Two important processes are highlighted in simulations of double-pulse ablation: (1) the crater depth decrease as a result of recoil flux formation in the nascent plume when the delay between the pulses increases; (2) the plume reheating by the second pulse that gives rise to two- three-fold growth of the electron temperature with the delay varying from 0 to 200 ps.

  19. Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation.

    Science.gov (United States)

    Huang, Nan-Lan; Lin, Jung-Hsin

    2015-08-18

    Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-01

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

  2. Atomistic simulations of a solid/liquid interface: a combined force field and first principles approach to the structure and dynamics of acetonitrile near an anatase surface

    Energy Technology Data Exchange (ETDEWEB)

    Schiffmann, Florian; Hutter, Juerg; VandeVondele, Joost [Physical Chemistry Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich (Switzerland)

    2008-02-13

    The acetonitrile/anatase(101) interface can be considered a prototypical interface between an oxide and a polar aprotic liquid, and is common in dye sensitized solar cells. Using first principles molecular dynamics simulations of a slab of TiO{sub 2} in contact with neat acetonitrile (MeCN), the liquid structure near this interface has been characterized. Furthermore, in order to investigate properties that require extensive sampling, a classical force field to describe the MeCN/TiO{sub 2} interaction has been optimized, and we show that this force field accurately describes the structure near the interface. We find a surprisingly strong interaction of MeCN with TiO{sub 2}, which leads to an ordered first MeCN layer displaying a significantly enhanced molecular dipole. The strong dipolar interactions between solvent molecules lead to pronounced layering further away from the interface, each successive layer having an alternate orientation of the molecular dipoles. At least seven distinct solvent layers (approximately 12 A) can be discerned in the orientational distribution function. The observed structure also strongly suppresses diffusion parallel to the interface in the first nanometer of the liquid. These results show that the properties of the liquid near the interface differ from those in the bulk, which suggests that solvation near the interface will be distinctly different from solvation in the bulk.

  3. Atomistic simulation of point defects in face centered cubic metals using MAEAM potential%面心立方金属中点缺陷的MAEAM模拟

    Institute of Scientific and Technical Information of China (English)

    宋祥磊; 张晓军; 张建民; 徐可为

    2005-01-01

    From the system energy minimization, the stable configuration and the rule of migration of mono-vacancy, di-vacancy and a single self-interstitial atom are analyzed using the modified analytical embedded atom method (MAEAM) combined with the molecular dynamics simulation in Al, Ni, Cu,Ag, Au and Pb. The results show that only the first-nearest neighbor di-vacancy is the stable configuration of di-vacancy. Compared with the mono-vacancy, the first-nearest neighbor di-vacancy is Ni, Cu, Ag and Au, but the body-centered configuration is favorable in Al and Pb. However compared with mono-vacancy, the single self-interstitial atom is also difficult to form.%将改进分析型嵌入原子法(MAEAM)模型与分子动力学模拟方法相结合,用能量最小化原理分析了面心立方金属Al、Ni、Cu、Ag、Au和Pb中的单空位、双空位及单自间隙原子3种点缺陷的稳定构型及其迁移规律.结果表明:最近邻双空位是双空位中惟一能够存在的构型,而且比单空位还容易迁移;尽管在4种构型的自间隙原子中,〈110〉哑铃状自间隙构型容易在Ni、Cu、Ag和Au中形成,体心自间隙构型也容易在Al和Pb中形成,但和单空位相比较还是较难形成的.

  4. 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.

  5. 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...

  6. 大规模并行原子模拟在钛合金界面行为研究中的应用%Implementing Large-Scale Parallel Atomistic Simulations in the Investigation of Interfacial Behaviors in Titanium Alloys

    Institute of Scientific and Technical Information of China (English)

    王皞; 徐东生; 杨锐

    2013-01-01

    界面对钛合金的力学性能有至关重要的影响。界面行为的原子模拟涉及的原子数目庞大,必须借助大规模并行计算。本研究组开发了大规模并行分子动力学程序,并将其应用于钛合金中不同种类界面行为的模拟研究。本文以钛铝金属间化合物中的孪晶界和α钛中的特殊大角晶界为例,介绍研究组在钛合金晶界行为的计算模拟方面的近期研究成果。所模拟的体系尺寸达到微米级,所需 CPU 核数几十至几百不等。研究发现,钛铝模拟晶胞沿伪孪晶方向剪切变形时,等静压力下可产生 L11结构的伪孪晶形核长大,而等静张力下剪切可产生真孪晶的形核长大,提出钛铝中一种新的孪晶长大机制。在α钛中,特定取向的两个晶粒所形成的晶界与位错发生相互作用,裂纹形核依赖于加载外力的取向而发生在晶界处或硬取向晶粒内,从而可能导致疲劳断裂行为与加载取向相关。这些结果有助于理解钛合金的塑性变形行为,并为更高尺度的模拟研究提供了原子尺度细节。%The mechanical behavior of titanium alloys is often inlfuenced signiifcantly by interfaces. The atomistic investigation of interfaces corresponds with large numbers of atoms, hence requiring large-scale parallel simulations. A molecular dynamics code for such simulations is developed in our group, and used in the investigations of interfacial behaviors in titanium alloys. The present paper introduces our recent works on the simulations of interfacial behaviors in titanium alloys, with the coherent twin boundary in TiAl and a special large-angle grain boundary inα-titanium as two examples. The size of the simulated cells is around micrometers, using tens to hundreds of CPU cores. It is found that, in TiAl under shear along the pseudo-twin direction, pseudo-twin and true twin nucleates and grows under hydrostatic compression and tension respectively

  7. 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.

  8. 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.

  9. 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

  10. An atomistic modelling of the porosity impact on UO{sub 2} matrix macroscopic properties

    Energy Technology Data Exchange (ETDEWEB)

    Jelea, A., E-mail: andrei.jelea@irsn.fr [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Institute of Physical Chemistry Ilie Murgulescu, Romanian Academy, 202 Spl Independentei St., 060021 Bucharest-12 (Romania); Colbert, M. [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Ribeiro, F. [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Treglia, G. [Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Pellenq, R.J.-M. [Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States)

    2011-08-15

    Highlights: > The porosity impact on the UO{sub 2} matrix thermomechanical properties was investigated. > Atomistic simulation techniques were used in this study. > The UO{sub 2} thermal expansion coefficient is modified due to the pore surface effects. > The elastic moduli at 0 K and at finite temperature decrease linearly with porosity. - Abstract: The porosity impact on the UO{sub 2} matrix thermomechanical properties was investigated using atomistic simulation techniques. The porosity modifies the thermal expansion coefficient and this is attributed to pore surface effects. The elastic moduli at 0 K and at finite temperature decrease with porosity, this variation being well approximated using affine functions. These results agree with other mesoscale model predictions and experimental data, showing the ability of the semiempirical potential atomistic simulations to give an overall good description of the porous UO{sub 2}. However, the surface effects are incompletely described.

  11. Quantum transport in RTD and atomistic modeling of nanostructures

    Science.gov (United States)

    Jiang, Zhengping

    As devices are scaled down to nanometer scale, new materials and device structures are introduced to extend Moore's law beyond Si devices. In this length scale, carrier transport moves from classical transport to quantum transport; material granularity has more and more impacts on performance. Computer Aided Design (CAD) becomes essential for both industrial and educational purposes. First part focuses on physical models and numerical issues in nano-scale devices modeling. Resonance Tunneling Diode (RTD) is simulated and used to illustrate phenomena in carrier transport. Non-Equilibrium Green's Function (NEGF) formulism is employed in quantum transport simulation. Inhomogeneous energy grid is used in energy integration, which is critical to capture essential physics in RTD simulation. All simulation results could be reproduced by developed simulators RTDNEGF and NEMO5. In nanostructures, device length becomes comparable to material granularity; it is not proper to consider materials as continuous in many situations. Second part of this work resolves this problem by introducing atomistic modeling method. Valley degeneracy in Si (110) QW is investigated. Inconsistency of experimental observations is resolved by introducing miscut in surface. Impacts of strain and electric field on electronic bandstructure are studied. Research of SiGe barrier disorder effects on valley splitting in Si (100) QW is then conducted. Behaviors of valley splitting in different well widths under electric field are predicted by atomistic simulation. Nearest neighbor empirical tight-binding method is used in electronic calculation and VFF Keating model is used in strain relaxation.

  12. 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

  13. Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-11-01

    The transbilayer pore of the nicotinic acetylcholine receptor (nAChR) is formed by a pentameric bundle of M2 helices. Models of pentameric bundles of M2 helices have been generated using simulated annealing via restrained molecular dynamics. The influence of: (a) the initial C alpha template; and (b) screening of sidechain electrostatic interactions on the geometry of the resultant M2 helix bundles is explored. Parallel M2 helices, in the absence of sidechain electrostatic interactions, pack in accordance with simple ridges-in-grooves considerations. This results in a helix crossing angle of ca. +12 degrees, corresponding to a left-handed coiled coil structure for the bundle as a whole. Tilting of M2 helices away from the central pore axis at their C-termini and/or inclusion of sidechain electrostatic interactions may perturb such ridges-in-grooves packing. In the most extreme cases right-handed coiled coils are formed. An interplay between inter-helix H-bonding and helix bundle geometry is revealed. The effects of changes in electrostatic screening on the dimensions of the pore mouth are described and the significance of these changes in the context of models for the nAChR pore domain is discussed.

  14. Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures

    NARCIS (Netherlands)

    Rzepiela, Andrzej J.; Schafer, Lars V.; Goga, Nicolae; Risselada, H. Jelger; De Vries, Alex H.; Marrink, Siewert J.

    2010-01-01

    We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which

  15. 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

  16. 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.

  17. Bundle Formation in Biomimetic Hydrogels

    NARCIS (Netherlands)

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

    2016-01-01

    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

  18. Vector Bundles And F Theory

    CERN Document Server

    Friedman, R; Witten, Edward

    1997-01-01

    To understand in detail duality between heterotic string and F theory compactifications, it is important to understand the construction of holomorphic G bundles over elliptic Calabi-Yau manifolds, for various groups G. In this paper, we develop techniques to describe these bundles, and make several detailed comparisons between the heterotic string and F theory.

  19. Vector Bundles And F Theory

    OpenAIRE

    Friedman, Robert; Morgan, John; Witten, Edward

    1997-01-01

    To understand in detail duality between heterotic string and F theory compactifications, it is important to understand the construction of holomorphic G bundles over elliptic Calabi-Yau manifolds, for various groups G. In this paper, we develop techniques to describe the bundles, and make several detailed comparisons between the heterotic string and F theory.

  20. 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.

  1. Fiber bundle phase conjugate mirror

    Science.gov (United States)

    Ward, Benjamin G.

    2012-05-01

    An improved method and apparatus for passively conjugating the phases of a distorted wavefronts resulting from optical phase mismatch between elements of a fiber laser array are disclosed. A method for passively conjugating a distorted wavefront comprises the steps of: multiplexing a plurality of probe fibers and a bundle pump fiber in a fiber bundle array; passing the multiplexed output from the fiber bundle array through a collimating lens and into one portion of a non-linear medium; passing the output from a pump collection fiber through a focusing lens and into another portion of the non-linear medium so that the output from the pump collection fiber mixes with the multiplexed output from the fiber bundle; adjusting one or more degrees of freedom of one or more of the fiber bundle array, the collimating lens, the focusing lens, the non-linear medium, or the pump collection fiber to produce a standing wave in the non-linear medium.

  2. 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.

  3. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations.

    Science.gov (United States)

    Lemmin, Thomas; Soto, Cinque S; Clinthorne, Graham; DeGrado, William F; Dal Peraro, Matteo

    2013-01-01

    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.

  4. 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.

  5. Predicting dislocation climb and creep from explicit atomistic details.

    Science.gov (United States)

    Kabir, Mukul; Lau, Timothy T; Rodney, David; Yip, Sidney; Van Vliet, Krystyn J

    2010-08-27

    Here we report kinetic Monte Carlo simulations of dislocation climb in heavily deformed, body-centered cubic iron comprising a supersaturation of vacancies. This approach explicitly incorporates the effect of nonlinear vacancy-dislocation interaction on vacancy migration barriers as determined from atomistic calculations, and enables observations of diffusivity and climb over time scales and temperatures relevant to power-law creep. By capturing the underlying microscopic physics, the calculated stress exponents for steady-state creep rates agree quantitatively with the experimentally measured range, and qualitatively with the stress dependence of creep activation energies.

  6. Atomistic Modelling of Si Nanoparticles Synthesis

    Directory of Open Access Journals (Sweden)

    Giovanni Barcaro

    2017-02-01

    Full Text Available Silicon remains the most important material for electronic technology. Presently, some efforts are focused on the use of Si nanoparticles—not only for saving material, but also for improving the efficiency of optical and electronic devices, for instance, in the case of solar cells coated with a film of Si nanoparticles. The synthesis by a bottom-up approach based on condensation from low temperature plasma is a promising technique for the massive production of such nanoparticles, but the knowledge of the basic processes occurring at the atomistic level is still very limited. In this perspective, numerical simulations can provide fundamental information of the nucleation and growth mechanisms ruling the bottom-up formation of Si nanoclusters. We propose to model the low temperature plasma by classical molecular dynamics by using the reactive force field (ReaxFF proposed by van Duin, which can properly describe bond forming and breaking. In our approach, first-principles quantum calculations are used on a set of small Si clusters in order to collect all the necessary energetic and structural information to optimize the parameters of the reactive force-field for the present application. We describe in detail the procedure used for the determination of the force field and the following molecular dynamics simulations of model systems of Si gas at temperatures in the range 2000–3000 K. The results of the dynamics provide valuable information on nucleation rate, nanoparticle size distribution, and growth rate that are the basic quantities for developing a following mesoscale model.

  7. Steric effects induce geometric remodeling of actin bundles in filopodia

    CERN Document Server

    Dobramysl, Ulrich; Erban, Radek

    2016-01-01

    Filopodia are ubiquitous fingerlike protrusions, spawned by many eukaryotic cells, to probe and interact with their environments. Polymerization dynamics of actin filaments, comprising the structural core of filopodia, largely determine their instantaneous lengths and overall lifetimes. The polymerization reactions at the filopodial tip require transport of G-actin, which enter the filopodial tube from the filopodial base and diffuse toward the filament barbed ends near the tip. Actin filaments are mechanically coupled into a tight bundle by cross-linker proteins. Interestingly, many of these proteins are relatively short, restricting the free diffusion of cytosolic G-actin throughout the bundle and, in particular, its penetration into the bundle core. To investigate the effect of steric restrictions on G-actin diffusion by the porous structure of filopodial actin filament bundle, we used a particle-based stochastic simulation approach. We discovered that excluded volume interactions result in partial and the...

  8. 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.

  9. Evaluating big deal journal bundles.

    Science.gov (United States)

    Bergstrom, Theodore C; Courant, Paul N; McAfee, R Preston; Williams, Michael A

    2014-07-01

    Large commercial publishers sell bundled online subscriptions to their entire list of academic journals at prices significantly lower than the sum of their á la carte prices. Bundle prices differ drastically between institutions, but they are not publicly posted. The data that we have collected enable us to compare the bundle prices charged by commercial publishers with those of nonprofit societies and to examine the types of price discrimination practiced by commercial and nonprofit journal publishers. This information is of interest to economists who study monopolist pricing, librarians interested in making efficient use of library budgets, and scholars who are interested in the availability of the work that they publish.

  10. 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.

  11. Vector bundles on toric varieties

    CERN Document Server

    Gharib, Saman

    2011-01-01

    Following Sam Payne's work, we study the existence problem of nontrivial vector bundles on toric varieties. The first result we prove is that every complete fan admits a nontrivial conewise linear multivalued function. Such functions could potentially be the Chern classes of toric vector bundles. Then we use the results of Corti\\~nas, Haesemeyer, Walker and Weibel to show that the (non-equivariant) Grothendieck group of the toric 3-fold studied by Payne is large, so the variety has a nontrivial vector bundle. Using the same computation, we show that every toric 3-fold X either has a nontrivial line bundle, or there is a finite surjective toric morphism from Y to X, such that Y has a large Grothendieck group.

  12. 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...

  13. 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...

  14. Fabrication of electrospun nanofibers bundles

    Science.gov (United States)

    Ye, Junjun; Sun, Daoheng

    2007-12-01

    Aligned nanofibers, filament bundle composed of large number of nanofibers have potential applications such as bio-material, composite material etc. A series of electrospinning experiments have been conducted to investigate the electrospinning process,in which some parameters such as polymer solution concentration, bias voltage, distance between spinneret and collector, solution flow rate etc have been setup to do the experiment of nanofibers bundles construction. This work firstly reports electrospun nanofiber bundle through non-uniform electrical field, and nanofibers distributed in different density on electrodes from that between them. Thinner nanofibers bundle with a few numbers of nanofiber is collected for 3 seconds; therefore it's also possible that the addressable single nanofiber could be collected to bridge two electrodes.

  15. Reconnection of superfluid vortex bundles.

    Science.gov (United States)

    Alamri, Sultan Z; Youd, Anthony J; Barenghi, Carlo F

    2008-11-21

    Using the vortex filament model and the Gross-Pitaevskii nonlinear Schroedinger equation, we show that bundles of quantized vortex lines in He II are structurally robust and can reconnect with each other maintaining their identity. We discuss vortex stretching in superfluid turbulence and show that, during the bundle reconnection process, kelvin waves of large amplitude are generated, in agreement with the finding that helicity is produced by nearly singular vortex interactions in classical Euler flows.

  16. 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.

  17. 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.

  18. 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

  19. Oscillation of carbon molecules inside carbon nanotube bundles

    Science.gov (United States)

    Thamwattana, Ngamta; Cox, Barry J.; Hill, James M.

    2009-04-01

    In this paper, we investigate the mechanics of a nanoscaled gigahertz oscillator comprising a carbon molecule oscillating within the centre of a uniform concentric ring or bundle of carbon nanotubes. Two kinds of oscillating molecules are considered, which are a carbon nanotube and a C60 fullerene. Using the Lennard-Jones potential and the continuum approach, we obtain a relation between the bundle radius and the radii of the nanotubes forming the bundle, as well as the optimum bundle size which gives rise to the maximum oscillatory frequency for both the nanotube-bundle and the C60-bundle oscillators. While previous studies in this area have been undertaken through molecular dynamics simulations, this paper emphasizes the use of applied mathematical modelling techniques, which provides considerable insight into the underlying mechanisms of the nanoscaled oscillators. The paper presents a synopsis of the major results derived in detail by the present authors (Cox et al 2007 Proc. R. Soc. A 464 691-710 and Cox et al 2007 J. Phys. A: Math. Theor. 40 13197-208).

  20. Cosmic multimuon bundles detected by DELPHI

    CERN Document Server

    Rídky, J

    2004-01-01

    The DELPHI detector located at LEP accelerator has been used also to measure multimuon bundles originated from cosmic ray interactions. Two subdetectors-hadron calorimeter and time projection chamber, are used for this purpose. The 1999 and 2000 data are analyzed over wide range of multiplicities. The multiplicity distribution is compared with prediction of Monte Carlo simulation based on CORSIKA/QGSJET. The Monte-Carlo does not describe the large multiplicity part of data. Even the extreme assumption on the cosmic ray composition (pure iron nuclei) hardly predicts comparable number of high-multiplicity events.

  1. 覆冰四分裂导线除冰过程模拟研究%Numerical simulation study on de-icing process of iced quad-bundled conductor

    Institute of Scientific and Technical Information of China (English)

    严波; 陈科全; 祖正华; 张宏雁; 周松

    2011-01-01

    针对提出的一种覆冰四分裂导线智能除冰方法,采用ABAQUS有限元软件建立覆冰四分裂导线及其除冰装置的有限元模型,实现除冰过程的数值模拟方法.通过数值模拟研究,验证智能除冰方法的可行性.覆冰破坏采用拉伸破坏强度理论,利用ABAQUS的用户材料子程序VUMAT定义覆冰的本构关系和破坏准则,实现破坏单元的删除.通过除冰装置不同张开位移和安装个数以及不同覆冰厚度下除冰效果的模拟研究,为智能除冰装置的设计提供参考.%Numerical model of iced quad-bundled conductor line with new intelligent de-icing equipments was set up by means of ABAQUS software, and the simulation of de-icing process was numerically carried out. The feasibility of the intelligent de-icing method was verified based on the numerical simulation. Tension failure criterion was employed in the simulation of ice failure, and the user material subroutine VUMAT of ABAQUS software was developed to introduce the constitutive relation of ice and the deletion of broken ice elements. Several de-icing scenarios were numerically studied considering the variables including the opening displacement of de-icing equipment,the number of installed de-icing equipments on the line and the thickness of ice covered on the conductors. The obtained numerical results provide a reference for design and realization of intelligent de-icing equipment.

  2. 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

    2016-08-08

    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.

  3. 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.

  4. 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.

  5. Atomistic insight into the minimum wear depth of Cu(111) surface

    OpenAIRE

    2013-01-01

    In the present work, we investigate the minimum wear depth of single crystalline Cu(111) under single asperity friction by means of molecular dynamics simulations. The atomistic mechanisms governing the incipient plasticity are elucidated by characterizing specific defect structures and are correlated to the observed mechanical and frictional responses of the material. Furthermore, the effect of probe radius on the friction process is studied. Our simulations indicate that the formation of we...

  6. CFD simulations of the single-phase and two-phase coolant flow of water inside the original and modified CANDU 37-element bundles

    Energy Technology Data Exchange (ETDEWEB)

    Abbasian, F.; Hadaller, G.I.; Fortman, R.A. [Stern Laboratories, Hamilton, Ontario (Canada)

    2010-07-01

    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)

  7. Multiscale Simulations Using Particles

    DEFF Research Database (Denmark)

    Walther, Jens Honore

    vortex methods for problems in continuum fluid dynamics, dissipative particle dynamics for flow at the meso scale, and atomistic molecular dynamics simulations of nanofluidic systems. We employ multiscale techniques to breach the atomistic and continuum scales to study fundamental problems in fluid...

  8. Creep rupture of fiber bundles

    DEFF Research Database (Denmark)

    Linga, G.; Ballone, P.; Hansen, Alex

    2015-01-01

    The creep deformation and eventual breaking of polymeric samples under a constant tensile load F is investigated by molecular dynamics based on a particle representation of the fiber bundle model. The results of the virtual testing of fibrous samples consisting of 40000 particles arranged on Nc=4...

  9. Vector Bundles over Elliptic Fibrations

    CERN Document Server

    Friedman, R; Witten, Edward; Friedman, Robert; Morgan, John W.; Witten, Edward

    1997-01-01

    This paper gives various methods for constructing vector bundles over elliptic curves and more generally over families of elliptic curves. We construct universal families over generalized elliptic curves via spectral cover methods and also by extensions, and then give a relative version of the construction in families. We give various examples and make Chern class computations.

  10. 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.

  11. 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.

  12. Strategic and welfare implications of bundling

    DEFF Research Database (Denmark)

    Martin, Stephen

    1999-01-01

    A standard oligopoly model of bundling shows that bundling by a firm with a monopoly over one product has a strategic effect because it changes the substitution relationships between the goods among which consumers choose. Bundling in appropriate proportions is privately profitable, reduces rival......' profits and overall welfare, and may drive rivals from the market...

  13. 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 $E$.

  14. Multipath packet switch using packet bundling

    DEFF Research Database (Denmark)

    Berger, Michael Stubert

    2002-01-01

    The basic concept of packet bundling is to group smaller packets into larger packets based on, e.g., quality of service or destination within the packet switch. This paper presents novel applications of bundling in packet switching. The larger packets created by bundling are utilized to extend...... switching capacity by use of parallel switch planes. During the bundling operation, packets will experience a delay that depends on the actual implementation of the bundling and scheduling scheme. Analytical results for delay bounds and buffer size requirements are presented for a specific scheduling...

  15. Dimensional Measurements of Fresh CANDU Fuel Bundle

    Energy Technology Data Exchange (ETDEWEB)

    Jun, Ji Su; Jo, Chang Keun; Jung, Jong Yeob; Koo, Dae Seo; Cho, Moon Sung [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    2005-07-01

    This paper intends to provide the dimensional measurements of fresh CANDU fuel (37-element) bundle for the estimation of deformation of post-irradiated (PI) bundle. It is expensive and difficult to measure the fretting wear of bearing pad, the element bowing and the waviness of endplate at the two-phase high flow condition (above 24 kg/s) of out-of-reactor test. So, it is recommended to compare the geometry of fresh bundle with that of PI bundle to estimate the integrity of fuel bundle in the CANDU-6 fuel channel with two-phase flow condition. The measurement system has been developed to provide the visual inspection and the dimensional measurements within the accuracy of 10 {mu}m. It is applicable in-air and underwater to the CANDU bundle as well as the CANFLEX bundle. The in-air measurements of the 36 fresh CANDU bundles (S/N: B400892 {approx} B400927) are done by this system from February 2004 to March 2004 in the PHWR fresh fuel storage building of KNFC. These bundles are produced by KNFC manufacturing procedure and are waiting for the delivery to the Wolsong-3 plant, and are planned to load into the proposed test channels. The detail measurements contain the outer rod profile (including the bearing pad), the diameter of bundle, the bowing of bundle, the rod length and the surface profile of end plate (waviness)

  16. Physically representative atomistic modeling of atomic-scale friction

    Science.gov (United States)

    Dong, Yalin

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

  17. Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

    OpenAIRE

    Lipp, Vladimir

    2015-01-01

    In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First...

  18. 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.

  19. 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)

  20. 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.

  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. ACM Bundles on Del Pezzo surfaces

    Directory of Open Access Journals (Sweden)

    Joan Pons-Llopis

    2009-11-01

    Full Text Available ACM rank 1 bundles on del Pezzo surfaces are classified in terms of the rational normal curves that they contain. A complete list of ACM line bundles is provided. Moreover, for any del Pezzo surface X of degree less or equal than six and for any n ≥ 2 we construct a family of dimension ≥ n − 1 of non-isomorphic simple ACM bundles of rank n on X.

  3. Entropy for frame bundle systems and Grassmann bundle systems induced by a diffeomorphism

    Institute of Scientific and Technical Information of China (English)

    SUN; Weniang(孙文祥)

    2002-01-01

    ALiao hyperbolic diffeomorphism has equal measure entropy and topological entropy to that ofits induced systems on frame bundles and Grassmann bundles. This solves a problem Liao posed in 1996 forLiao hyperbolic diffeomorphisms.

  4. Hydraulic characteristics of HANARO fuel bundles

    Energy Technology Data Exchange (ETDEWEB)

    Cho, S.; Chung, H. J.; Chun, S. Y.; Yang, S. K.; Chung, M. K. [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1997-12-31

    This paper presents the hydraulic characteristics measured by using LDV (Laser Doppler Velocimetry) in subchannels of HANARO, KAERI research reactor, fuel bundle. The fuel bundle consists of 18 axially finned rods with 3 spacer grids, which are arranged in cylindrical configuration. The effects of the spacer grids on the turbulent flow were investigated by the experimental results. Pressure drops for each component of the fuel bundle were measured, and the friction factors of fuel bundle and loss coefficients for the spacer grids were estimated from the measured pressure drops. Implications regarding the turbulent thermal mixing were discussed. Vibration test results measured by using laser vibrometer were presented. 9 refs., 12 figs. (Author)

  5. Thermal Hydraulic Performance of Tight Lattice Bundle

    Science.gov (United States)

    Yamamoto, Yasushi; Akiba, Miyuki; Morooka, Shinichi; Shirakawa, Kenetsu; Abe, Nobuaki

    Recently, the reduced moderation spectrum BWR has been studied. The fast neutron spectrum is obtained through triangular tight lattice fuel. However, there are few thermal hydraulic test data and thermal hydraulic correlation applicable to critical power prediction in such a tight lattice bundle. This study aims to enhance the database of the thermal hydraulic performance of the tight lattice bundle whose rod gap is about 1mm. Therefore, thermal hydraulic performance measurement tests of tight lattice bundles for the critical power, the pressure drop and the counter current flow limiting were performed. Moreover, the correlations to evaluate the thermal-hydraulic performance of the tight lattice bundle were developed.

  6. Principal $G$-bundles over elliptic curves

    CERN Document Server

    Friedman, R; Witten, Edward; Friedman, Robert; Morgan, John W.; Witten, Edward

    1997-01-01

    Let $G$ be a simple and simply connected complex Lie group. We discuss the moduli space of holomorphic semistable principal $G$-bundles over an elliptic curve $E$. In particular, we give a new proof of a theorem of Looijenga and Bernshtein-Shvartsman, that the moduli space is a weighted projective space. The method of proof is to study the deformations of certain unstable bundles coming from special maximal parabolic subgroups of $G$. We also discuss the associated automorphism sheaves and universal bundles, as well as the relation between various universal bundles and spectral covers.

  7. 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.

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

    Science.gov (United States)

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

    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 Sánchez et al. [J. Chem. Phys. 2006, 124, 214708] and Subotnik et al. [J. Chem. Phys. 2009, 130, 144105]. 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 define the bias voltage across the system while maintaining a proper thermal electronic distribution within the finite lead models. Furthermore, it allows us to investigate complex molecular junctions, including multilead configurations. A heuristic derivation of our working equation leads to explicit expressions for the damping and driving terms, which serve as appropriate electron sources and sinks that effectively "open" the finite model system. Although the method does not forbid it, in practice we find neither violation of Pauli's exclusion principles nor deviation from density matrix positivity throughout our numerical simulations of various tight-binding model systems. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic molecular junction models.

  9. 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.

  10. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. Atomistic modeling of electronic structure and transport in disordered nanostructures

    Science.gov (United States)

    Kharche, Neerav

    and illuminate the interesting physics of these disordered nanostructures that otherwise can not be explained using the traditional averaging methods such as the virtual crystal approximation. Finally, a multiscale modeling approach is employed, which combines the atomistic tight-binding method to compute the electronic structure and the real-space effective mass based quantum transport model including gate leakage to simulate the three terminal characteristics of III-V quantum well field effect transistors (QWFETs). The simulation methodology has been benchmarked against experimental data and it is then applied to investigate the logic performance of ultra-scaled III-V QWFETs with high mobility InAs channels.

  17. 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.

  18. Cold melting of beryllium: Atomistic view on Z-machine experiments

    Science.gov (United States)

    Dremov, V. V.; Rykounov, A. A.; Sapozhnikov, F. A.; Karavaev, A. V.; Yakovlev, S. V.; Ionov, G. V.; Ryzhkov, M. V.

    2015-07-01

    Analysis of phase diagram of beryllium at high pressures and temperatures obtained as a result of ab initio calculations and large scale classical molecular dynamics simulations of beryllium shock loading have shown that the so called cold melting takes place when shock wave propagates through polycrystalline samples. Comparison of ab initio calculation results on sound speed along the Hugoniot with experimental data obtained on Z-machine also evidences for possible manifestation of the cold melting. The last may explain the discrepancy between atomistic simulations and experimental data on the onset of the melting on the Hugoniot.

  19. 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.

  20. Line bundle embeddings for heterotic theories

    Science.gov (United States)

    Nibbelin, Stefan Groot; Ruehle, Fabian

    2016-04-01

    In heterotic string theories consistency requires the introduction of a non-trivial vector bundle. This bundle breaks the original ten-dimensional gauge groups E8 × E8 or SO(32) for the supersymmetric heterotic string theories and SO(16) × 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. 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.

  2. Composite spinor bundles in gravitation theory

    CERN Document Server

    Sardanashvily, G

    1995-01-01

    In gravitation theory, the realistic fermion matter is described by spinor bundles associated with the cotangent bundle of a world manifold X. In this case, the Dirac operator can be introduced. There is the 1:1 correspondence between these spinor bundles and the tetrad gravitational fields represented by sections of the quotient \\Si of the linear frame bundle over X by the Lorentz group. The key point lies in the fact that different tetrad fields imply nonequivalent representations of cotangent vectors to X by the Dirac's matrices. It follows that a fermion field must be regarded only in a pair with a certain tetrad field. These pairs can be represented by sections of the composite spinor bundle S\\to\\Si\\to X where values of tetrad fields play the role of parameter coordinates, besides the familiar world coordinates.

  3. 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.

  4. 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...

  5. 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.

  6. 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.

  7. Functional bundles of the medial patellofemoral ligament.

    Science.gov (United States)

    Kang, Hui Jun; Wang, Fei; Chen, Bai Cheng; Su, Yan Ling; Zhang, Zhan Chi; Yan, Chang Bao

    2010-11-01

    The purpose of this study was to explore the anatomy and evaluate the function of the medial patellofemoral ligament (MPFL). Anatomical dissection was performed on 12 fresh-frozen knee specimens. The MPFL is a condensation of capsular fibers, which originates at the medial femoral condyle. It runs transversely and inserts to the medial edge of the patella. With the landmark of the medial femur epicondyle (MFE), the femoral origination was located: just 8.90 ± 3.27 mm proximally and 13.47 ± 3.68 mm posteriorly to the MFE. The most interesting finding in present study was functional bundles of its patellar insertion. Approximately from the femoral origination point, fibers of the MPFL form two relatively concentrated fiber bundles: the inferior-straight bundle and the superior-oblique bundle. The whole length of each was 71.78 ± 5.51 and 73.67 ± 5.40 mm, respectively. The included angle between bundles was 15.1° ± 2.1°. Although the superior-oblique bundle and the inferior-straight bundle run on the patellar MPFL inferiorly and superiorly, respectively, as their name indicates, the two bundles are not entirely separated, which make MPFL one intact structure. The inferior-straight bundle is the main static soft tissue restraints where the superior-oblique bundle associated with vastus medialis obliquus (VMO) is to serve as the main dynamic soft tissue restraints. So this finding may provide the theoretical foundation for the anatomical reconstruction of the MPFL and shed lights on the future researchers.

  8. 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.

  9. The injection of a screw dislocation into a crystal: Atomistics vs. continuum elastodynamics

    Science.gov (United States)

    Verschueren, J.; Gurrutxaga-Lerma, B.; Balint, D. S.; Dini, D.; Sutton, A. P.

    2017-01-01

    The injection (creation) process of a straight screw dislocation is compared atomistically with elastodynamic continuum theory. A method for injecting quiescent screw dislocations into a crystal of tungsten is simulated using non-equilibrium molecular dynamics. The resulting stress fields are compared to the those of elastodynamic solutions for the injection of a quiescent screw dislocation. A number of differences are found: a plane wave emission is observed to emanate from the whole surface of the cut used to create the dislocation, affecting the displacement field along the dislocation line (z), and introducing displacement field components perpendicular to the line (along x and y). It is argued that, in part, this emission is the result of the finite time required to inject the dislocation, whereby the atoms in the cut surface must temporarily be displaced to unstable positions in order to produce the required slip. By modelling this process in the continuum it is shown that the displacements components normal to the dislocation line arise from transient displacements of atoms in the cut surface parallel to x and y. It is shown that once these displacements are included in the elastodynamic continuum formulation the plane wave emission in uz is correctly captured. A detailed comparison between the atomistic and continuum models is then offered, showing that the main atomistic features can also be captured in the continuum.

  10. Atomistic Simulation of Fcc-bcc Phase Transition in Single Crystal Al Under Uniform Deformation Compression%等变形压加载下单晶铝fcc-bcc相变的分子动力学模拟

    Institute of Scientific and Technical Information of China (English)

    郭钰; 何凯; 李莉; 梁九卿

    2012-01-01

    By molecular dynamics simulations employing an embedded atom method potential, we simulate structural transformations in single crystal Al caused by high rate uniform strain loading. The simulations show that the phase transition takes place at about 270 GPa, corresponding to the reduced volume of 0. 55V0,in reasonable agreement with the calculated value through density functional theory.%采用EAM势,利用分子动力学方法模拟了单晶铝在高速率等变形压加载条件下的fcc-bcc的结构相变.模拟结果表明,在等变形压加载条件下,单晶铝在加压至270 GPa左右,体积缩小至0.55V0时,由面心立方结构转变为体心立方结构.这一结果与第一原理计算的结果大致符合.

  11. ORNL rod-bundle heat-transfer test data. Volume 6. Thermal-hydraulic test facility experimental data report for test 3. 05. 5B - double-ended cold-leg break simulation

    Energy Technology Data Exchange (ETDEWEB)

    Mullins, C.B.; Felde, D.K.; Sutton, A.G.; Gould, S.S.; Morris, D.G.; Robinson, J.J.; Schwinkendorf, K.N.

    1982-05-18

    Thermal-Hydraulic Test Facility (THTF) Test 3.05.5B was conducted by members of the ORNL PWR Blowdown Heat Transfer Separate-Effects Program on July 3, 1980. The objective of the program is to investigate heat transfer phenomena believed to occur in PWRs during accidents, including small and large break loss-of-coolant accidents. Test 3.05.5B was designed to provide transient thermal-hydraulics data in rod bundle geometry under reactor accident-type conditions. Reduced instrument responses are presented. Also included are uncertainties in the instrument responses, calculated mass flows, and calculated rod powers.

  12. Numerical simulation of heat transfer enhancement by strip-coil-baffles in tube-bundle for a tube-shell heat exchanger%螺旋折流片强化管壳式换热器内管束传热数值模拟

    Institute of Scientific and Technical Information of China (English)

    陈亚平; 梅娜; 施明恒

    2007-01-01

    介绍了一种用于强化管壳式换热器壳侧传热和支撑管束的螺旋折流片新型结构,该结构是对换热器管子相间地套上螺旋折流片以产生旋涡流动.研究模型是在正方形布置的4个管子中的2个对角管子套上螺旋折流片后形成的通道,利用FLUENT软件对该上述四管通道模型的流场和温度分布情况进行了数值模拟;分析了四管通道模型中螺旋折流片对强化传热和流动阻力随雷诺数的变化关系的影响.算例结果显示该新型结构可比相同尺寸的光管通道中的情形传热系数提高约40%~55%,同时也将伴随较高的流动阻力.可以相信螺旋折流片式换热器将会在许多工业领域有良好的应用前景.%A novel strip-coil-baffle structure used to enhance heat transfer and support the tube bundle for a tube-shell heat exchanger is proposed.The new structure can sleeve the tubes in bundle alternatively to create a vortex flow in a heat exchanger.The numerical simulation on the flow and heat transfer characteristics for this new structure heat exchanger is conducted.The computational domain consists of two strip-coil sleeved tubes and two bare tubes oppositely placed at each corner of a square.The velocity and temperature fields in such strip-coil-baffled channel are simulated using FLUENT software.The effects of the strip-coil-baffles on heat transfer enhancement and flow resistance in relation to the Reynolds number are analyzed.The results show that this new structure bundle can enhance the heat transfer coefficient up to a range of 40% to 55% in comparison with a bare tube bundle;meanwhile,higher flow resistance is also accompanied.It is believe that the strip-coil-baffled heat exchanger should have promising applications in many industry fields.

  13. Dislocation climb models from atomistic scheme to dislocation dynamics

    Science.gov (United States)

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

    2017-02-01

    We develop a mesoscopic dislocation dynamics model for vacancy-assisted dislocation climb by upscalings from a stochastic model on the atomistic scale. Our models incorporate microscopic mechanisms of (i) bulk diffusion of vacancies, (ii) vacancy exchange dynamics between bulk and dislocation core, (iii) vacancy pipe diffusion along the dislocation core, and (iv) vacancy attachment-detachment kinetics at jogs leading to the motion of jogs. Our mesoscopic model consists of the vacancy bulk diffusion equation and a dislocation climb velocity formula. The effects of these microscopic mechanisms are incorporated by a Robin boundary condition near the dislocations for the bulk diffusion equation and a new contribution in the dislocation climb velocity due to vacancy pipe diffusion driven by the stress variation along the dislocation. Our climb formulation is able to quantitatively describe the translation of prismatic loops at low temperatures when the bulk diffusion is negligible. Using this new formulation, we derive analytical formulas for the climb velocity of a straight edge dislocation and a prismatic circular loop. Our dislocation climb formulation can be implemented in dislocation dynamics simulations to incorporate all the above four microscopic mechanisms of dislocation climb.

  14. Atomistic modeling at experimental strain rates and timescales

    Science.gov (United States)

    Yan, Xin; Cao, Penghui; Tao, Weiwei; Sharma, Pradeep; Park, Harold S.

    2016-12-01

    Modeling physical phenomena with atomistic fidelity and at laboratory timescales is one of the holy grails of computational materials science. Conventional molecular dynamics (MD) simulations enable the elucidation of an astonishing array of phenomena inherent in the mechanical and chemical behavior of materials. However, conventional MD, with our current computational modalities, is incapable of resolving timescales longer than microseconds (at best). In this short review article, we briefly review a recently proposed approach—the so-called autonomous basin climbing (ABC) method—that in certain instances can provide valuable information on slow timescale processes. We provide a general summary of the principles underlying the ABC approach, with emphasis on recent methodological developments enabling the study of mechanically-driven processes at slow (experimental) strain rates and timescales. Specifically, we show that by combining a strong physical understanding of the underlying phenomena, kinetic Monte Carlo, transition state theory and minimum energy pathway methods, the ABC method has been found to be useful in a variety of mechanically-driven problems ranging from the prediction of creep-behavior in metals, constitutive laws for grain boundary sliding, void nucleation rates, diffusion in amorphous materials to protein unfolding. Aside from reviewing the basic ideas underlying this approach, we emphasize some of the key challenges encountered in our own personal research work and suggest future research avenues for exploration.

  15. Some recent developments in the theory of acoustic transmission in tube bundles

    Science.gov (United States)

    Heckl, Maria A.; Mulholland, L. S.

    1995-01-01

    A comprehensive theoretical model for acoustic transmission in a tube bundle is presented. The tube bundle is considered as a series of diffraction gratings. Each grating consists of periodically spaced cylindrical tubes which obey the equations of motion of a cylindrical shell. Fluid loading is included. The model can be used for numerical simulations to calculate the sound field at any point in a tube bundle. Various phenomena can be predicted which are of interest for the development of acoustic diagnostics in heat exchangers. These include diffraction of a plane incident wave into several directions, the occurrence of passing and stopping bands in the transmission spectrum, features specific to oblique waves and the effect of dissipative losses. Tube bundles with baffle plates are also examined. The validity of the theoretical model is confirmed by comparison with experimental results.

  16. Adsorption behavior of ternary mixtures of noble gases inside single-walled carbon nanotube bundles

    Science.gov (United States)

    Foroutan, Masumeh; Nasrabadi, Amir Taghavi

    2010-09-01

    In order to study the gas-storage and gas-filtering capability of carbon nanotube (CNT) bundles simultaneously, we considered the adsorption behavior of a ternary mixture of noble gases, including Argon (Ar), Krypton (Kr), and Xenon (Xe), i.e., Ar-Kr-Xe mixture, on (10, 10) single-walled carbon nanotube (SWCNT) bundles. Molecular dynamics (MD) simulations at different temperatures of (75, 100, 150, 200, 250, and 300) K were performed, and adsorption energies, self-diffusion coefficients, activation energies, and radial distribution functions (RDFs) were computed to analyze the thermodynamics, transport and structural properties of the adsorption systems. It is observed that the SWCNT bundles have larger contents of heavier noble gases compared to the lighter ones. This interesting behavior of SWCNT bundles makes them proper candidates for gas-storage and gas molecular-sieving processes.

  17. Higgs bundles and the real symplectic group

    CERN Document Server

    Gothen, Peter B

    2011-01-01

    We give an overview of the work of Corlette, Donaldson, Hitchin and Simpson leading to the non-abelian Hodge theory correspondence between representations of the fundamental group of a surface and the moduli space of Higgs bundles. We then explain how this can be generalized to a correspondence between character varieties for representations of surface groups in real Lie groups G and the moduli space of G-Higgs bundles. Finally we survey recent joint work with Bradlow, Garc\\'ia-Prada and Mundet i Riera on the moduli space of maximal Sp(2n,R)-Higgs bundles.

  18. 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.

  19. Primary and secondary modes of deformation twinning in HCP Mg based on atomistic simulations%基于原子尺度模拟研究HCP镁中的一次及二次孪生模式

    Institute of Scientific and Technical Information of China (English)

    徐泓鹭; 苏小明; 袁广银; 金朝晖

    2014-01-01

    通过分子动力学模拟(MD),研究在HCP镁中的一个对称倾斜晶界与基面滑移的位错相互作用而激发的变形孪晶,也就是孪晶形核与长大的过程(或者是孪晶界迁移,TBM)。{1121}孪晶在该过程中是最易被激发的孪生模式。一旦这样的孪晶形成了,它们就会不断长大。该种孪晶界迁移是由单纯的原子位置局域调整造成的。在模拟过程中同时也产生了二次孪晶{1122}。该二次孪晶模型的孪晶形核与长大需要克服的能垒与{1121}孪晶不同。同时,二次孪晶的孪晶界迁移过程是通过孪晶界上的锥形滑移而激发的。%Deformation twinning, i.e., twin nucleation and twin growth (or twin boundary migration, TBM) activated by impinged basal slip at a symmetrical tilt grain boundary in HCP Mg, was examined with molecular dynamics (MD) simulations. The results show that the {1 1 21}-type twinning acts as the most preferential mode of twinning. Once such twins are formed, they are almost ready to grow. The TBM of such twins is led by pure atomic shuffling events. A secondary mode of twinning can also occur in our simulations. The {1122} twinning is observed at 10 K as the secondary twin. This secondary mode of twinning shows different energy barriers for nucleation as well as for growth compared with the {1 1 21}-type twining. In particular, TBMs in this case is triggered intrinsically by pyramidal slip at its twin boundary.

  20. Strain Functionals for Characterizing Atomistic Geometries

    Science.gov (United States)

    Kober, Edward; Rudin, Sven

    The development of a set of strain tensor functionals that are capable of characterizing arbitrarily ordered atomistic structures is described. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the moments of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. Other methods used to characterize atomic structures, such as the Steinhardt parameters or the centrosymmetry metric, can be derived from this more general approach. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. They allow material phases, deformations, and a large number of defect structures to be readily identified and classified. Applications to the analysis of shock-loaded samples of Cu, Ta and Ti will be presented. This strain functional basis can also then be used for developing interatomic potential functions, and an initial application to Cu will be presented.

  1. 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.

  2. Bundled Hybrid Offset Riser Global Strength Analysis

    Institute of Scientific and Technical Information of China (English)

    William C.Webster; Zhuang Kang; Wenzhou Liang; Youwei Kang; Liping Sun

    2011-01-01

    Bundled hybrid offset riser(BHOR)global strength analysis,which is more complex than single line offset riser global strength analysis,was carried out in this paper.At first,the equivalent theory is used to deal with BHOR,and then its global strength in manifold cases was analyzed,along with the use of a three-dimensional nonlinear time domain finite element program.So the max bending stress,max circumferential stress,and max axial stress in the BHOR bundle main section(BMS)were obtained,and the values of these three stresses in each riser were obtained through the "stress distribution method".Finally,the Max Von Mises stress in each riser was given and a check was made whether or not they met the demand.This paper provides a reference for strength analysis of the bundled hybrid offset riser and some other bundled pipelines.

  3. Noncommutative principal bundles through twist deformation

    CERN Document Server

    Aschieri, Paolo; Pagani, Chiara; Schenkel, Alexander

    2016-01-01

    We construct noncommutative principal bundles deforming principal bundles with a Drinfeld twist (2-cocycle). If the twist is associated with the structure group then we have a deformation of the fibers. If the twist is associated with the automorphism group of the principal bundle, then we obtain noncommutative deformations of the base space as well. Combining the two twist deformations we obtain noncommutative principal bundles with both noncommutative fibers and base space. More in general, the natural isomorphisms proving the equivalence of a closed monoidal category of modules and its twist related one are used to obtain new Hopf-Galois extensions as twists of Hopf-Galois extensions. A sheaf approach is also considered, and examples presented.

  4. 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.

  5. Supporting the Secure Deployment of OSGi Bundles

    OpenAIRE

    Parrend, Pierre; Frénot, Stéphane

    2007-01-01

    International audience; The OSGi platform is a lightweight management layer over a Java virtual machine that makes runtime extensi- bility and multi-application support possible in mobile and constraint environments. This powerfull capability opens a particular attack vector against mobile platforms: the in- stallation of malicious OSGi bundles. The first countermea- sure is the digital signature of the bundles. We developed a tool suite that supports the signature, the publication and the va...

  6. 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.

  7. Is It Complete Left Bundle Branch Block? Just Ablate the Right Bundle.

    Science.gov (United States)

    Ali, Hussam; Lupo, Pierpaolo; Foresti, Sara; De Ambroggi, Guido; Epicoco, Gianluca; Fundaliotis, Angelica; Cappato, Riccardo

    2017-03-01

    Complete left bundle branch block (LBBB) is established according to standard electrocardiographic criteria. However, functional LBBB may be rate-dependent or can perpetuate during tachycardia due to repetitive concealed retrograde penetration of impulses through the contralateral bundle "linking phenomenon." In this brief article, we present two patients with basal complete LBBB in whom ablating the right bundle unmasked the actual antegrade conduction capabilities of the left bundle. These cases highlight intriguing overlap between electrophysiological concepts of complete block, linking, extremely slow, and concealed conduction.

  8. Elastic behavior of amorphous-crystalline silicon nanocomposite: An atomistic view

    Science.gov (United States)

    Das, Suvankar; Dutta, Amlan

    2017-01-01

    In the context of mechanical properties, nanocomposites with homogeneous chemical composition throughout the matrix and the dispersed phase are of particular interest. In this study, the elastic moduli of amorphous-crystalline silicon nanocomposite have been estimated using atomistic simulations. A comparison with the theoretical model reveals that the elastic behavior is significantly influenced by the crystal-amorphous interphase. On observing the effect of volume-fraction of the crystalline phase, an anomalous trend for the bulk modulus is obtained. This phenomenon is attributed to the relaxation displacements of the amorphous atoms.

  9. 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.

  10. 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

  11. Twisted Bundle on Noncommutative Space and U(1) Instanton

    CERN Document Server

    Ho, P M

    2000-01-01

    We study the notion of twisted bundles on noncommutative space. Due to theexistence of projective operators in the algebra of functions on thenoncommutative space, there are twisted bundles with non-constant dimension.The U(1) instanton solution of Nekrasov and Schwarz is such an example. As amathematical motivation for not excluding such bundles, we find gaugetransformations by which a bundle with constant dimension can be equivalent toa bundle with non-constant dimension.

  12. Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics

    Energy Technology Data Exchange (ETDEWEB)

    Amani, Ehsan, E-mail: eamani@aut.ac.ir; Movahed, Saeid, E-mail: smovahed@aut.ac.ir

    2016-06-07

    In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. - Highlights: • A hybrid continuum-atomistic model is proposed for electrokinetics in nanochannels. • The model is validated by molecular dynamics. • This is a promising approach to model more complicated geometries and physics.

  13. 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.

  14. 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.

  15. 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.

  16. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

    Science.gov (United States)

    Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

    2016-08-25

    The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

  17. LWR nuclear fuel bundle data for use in fuel bundle handling

    Energy Technology Data Exchange (ETDEWEB)

    Weihermiller, W.B.; Allison, G.S.

    1979-09-01

    Although increasing numbers of spent light water reactor (LWR) fuel bundles are moved into storage, no handling equipment is set up to manipulate all of the various types of fuel bundles. This report summarizes fuel bundle information of interest to the designer of such handling equipment. Dimensional descriptions are included with discussions of assembly procedure and manufacturer provisions for handling equipment. No attempt is made to make a complete compilation of dimensional information; the number of fuel bundle designs and design revisions makes it impractical. Because the fuel bundle designs are so varied, any equipment intended for handling all types of bundles will have to be designed with flexibility in mind. Besides the ability to manipulate fuel bundles in space, handling equipment may be required to locate an external surface or to position a cutting operation to avoid breaking a fuel rod pressure boundary. Even with the most sophisticated and flexible handling equipment, some situations will require use of the manufacturers' as-built descriptions of individual fuel bundles.

  18. The histology of retinal nerve fiber layer bundles and bundle defects.

    Science.gov (United States)

    Radius, R L; Anderson, D R

    1979-05-01

    The fiber bundle striations recognized clinically in normal monkey eyes appear to be bundles of axons compartmentalized within glial tunnels formed by Müller's-cell processes, when viewed histologically. The dark boundaries that separate individual bundles are the broadened foot endings of these cells near the inner surface of the retina. Within one week after focal retinal photocoagulation, characteristic fundus changes could be seen in experimental eyes. In histologic sections of the involved retina, there was marked cystic degeneration of the retinal nerve fiber layer. Within one month, atrophy of distal axon segments was complete. With the drop-out of damaged axons and thinning of individual fiber bundles, retinal striations became less prominent. The resulting fundus picture in these experimental eyes is similar to fiber bundle defects that can be seen clinically in various neuro-ophthalmic disorders.

  19. Atomistic simulation of damage accumulation and amorphization in Ge

    Energy Technology Data Exchange (ETDEWEB)

    Gomez-Selles, Jose L., E-mail: joseluis.gomezselles@imdea.org; Martin-Bragado, Ignacio [IMDEA Materials Institute, Eric Kandel 2, 28906 Getafe, Madrid (Spain); Claverie, Alain [CEMES/CNRS, 29 rue J. Marvig, 31055 Toulouse Cedex (France); Sklenard, Benoit [CEA, LETI, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Benistant, Francis [GLOBALFOUNDRIES Singapore Pte Ltd., 60 Woodlands Industrial Park D Street 2, Singapore 738406 (Singapore)

    2015-02-07

    Damage accumulation and amorphization mechanisms by means of ion implantation in Ge are studied using Kinetic Monte Carlo and Binary Collision Approximation techniques. Such mechanisms are investigated through different stages of damage accumulation taking place in the implantation process: from point defect generation and cluster formation up to full amorphization of Ge layers. We propose a damage concentration amorphization threshold for Ge of ∼1.3 × 10{sup 22} cm{sup −3} which is independent on the implantation conditions. Recombination energy barriers depending on amorphous pocket sizes are provided. This leads to an explanation of the reported distinct behavior of the damage generated by different ions. We have also observed that the dissolution of clusters plays an important role for relatively high temperatures and fluences. The model is able to explain and predict different damage generation regimes, amount of generated damage, and extension of amorphous layers in Ge for different ions and implantation conditions.

  20. Ultrafast laser melting of Au nanoparticles: atomistic simulations

    Science.gov (United States)

    Wang, Ningyu; Rokhlin, S. I.; Farson, D. F.

    2011-10-01

    In spite of the technological importance of laser modification and processing of nanoparticles, the interaction of laser energy with nanoparticles is not well understood. In this work, integrated molecular dynamics (MD) and two-temperature (TTM) computational models have been developed to study ultrafast laser interaction with free Au nanoparticles with sizes 2.44-6.14 nm. At low intensity, when surface premelting and solid-liquid phase transition dominate, a nonhomogeneous surface premelting mechanism was identified. The appearance of a contiguous surface liquid layer (complete surface premelting) is size dependent and is not related to surface premelting history. The effects of temporary superheating and stable supercooling of nanoparticles were found and examined.

  1. 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.

  2. 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.

  3. Atomistic Simulation Study of Vacancy Clusters in Copper.

    Science.gov (United States)

    1985-01-01

    found to be very mobile with migration energies of 0.56 and 0.39 eV, respectively, compared to previously calculated single and divacancy migration...CF 1985 Massachusetts Institute of Techonology Signature of Author Department of Nuclear Engineering December 4, 1985 C e r t i f i e d b y S i d n...using molecular statics with an interatomic potential recently derived from first principles. Tri- and tetravacancies are found to be very mobile with

  4. 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.

  5. 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.

  6. A fully atomistic model of the Cx32 connexon.

    Directory of Open Access Journals (Sweden)

    Sergio Pantano

    Full Text Available Connexins are plasma membrane proteins that associate in hexameric complexes to form channels named connexons. Two connexons in neighboring cells may dock to form a "gap junction" channel, i.e. an intercellular conduit that permits the direct exchange of solutes between the cytoplasm of adjacent cells and thus mediate cell-cell ion and metabolic signaling. The lack of high resolution data for connexon structures has hampered so far the study of the structure-function relationships that link molecular effects of disease-causing mutations with their observed phenotypes. Here we present a combination of modeling techniques and molecular dynamics (MD to infer side chain positions starting from low resolution structures containing only C alpha atoms. We validated this procedure on the structure of the KcsA potassium channel, which is solved at atomic resolution. We then produced a fully atomistic model of a homotypic Cx32 connexon starting from a published model of the C alpha carbons arrangement for the connexin transmembrane helices, to which we added extracellular and cytoplasmic loops. To achieve structural relaxation within a realistic environment, we used MD simulations inserted in an explicit solvent-membrane context and we subsequently checked predictions of putative side chain positions and interactions in the Cx32 connexon against a vast body of experimental reports. Our results provide new mechanistic insights into the effects of numerous spontaneous mutations and their implication in connexin-related pathologies. This model constitutes a step forward towards a structurally detailed description of the gap junction architecture and provides a structural platform to plan new biochemical and biophysical experiments aimed at elucidating the structure of connexin channels and hemichannels.

  7. 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.

  8. New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

    Science.gov (United States)

    Saether, E.; Yamakov, V.; Glaessgen, E.

    2008-01-01

    A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

  9. 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.

  10. Atomistic studies of dislocations in {alpha}-iron using bond-order potential

    Energy Technology Data Exchange (ETDEWEB)

    Mrovec, Matous; Elsaesser, Christian; Gumbsch, Peter [Fraunhofer-Institut fuer Werkstoffmechanik IWM, Freiburg (Germany); IZBS, Universitaet Karlsruhe, Karlsruhe (Germany)

    2010-07-01

    Macroscopic plastic behavior is closely linked to properties of dislocations at the nanometer scale. Direct experimental observations of the dislocation core region and of its changes during dislocation motion are unfortunately impossible and better understanding of these phenomena can be obtained only with the help of atomistic simulations. Recent atomistic studies of dislocations in iron have provided however very different outcomes, both in terms of atomic structures and energetics. The most likely reason of these large differences is a lack of reliable interatomic potentials, which would be able to describe adequately the atomic bonding and magnetic interactions in iron. In the present work we present studies of dislocations in {alpha}-iron using a bond-order potential, which is based on a tight-binding bond representation. The model is able to capture the directional character of bonds present in transition metals and includes a description of magnetic effects within the Stoner model of itinerant magnetism. We compare results of our simulations with available first-principles predictions as well as with predictions of other empirical interatomic potentials and discuss underlying causes of the differences.

  11. 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...

  12. 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.

  13. Abelian conformal field theory and determinant bundles

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Ueno, K.

    2007-01-01

    Following [10], we study a so-called bc-ghost system of zero conformal dimension from the viewpoint of [14, 16]. We show that the ghost vacua construction results in holomorphic line bundles with connections over holomorphic families of curves. We prove that the curvature of these connections...... are up to a scale the same as the curvature of the connections constructed in [14, 16]. We study the sewing construction for nodal curves and its explicit relation to the constructed connections. Finally we construct preferred holomorphic sections of these line bundles and analyze their behaviour near...

  14. Classical Higgs fields on gauge gluon bundles

    Directory of Open Access Journals (Sweden)

    Palese Marcella

    2016-01-01

    Full Text Available Classical Higgs fields and related canonical conserved quantities are defined by invariant variational problems on suitably defined gauge gluon bundles. We consider Lagrangian field theories which are assumed to be invariant with respect to the action of a gauge-natural group. As an illustrative example we exploit the ‘gluon Lagrangian’, i.e. a Yang-Mills Lagrangian on the (1, 1-order gauge-natural bundle of SU(3-principal connections. The kernel of the gauge-natural Jacobi morphism for such a Lagrangian, by inducing a reductive split structure, canonically defines a ‘gluon classical Higgs field’.

  15. 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...

  16. Atomistic Mechanisms for Viscoelastic Damping in Inorganic Solids

    Science.gov (United States)

    Ranganathan, Raghavan

    Viscoelasticity, a ubiquitous material property, can be tuned to engineer a wide range of fascinating applications such as mechanical dampers, artificial tissues, functional foams and optoelectronics, among others. Traditionally, soft matter such as polymers and polymer composites have been used extensively for viscoelastic damping applications, owing to the inherent viscous nature of interactions between polymer chains. Although this leads to good damping characteristics, the stiffness in these materials is low, which in turn leads to limitations. In this context, hard inorganic materials and composites are promising candidates for enhanced damping, owing to their large stiffness and, in some cases large loss modulus. Viscoelasticity in these materials has been relatively unexplored and atomistic mechanisms responsible for damping are not apparent. Therefore, the overarching goal of this work is to understand mechanisms for viscoelastic damping in various classes of inorganic composites and alloys at an atomistic level from molecular dynamics simulations. We show that oscillatory shear deformation serves as a powerful probe to explain mechanisms for exceptional damping in hitherto unexplored systems. The first class of inorganic materials consists of crystalline phases of a stiff inclusion in a soft matrix. The two crystals within the composite, namely the soft and a stiff phase, individually show a highly elastic behavior and a very small loss modulus. On the other hand, a composite with the two phases is seen to exhibit damping that is about 20 times larger than predicted theoretical bounds. The primary reason for the damping is due to large anharmonicity in phonon-phonon coupling, resulting from the composite microstructure. A concomitant effect is the distribution of shear strain, which is observed to be highly inhomogeneous and mostly concentrated in the soft phase. Interestingly, the shear frequency at which the damping is greatest is observed to scale with

  17. Continuum simulations of water flow past fullerene molecules

    Science.gov (United States)

    Popadić, A.; Praprotnik, M.; Koumoutsakos, P.; Walther, J. H.

    2015-09-01

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

  18. 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.

  19. Graphitization of single-wall nanotube bundles at extreme conditions: Collapse or coalescence route

    NARCIS (Netherlands)

    Colonna, F.; Fasolino, A.; Meijer, E.J.

    2013-01-01

    We determine the reaction phase diagram and the transformation mechanism of (5,5) and (10,10) single-walled carbon nanotube bundles up to 20 GPa and 4000 K. We use Monte Carlo simulations, based on the state-of-the-art reactive potential LCBOPII, that incorporates both covalent and van der Waals int

  20. 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

  1. 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.

  2. 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)

  3. Lazarsfeld-Mukai bundles and applications

    CERN Document Server

    Aprodu, Marian

    2012-01-01

    We survey the development of the notion of Lazarsfeld-Mukai bundles together with various applications, from the classification of Mukai manifolds to Brill-Noether theory and syzygies of $K3$ sections. To see these techniques at work, we present a short proof of a result of M. Reid on the existence of elliptic pencils.

  4. The Hodge bundle on Hurwitz spaces

    NARCIS (Netherlands)

    van der Geer, G.; Kouvidakis, A.

    2011-01-01

    In 2009 Kokotov, Korotkin and Zograf gave in [7] a formula for the class of the Hodge bundle on the Hurwitz space of admissible covers of genus g and degree d of the projective line. They gave an analytic proof of it. In this note we give an algebraic proof and an extension of the result.

  5. 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.

  6. Meromorphic Higgs bundles And Related Geometries

    OpenAIRE

    Dalakov, Peter

    2016-01-01

    The present note is mostly a survey on the generalised Hitchin integrable system and moduli spaces of meromorphic Higgs bundles. We also fill minor gaps in the existing literature, outline a calculation of the infinitesimal period map and review briefly some related geometries.

  7. Meromorphic Higgs bundles and related geometries

    Science.gov (United States)

    Dalakov, Peter

    2016-11-01

    The present note is mostly a survey on the generalised Hitchin integrable system and moduli spaces of meromorphic G-Higgs bundles. We also fill minor gaps in the existing literature, outline a calculation of the infinitesimal period map and review some related geometries.

  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. 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

  10. Active Hair-Bundle Motility by the Vertebrate Hair Cell

    Science.gov (United States)

    Tinevez, J.-Y.; Martin, P.; Jülicher, F.

    2009-02-01

    The hair bundle is both a mechano-sensory antenna and a force generator that might help the vertebrate hair cell from the inner ear to amplify its responsiveness to small stimuli. To study active hair-bundle motility, we combined calcium iontophoresis with mechanical stimulation of single hair bundles from the bullfrog's sacculus. A hair bundle could oscillate spontaneously, or be quiescent but display non-monotonic movements in response to abrupt force steps. Extracellular calcium changes or static biases to the bundle's position at rest could affect the kinetics of bundle motion and evoke transitions between the different classes of motility. The calcium-dependent location of a bundle's operating point within its nonlinear force-displacement relation controlled the type of movements observed. A unified theoretical description, in which mechanical activity stems from myosin-based adaptation and electro-mechanical feedback by Ca2+, could account for the fast and slow manifestations of active hair-bundle motility.

  11. 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.

  12. LUSTERNIK-S CHNIRELMANN CATEGORY AND EMBEDDING FINITE COVERING MAPS, PRINCIPAL G-BUNDLES INTO BUNDLES

    Institute of Scientific and Technical Information of China (English)

    LIULUOFEI

    1996-01-01

    The author proves several embedding theorems for finite covering maps,principal G-bundies into bundles.The main results are 1. Let π:E→X be a finite covering map, and X a connected locally path-connected paracompact space. If cat X≤k, then the finite covering space π:E→X can be embedded into the trivial real k-plane bundle. 2. Let π:E→X be a principal G-bundle over a paracompact space. If there exists a linera action of Gon F(F=R or C)and cat X≤k ,then π:E→X can be embedded into ξ1 … ξn for any F-vector bundles ξi,i=1,…k.

  13. Atomistic and continuums modeling of cluster migration and coagulation in precipitation reactions.

    Science.gov (United States)

    Warczok, Piotr; Ženíšek, Jaroslav; Kozeschnik, Ernst

    2012-07-01

    The influence of vacancy preference towards one of the constituents in a binary system on the formation of precipitates was investigated by atomistic and continuums modeling techniques. In case of vacancy preference towards the solute atoms, we find that the mobility of individual clusters as well as entire atom clusters is significantly altered compared to the case of vacancy preference towards the solvent atoms. The increased cluster mobility leads to pronounced cluster collisions, providing a precipitate growth and coarsening mechanism competitive to that of pure solute evaporation and adsorption considered in conventional diffusional growth and Ostwald ripening. A modification of a numerical Kampmann-Wagner type continuum model for precipitate growth is proposed, which incorporates the influence of both mechanisms. The prognoses of the modified model are validated against the growth laws obtained with lattice Monte Carlo simulations and a growth simulation considering solely the coalescence mechanism.

  14. Atomistic Investigation of Cu-Induced Misfolding in the Onset of Parkinson's Disease

    Science.gov (United States)

    Rose, Francis; Hodak, Miroslav; Bernholc, Jerry

    2009-03-01

    A nucleation mechanism for the misfolding of α-synuclein, the protein implicated in Parkinson's Disease (PD), is investigated using computer simulations. Through a combination of ab initio and classical simulation techniques, the conformational evolution of copper-ion-initiated misfolding of α-synuclein is determined. Based on these investigations and available experimental evidence, an atomistic model detailing the nucleation-initiated pathogenesis of PD is proposed. Once misfolded, the proteins can assemble into fibrils, the primary structural components of the deleterious PD plaques. Our model identifies a process of structural modifications to an initially unfolded α-synuclein that results in a partially folded intermediate with a well defined nucleation site as a precursor to the fully misfolded protein. The identified pathway can enable studies of reversal mechanisms and inhibitory agents, potentially leading to the development of effective therapies.

  15. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    Science.gov (United States)

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; Stocks, G. Malcolm; Landau, David P.

    2017-01-01

    Using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. By calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. Comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnons leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.

  16. 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.

  17. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-12-27

    The ion channel of the nicotinic acetylcholine receptor is a water-filled pore formed by five M2 helix segments, one from each subunit. Molecular dynamics simulations on bundles of five M2 alpha 7 helices surrounding a central column of water and with caps of water molecules at either end of the pore have been used to explore the effects of intrapore water on helix packing. Interactions of water molecules with the N-terminal polar sidechains lead to a conformational transition from right- to left-handed supercoils during these stimulations. These studies reveal that the pore formed by the bundle of M2 helices is flexible. A structural role is proposed for water molecules in determining the geometry of bundles of isolated pore-forming helices.

  18. Stochastic mechanical degradation of multi-cracked fiber bundles with elastic and viscous interactions.

    Science.gov (United States)

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

    2015-05-01

    The mechanics of fiber bundles has been largely investigated in order to understand their complex failure modes. Under a mechanical load, the fibers fail progressively while the load is redistributed among the unbroken fibers. The classical fiber bundle model captures the most important features of this rupture process. On the other hand, the homogenization techniques are able to evaluate the stiffness degradation of bulk solids with a given population of cracks. However, these approaches are inadequate to determine the effective response of a degraded bundle where breaks are induced by non-mechanical actions. Here, we propose a method to analyze the behavior of a fiber bundle, undergoing a random distribution of breaks, by considering the intrinsic response of the fibers and the visco-elastic interactions among them. We obtain analytical solutions for simple configurations, while the most general cases are studied by Monte Carlo simulations. We find that the degradation of the effective bundle stiffness can be described by two scaling regimes: a first exponential regime for a low density of breaks, followed by a power-law regime at increasingly higher break density. For both regimes, we find analytical effective expressions described by specific scaling exponents.

  19. 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.

  20. 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

  1. QTLs analysis of rice peduncle vascular bundle and panicle traits

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@The vascular bundle in plants plays an important role in transportation of photosynthetic products, mineral nutrients, water, and so on. Significant positive correlations were found between grain yield, panicle traits and the No. Of peduncle vascular bundles. So, it is very important to study the inheritance of peduncle vascular bundle, which is a quantitative trait.

  2. VECTOR BUNDLE, KILLING VECTOR FIELD AND PONTRYAGIN NUMBERS

    Institute of Scientific and Technical Information of China (English)

    周建伟

    1991-01-01

    Let E be a vector bundle over a compact Riemannian manifold M. We construct a natural metric on the bundle space E and discuss the relationship between the killing vector fields of E and M. Then we give a proof of the Bott-Baum-Cheeger Theorem for vector bundle E.

  3. Heat exchanger with helical bundles of finned tubes

    Energy Technology Data Exchange (ETDEWEB)

    Eyking, H.J.

    1975-01-23

    The invention applies to a heat exchanger with helical bundles of tubes consisting of finned tubes separated by spacers. The spacers are designed as closed holding cylinders with holding devices for the tube bundles, each ot which surrounds a bundle of tubes. This construction serves to simplify the production process and to enable the use of the heat exchanger at higher loads.

  4. Stability of Picard Bundle Over Moduli Space of Stable Vector Bundles of Rank Two Over a Curve

    Indian Academy of Sciences (India)

    Indranil Biswas; Tomás L Gómez

    2001-08-01

    Answering a question of [BV] it is proved that the Picard bundle on the moduli space of stable vector bundles of rank two, on a Riemann surface of genus at least three, with fixed determinant of odd degree is stable.

  5. Motor-mediated bidirectional transport along an antipolar microtubule bundle: a mathematical model.

    Science.gov (United States)

    Lin, Congping; Ashwin, Peter; Steinberg, Gero

    2013-05-01

    Long-distance bidirectional transport of organelles depends on the coordinated motion of various motor proteins on the cytoskeleton. Recent quantitative live cell imaging in the elongated hyphal cells of Ustilago maydis has demonstrated that long-range motility of motors and their endosomal cargo occurs on unipolar microtubules (MTs) near the extremities of the cell. These MTs are bundled into antipolar bundles within the central part of the cell. Dynein and kinesin-3 motors coordinate their activity to move early endosomes (EEs) in a bidirectional fashion where dynein drives motility towards MT minus ends and kinesin towards MT plus ends. Although this means that one can easily assign the drivers of bidirectional motion in the unipolar section, the bipolar orientations in the bundle mean that it is possible for either motor to drive motion in either direction. In this paper we use a multilane asymmetric simple exclusion process modeling approach to simulate and investigate phases of bidirectional motility in a minimal model of an antipolar MT bundle. In our model, EE cargos (particles) change direction on each MT with a turning rate Ω and there is switching between MTs in the bundle at the minus ends. At these ends, particles can hop between MTs with rate q(1) on passing from a unipolar to a bipolar section (the obstacle-induced switching rate) or q(2) on passing in the other direction (the end-induced switching rate). By a combination of numerical simulations and mean-field approximations, we investigate the distribution of particles along the MTs for different values of these parameters and of Θ, the overall density of particles within this closed system. We find that even if Θ is low, the system can exhibit a variety of phases with shocks in the density profiles near plus and minus ends caused by queuing of particles. We discuss how the parameters influence the type of particle that dominates active transport in the bundle.

  6. Motor-mediated bidirectional transport along an antipolar microtubule bundle: A mathematical model

    Science.gov (United States)

    Lin, Congping; Ashwin, Peter; Steinberg, Gero

    2013-05-01

    Long-distance bidirectional transport of organelles depends on the coordinated motion of various motor proteins on the cytoskeleton. Recent quantitative live cell imaging in the elongated hyphal cells of Ustilago maydis has demonstrated that long-range motility of motors and their endosomal cargo occurs on unipolar microtubules (MTs) near the extremities of the cell. These MTs are bundled into antipolar bundles within the central part of the cell. Dynein and kinesin-3 motors coordinate their activity to move early endosomes (EEs) in a bidirectional fashion where dynein drives motility towards MT minus ends and kinesin towards MT plus ends. Although this means that one can easily assign the drivers of bidirectional motion in the unipolar section, the bipolar orientations in the bundle mean that it is possible for either motor to drive motion in either direction. In this paper we use a multilane asymmetric simple exclusion process modeling approach to simulate and investigate phases of bidirectional motility in a minimal model of an antipolar MT bundle. In our model, EE cargos (particles) change direction on each MT with a turning rate Ω and there is switching between MTs in the bundle at the minus ends. At these ends, particles can hop between MTs with rate q1 on passing from a unipolar to a bipolar section (the obstacle-induced switching rate) or q2 on passing in the other direction (the end-induced switching rate). By a combination of numerical simulations and mean-field approximations, we investigate the distribution of particles along the MTs for different values of these parameters and of Θ, the overall density of particles within this closed system. We find that even if Θ is low, the system can exhibit a variety of phases with shocks in the density profiles near plus and minus ends caused by queuing of particles. We discuss how the parameters influence the type of particle that dominates active transport in the bundle.

  7. Synergetic driving concepts for bundled miniature ultrasonic linear motors.

    Science.gov (United States)

    Mracek, Maik; Hemsel, Tobias

    2006-12-22

    Rotary ultrasonic motors have found broad industrial application in camera lens drives and other systems. Linear ultrasonic motors in contrast have only found limited applications. The main reason for the limited range of application of these very attractive devices seems to be their small force and power range. Attempts to build linear ultrasonic motors for high forces and high power applications have not been truly successful yet. To achieve larger force and higher power, multiple miniaturized motors can be combined. This approach, however, is not as simple as it appears at first glance. The electromechanical behaviour of the individual motors differs slightly due to manufacturing and assembly tolerances. The individual motor characteristics are strongly dependent on the driving parameters (frequency, voltage, temperature, pre-stress, etc.) and the driven load and the collective behaviour of the swarm of motors is not just the linear superposition of the individual drive's forces. Thus, the bundle of motors has to be synchronized and controlled appropriately in order to obtain an optimized drive that is not oversized and costly. We have investigated driving and control strategies of a set of linear ultrasonic motors. Our contribution will be divided into three main parts. In part I ultrasonic linear motors will be introduced. In part II driving strategies for a single motor as well as for a bundle of motors will be presented. These concepts will be verified by simulation results and experimental data. In part III a simplified model for the motor's electromechanical behaviour will be given.

  8. Bundling of harvesting residues and whole-trees and the treatment of bundles; Hakkuutaehteiden ja kokopuiden niputus ja nippujen kaesittely

    Energy Technology Data Exchange (ETDEWEB)

    Kaipainen, H.; Seppaenen, V.; Rinne, S.

    1996-12-31

    The conditions on which the bundling of the harvesting residues from spruce regeneration fellings would become profitable were studied. The calculations showed that one of the most important features was sufficient compaction of the bundle, so that the portion of the wood in the unit volume of the bundle has to be more than 40 %. The tests showed that the timber grab loader of farm tractor was insufficient for production of dense bundles. The feeding and compression device of the prototype bundler was constructed in the research and with this device the required density was obtained.The rate of compaction of the dry spruce felling residues was about 40 % and that of the fresh residues was more than 50 %. The comparison between the bundles showed that the calorific value of the fresh bundle per unit volume was nearly 30 % higher than that of the dry bundle. This means that the treatment of the bundles should be done of fresh felling residues. Drying of the bundles succeeded well, and the crushing and chipping tests showed that the processing of the bundles at the plant is possible. The treatability of the bundles was also excellent. By using the prototype, developed in the research, it was possible to produce a bundle of the fresh spruce harvesting residues, the diameter of which was about 50 cm and the length about 3 m, and the rate of compaction over 50 %. By these values the reduction target of the costs is obtainable

  9. Transversal thermal transport in single-walled carbon nanotube bundles: Influence of axial stretching and intertube bonding

    Science.gov (United States)

    Gharib-Zahedi, Mohammad Reza; Tafazzoli, Mohsen; Böhm, Michael C.; Alaghemandi, Mohammad

    2013-11-01

    Using reverse nonequilibrium molecular dynamics simulations the influence of intermolecular bridges on the thermal conductivity (λ) in carbon nanotube (CNT) bundles has been investigated. The chosen cross linkers (CH2, O, CO) strengthen the transversal energy transport relative to the one in CNT bundles without bridges. The results showed that λ does not increase linearly with the linker density. The efficiency of the heat transport is determined by the number of linkers in the direction of the heat flux, the type of the linker, and their spatial ordering. The influence of a forced axial stress on the transversal λ has been also studied. The observed λ reduction with increasing axial stretching in a neat CNT bundle can be (over)compensated by cross linkers. The present computational data emphasize the contribution of phonons to the transversal heat transport in CNT bundles with intertube bonds.

  10. Multiscale simulations and ductile-brittle analyses of the atomistic cracks in BCC Ta, Fe and W%钽、铁、钨三种体心立方金属裂纹的多尺度模拟及韧脆性分析∗

    Institute of Scientific and Technical Information of China (English)

    杜浩; 倪玉山

    2016-01-01

    In order to better understand the fracture mechanism of body-centered-cubic (BCC) metal, the multiscale quasi-continuum method (QC) is employed to analyze the nano-sized mode I cracks of three kinds of BCC metal materials, i.e., Ta, Fe and W. The plastic deformation near the crack tip and the brittle cleavage process are both investigated. The simulation result shows that there are different ductile-brittle behaviors in the cracks of different BCC materials. In the same loading range, the plastic deformation, such as dislocation nucleation and emission, stacking faults and twinning, is the main phenomenon for the crack of BCC-Ta. For the crack of BCC-Fe, plastic deformation and brittle cleavage are observed successively. At the initial stage, plastic deformation is dominant, which is similar to the crack of Ta. As loading increases, the crack begins to propagate, which differs from the crack of Ta. At first, the crack propagates along the initial direction [001], but then turns to [0ˆ11] as the surface energy of {110} is lower than that of {0ˆ11}. With the crack propagating, the crack tip is blunted by the plastic deformation, which is consistent with experimental results. As for BCC-W, the crack is found to propagate as brittle cleavage without plastic deformation at first. And the brittle cleavage is dominant all the time, which is a significant difference between W and the other two materials. In addition to the atomistic simulation, some theoretical calculations are also performed to analyze the ductile-brittle behaviors of the cracks. By an atomic slip model, the generalized stacking fault curves of BCC Ta, Fe and W are generated, which exhibit the unstable stacking fault energies of these materials. Based on the unstable stacking fault energy, two theoretical ductile-brittle criterions are analyzed. For the Rice-criterion, the result shows that the dislocation condition is met before cleavage for Ta and Fe, while for W the cleavage occurs before dislocation

  11. Emitters of N-photon bundles.

    Science.gov (United States)

    Muñoz, C Sánchez; Del Valle, E; Tudela, A González; Müller, K; Lichtmannecker, S; Kaniber, M; Tejedor, C; Finley, J J; Laussy, F P

    2014-07-01

    Controlling the ouput of a light emitter is one of the basic tasks of photonics, with landmarks such as the laser and single-photon sources. The development of quantum applications makes it increasingly important to diversify the available quantum sources. Here, we propose a cavity QED scheme to realize emitters that release their energy in groups, or "bundles" of N photons, for integer N. Close to 100% of two-photon emission and 90% of three-photon emission is shown to be within reach of state of the art samples. The emission can be tuned with system parameters so that the device behaves as a laser or as a N-photon gun. The theoretical formalism to characterize such emitters is developed, with the bundle statistics arising as an extension of the fundamental correlation functions of quantum optics. These emitters will be useful for quantum information processing and for medical applications.

  12. Care bundles reduce readmissions for COPD.

    Science.gov (United States)

    Matthews, Healther; Tooley, Cathy; Nicholls, Carol; Lindsey-Halls, Anna

    In 2011, the respiratory nursing team at the James Paget University Hospital Foundation Trust were considering introducing a discharge care bundle for patients admitted with an acute exacerbation of chronic obstructive pulmonary disease. At the same time, the trust was asking for applications for Commissioning for Quality and Innovation schemes (CQUINs). These are locally agreed packages of quality improvement goals and indicators, which, if achieved in total, enable the provider to earn its full CQUIN payment. A CQUIN scheme should address the three domains of quality, safety and effectiveness, patient experience and also show innovation. This article discusses how the care bundle was introduced and how, over a 12-month period, it showed tangible results in improving the care pathway for COPD patients as well as reducing readmissions and saving a significant amount of money.

  13. Phase Slips in Oscillatory Hair Bundles

    Science.gov (United States)

    Roongthumskul, Yuttana; Shlomovitz, Roie; Bruinsma, Robijn; Bozovic, Dolores

    2013-01-01

    Hair cells of the inner ear contain an active amplifier that allows them to detect extremely weak signals. As one of the manifestations of an active process, spontaneous oscillations arise in fluid immersed hair bundles of in vitro preparations of selected auditory and vestibular organs. We measure the phase-locking dynamics of oscillatory bundles exposed to low-amplitude sinusoidal signals, a transition that can be described by a saddle-node bifurcation on an invariant circle. The transition is characterized by the occurrence of phase slips, at a rate that is dependent on the amplitude and detuning of the applied drive. The resultant staircase structure in the phase of the oscillation can be described by the stochastic Adler equation, which reproduces the statistics of phase slip production. PMID:25167040

  14. Client Provider Collaboration for Service Bundling

    Directory of Open Access Journals (Sweden)

    LETIA, I. A.

    2008-04-01

    Full Text Available The key requirement for a service industry organization to reach competitive advantages through product diversification is the existence of a well defined method for building service bundles. Based on the idea that the quality of a service or its value is given by the difference between expectations and perceptions, we draw the main components of a frame that aims to support the client and the provider agent in an active collaboration meant to co-create service bundles. Following e3-value model, we structure the supporting knowledge around the relation between needs and satisfying services. We deal with different perspectives about quality through an ontological extension of Value Based Argumentation. The dialog between the client and the provider takes the form of a persuasion whose dynamic object is the current best configuration. Our approach for building service packages is a demand driven approach, allowing progressive disclosure of private knowledge.

  15. Deformations of Fell bundles and twisted graph algebras

    Science.gov (United States)

    Raeburn, Iain

    2016-11-01

    We consider Fell bundles over discrete groups, and the C*-algebra which is universal for representations of the bundle. We define deformations of Fell bundles, which are new Fell bundles with the same underlying Banach bundle but with the multiplication deformed by a two-cocycle on the group. Every graph algebra can be viewed as the C*-algebra of a Fell bundle, and there are are many cocycles of interest with which to deform them. We thus obtain many of the twisted graph algebras of Kumjian, Pask and Sims. We demonstate the utility of our approach to these twisted graph algebras by proving that the deformations associated to different cocycles can be assembled as the fibres of a C*-bundle.

  16. Quantum principal bundles and their characteristic classes

    CERN Document Server

    Durdevic, M

    1996-01-01

    A brief exposition of the general theory of characteristic classes of quantum principal bundles is given. The theory of quantum characteristic classes incorporates ideas of classical Weil theory into the conceptual framework of non-commutative differential geometry. A purely cohomological interpretation of the Weil homomorphism is given, together with a standard geometrical interpretation via quantum invariant polynomials. A natural spectral sequence is described. Some quantum phenomena appearing in the formalism are discussed.

  17. On Complex Supermanifolds with Trivial Canonical Bundle

    CERN Document Server

    Groeger, Josua

    2016-01-01

    We give an algebraic characterisation for the triviality of the canonical bundle of a complex supermanifold in terms of a certain Batalin-Vilkovisky superalgebra structure. As an application, we study the Calabi-Yau case, in which an explicit formula in terms of the Levi-Civita connection is achieved. Our methods include the use of complex integral forms and the recently developed theory of superholonomy.

  18. Uncontrolled inexact information within bundle methods

    OpenAIRE

    Malick, Jérôme; Welington De Oliveira, ·; Zaourar-Michel, Sofia

    2016-01-01

    International audience; We consider convex nonsmooth optimization problems where additional information with uncontrolled accuracy is readily available. It is often the case when the objective function is itself the output of an optimization solver, as for large-scale energy optimization problems tackled by decomposition. In this paper, we study how to incorporate the uncontrolled linearizations into (proximal and level) bundle algorithms in view of generating better iterates and possibly acc...

  19. Uncovering ecosystem service bundles through social preferences.

    Directory of Open Access Journals (Sweden)

    Berta Martín-López

    Full Text Available Ecosystem service assessments have increasingly been used to support environmental management policies, mainly based on biophysical and economic indicators. However, few studies have coped with the social-cultural dimension of ecosystem services, despite being considered a research priority. We examined how ecosystem service bundles and trade-offs emerge from diverging social preferences toward ecosystem services delivered by various types of ecosystems in Spain. We conducted 3,379 direct face-to-face questionnaires in eight different case study sites from 2007 to 2011. Overall, 90.5% of the sampled population recognized the ecosystem's capacity to deliver services. Formal studies, environmental behavior, and gender variables influenced the probability of people recognizing the ecosystem's capacity to provide services. The ecosystem services most frequently perceived by people were regulating services; of those, air purification held the greatest importance. However, statistical analysis showed that socio-cultural factors and the conservation management strategy of ecosystems (i.e., National Park, Natural Park, or a non-protected area have an effect on social preferences toward ecosystem services. Ecosystem service trade-offs and bundles were identified by analyzing social preferences through multivariate analysis (redundancy analysis and hierarchical cluster analysis. We found a clear trade-off among provisioning services (and recreational hunting versus regulating services and almost all cultural services. We identified three ecosystem service bundles associated with the conservation management strategy and the rural-urban gradient. We conclude that socio-cultural preferences toward ecosystem services can serve as a tool to identify relevant services for people, the factors underlying these social preferences, and emerging ecosystem service bundles and trade-offs.

  20. Adhesive contact:from atomistic model to continuum model

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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